Multiple platform build/check report for BioC 3.13 - CHECK results for msa on nebbiolo1

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL msa
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘msa’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -g -O2  -Wall -c R_init_msa.cpp -o R_init_msa.o
In file included from ./Muscle/RMuscle.h:4,
                 from R_init_msa.cpp:3:
./Muscle/muscle.h:54: warning: "assert" redefined
   54 | #define assert(exp)     ((void)0)
      | 
In file included from /usr/include/c++/9/cassert:44,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:137,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/utils/tinyformat.h:40,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:72,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ./ClustalOmega/src/RClustalOmega.h:4,
                 from R_init_msa.cpp:1:
/usr/include/assert.h:50: note: this is the location of the previous definition
   50 | # define assert(expr)  (__ASSERT_VOID_CAST (0))
      | 
In file included from ./Muscle/muscle.h:38,
                 from ./Muscle/RMuscle.h:4,
                 from R_init_msa.cpp:3:
./Muscle/intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -g -O2  -Wall -c SplitCharVector2List.cpp -o SplitCharVector2List.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -g -O2  -Wall -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
make --file=msaMakefile --directory=gc-7.2
make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2'
./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
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... /usr/bin/mkdir -p
checking for gawk... gawk
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 for dlopen in -ldl... 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/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
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... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
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/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
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/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
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/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
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 (/home/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2/libatomic_ops)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  '--enable-cplusplus' '--enable-threads=pthreads' '--enable-shared' '--with-pic' --cache-file=/dev/null --srcdir=.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
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
make[2]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2'
make[3]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2'
depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fPIC -DPIC -o .libs/allchblk.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fPIC -DPIC -o allchblk.o >/dev/null 2>&1
depbase=`echo alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fPIC -DPIC -o .libs/alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fPIC -DPIC -o alloc.o >/dev/null 2>&1
depbase=`echo blacklst.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fPIC -DPIC -o .libs/blacklst.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fPIC -DPIC -o blacklst.o >/dev/null 2>&1
depbase=`echo checksums.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fPIC -DPIC -o .libs/checksums.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fPIC -DPIC -o checksums.o >/dev/null 2>&1
depbase=`echo dbg_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fPIC -DPIC -o .libs/dbg_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fPIC -DPIC -o dbg_mlc.o >/dev/null 2>&1
depbase=`echo dyn_load.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fPIC -DPIC -o .libs/dyn_load.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fPIC -DPIC -o dyn_load.o >/dev/null 2>&1
depbase=`echo finalize.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fPIC -DPIC -o .libs/finalize.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fPIC -DPIC -o finalize.o >/dev/null 2>&1
depbase=`echo gc_dlopen.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fPIC -DPIC -o .libs/gc_dlopen.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fPIC -DPIC -o gc_dlopen.o >/dev/null 2>&1
depbase=`echo gcj_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fPIC -DPIC -o .libs/gcj_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fPIC -DPIC -o gcj_mlc.o >/dev/null 2>&1
depbase=`echo headers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fPIC -DPIC -o .libs/headers.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fPIC -DPIC -o headers.o >/dev/null 2>&1
depbase=`echo malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fPIC -DPIC -o .libs/malloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fPIC -DPIC -o malloc.o >/dev/null 2>&1
depbase=`echo mallocx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fPIC -DPIC -o .libs/mallocx.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fPIC -DPIC -o mallocx.o >/dev/null 2>&1
depbase=`echo mark.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fPIC -DPIC -o .libs/mark.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fPIC -DPIC -o mark.o >/dev/null 2>&1
depbase=`echo mark_rts.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fPIC -DPIC -o .libs/mark_rts.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fPIC -DPIC -o mark_rts.o >/dev/null 2>&1
depbase=`echo misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fPIC -DPIC -o .libs/misc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fPIC -DPIC -o misc.o >/dev/null 2>&1
depbase=`echo new_hblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fPIC -DPIC -o .libs/new_hblk.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fPIC -DPIC -o new_hblk.o >/dev/null 2>&1
depbase=`echo obj_map.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fPIC -DPIC -o .libs/obj_map.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fPIC -DPIC -o obj_map.o >/dev/null 2>&1
depbase=`echo os_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fPIC -DPIC -o .libs/os_dep.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fPIC -DPIC -o os_dep.o >/dev/null 2>&1
depbase=`echo pcr_interface.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fPIC -DPIC -o .libs/pcr_interface.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fPIC -DPIC -o pcr_interface.o >/dev/null 2>&1
depbase=`echo ptr_chck.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fPIC -DPIC -o .libs/ptr_chck.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fPIC -DPIC -o ptr_chck.o >/dev/null 2>&1
depbase=`echo real_malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fPIC -DPIC -o .libs/real_malloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fPIC -DPIC -o real_malloc.o >/dev/null 2>&1
depbase=`echo reclaim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fPIC -DPIC -o .libs/reclaim.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fPIC -DPIC -o reclaim.o >/dev/null 2>&1
depbase=`echo specific.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fPIC -DPIC -o .libs/specific.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fPIC -DPIC -o specific.o >/dev/null 2>&1
depbase=`echo stubborn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fPIC -DPIC -o .libs/stubborn.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fPIC -DPIC -o stubborn.o >/dev/null 2>&1
depbase=`echo typd_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fPIC -DPIC -o .libs/typd_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fPIC -DPIC -o typd_mlc.o >/dev/null 2>&1
depbase=`echo backgraph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fPIC -DPIC -o .libs/backgraph.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fPIC -DPIC -o backgraph.o >/dev/null 2>&1
depbase=`echo thread_local_alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fPIC -DPIC -o .libs/thread_local_alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fPIC -DPIC -o thread_local_alloc.o >/dev/null 2>&1
depbase=`echo pthread_start.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fPIC -DPIC -o .libs/pthread_start.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fPIC -DPIC -o pthread_start.o >/dev/null 2>&1
depbase=`echo pthread_support.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fPIC -DPIC -o .libs/pthread_support.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fPIC -DPIC -o pthread_support.o >/dev/null 2>&1
depbase=`echo pthread_stop_world.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fPIC -DPIC -o .libs/pthread_stop_world.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fPIC -DPIC -o pthread_stop_world.o >/dev/null 2>&1
depbase=`echo libatomic_ops/src/atomic_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c  -fPIC -DPIC -o libatomic_ops/src/.libs/atomic_ops.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c  -fPIC -DPIC -o libatomic_ops/src/atomic_ops.o >/dev/null 2>&1
depbase=`echo mach_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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  -fPIC -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  -fPIC -DPIC -o mach_dep.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=link gcc -fexceptions -g -O2 -fno-strict-aliasing  -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   libatomic_ops/src/atomic_ops.lo mach_dep.lo -lpthread -ldl   
libtool: link: gcc -shared  -fPIC -DPIC  .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 libatomic_ops/src/.libs/atomic_ops.o .libs/mach_dep.o   -lpthread -ldl  -g -O2   -Wl,-soname -Wl,libgc.so.1 -o .libs/libgc.so.1.0.3
libtool: link: (cd ".libs" && rm -f "libgc.so.1" && ln -s "libgc.so.1.0.3" "libgc.so.1")
libtool: link: (cd ".libs" && rm -f "libgc.so" && ln -s "libgc.so.1.0.3" "libgc.so")
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 libatomic_ops/src/atomic_ops.o mach_dep.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libgc.a
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/bash ./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 $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc  -fPIC -DPIC -o .libs/gc_cpp.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc  -fPIC -DPIC -o gc_cpp.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CXX   --mode=link g++ -fexceptions -g -O2 -version-info 1:3:0 -no-undefined  -o libgccpp.la -rpath /usr/local/lib gc_cpp.lo ./libgc.la 
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/9/crtbeginS.o  .libs/gc_cpp.o   -Wl,-rpath -Wl,/home/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2/.libs ./.libs/libgc.so -lpthread -ldl -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/9/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crtn.o  -g -O2   -Wl,-soname -Wl,libgccpp.so.1 -o .libs/libgccpp.so.1.0.3
libtool: link: (cd ".libs" && rm -f "libgccpp.so.1" && ln -s "libgccpp.so.1.0.3" "libgccpp.so.1")
libtool: link: (cd ".libs" && rm -f "libgccpp.so" && ln -s "libgccpp.so.1.0.3" "libgccpp.so")
libtool: link: ar cru .libs/libgccpp.a  gc_cpp.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libgccpp.a
libtool: link: ( cd ".libs" && rm -f "libgccpp.la" && ln -s "../libgccpp.la" "libgccpp.la" )
depbase=`echo cord/cordbscs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c  -fPIC -DPIC -o cord/.libs/cordbscs.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c  -fPIC -DPIC -o cord/cordbscs.o >/dev/null 2>&1
depbase=`echo cord/cordprnt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c  -fPIC -DPIC -o cord/.libs/cordprnt.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c  -fPIC -DPIC -o cord/cordprnt.o >/dev/null 2>&1
depbase=`echo cord/cordtest.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c  -fPIC -DPIC -o cord/.libs/cordtest.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c  -fPIC -DPIC -o cord/cordtest.o >/dev/null 2>&1
depbase=`echo cord/cordxtra.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./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  -fPIC -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  -fPIC -DPIC -o cord/cordxtra.o >/dev/null 2>&1
/bin/bash ./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 -shared  -fPIC -DPIC  cord/.libs/cordbscs.o cord/.libs/cordprnt.o cord/.libs/cordtest.o cord/.libs/cordxtra.o   -Wl,-rpath -Wl,/home/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2/.libs ./.libs/libgc.so -lpthread -ldl  -g -O2   -Wl,-soname -Wl,libcord.so.1 -o .libs/libcord.so.1.0.3
libtool: link: (cd ".libs" && rm -f "libcord.so.1" && ln -s "libcord.so.1.0.3" "libcord.so.1")
libtool: link: (cd ".libs" && rm -f "libcord.so" && ln -s "libcord.so.1.0.3" "libcord.so")
libtool: link: ar cru .libs/libcord.a  cord/cordbscs.o cord/cordprnt.o cord/cordtest.o cord/cordxtra.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libcord.a
libtool: link: ( cd ".libs" && rm -f "libcord.la" && ln -s "../libcord.la" "libcord.la" )
make[3]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2'
make[2]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2'
cp .libs/libgc.a ../
cp .libs/libgccpp.a ../ 
make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2'
----------------------------------------
------------------ GC  -----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=Muscle
make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/Muscle'
export PKG_CXXFLAGS=" -I../gc-7.2/include"
/home/biocbuild/bbs-3.13-bioc/R/bin/R CMD SHLIB -o libMuscle.so aligngivenpath.cpp aligngivenpathsw.cpp aligntwomsas.cpp aligntwoprofs.cpp aln.cpp alpha.cpp anchors.cpp bittraceback.cpp blosum62.cpp blosumla.cpp clust.cpp cluster.cpp clwwt.cpp color.cpp cons.cpp diaglist.cpp diffobjscore.cpp diffpaths.cpp difftrees.cpp difftreese.cpp distcalc.cpp distfunc.cpp distpwkimura.cpp domuscle.cpp dosp.cpp dpreglist.cpp drawtree.cpp edgelist.cpp enumopts.cpp enumtostr.cpp estring.cpp fasta.cpp fasta2.cpp fastclust.cpp fastdist.cpp fastdistjones.cpp fastdistkbit.cpp fastdistkmer.cpp fastdistmafft.cpp fastdistnuc.cpp fastscorepath2.cpp finddiags.cpp finddiagsn.cpp glbalign.cpp glbalign352.cpp glbaligndiag.cpp glbalignle.cpp glbalignsimple.cpp glbalignsp.cpp glbalignspn.cpp glbalignss.cpp glbalndimer.cpp globals.cpp globalslinux.cpp globalsosx.cpp globalsother.cpp globalswin32.cpp gonnet.cpp henikoffweight.cpp henikoffweightpb.cpp html.cpp hydro.cpp intmath.cpp local.cpp main.cpp makerootmsa.cpp makerootmsab.cpp maketree.cpp mhack.cpp mpam200.cpp msa.cpp msa2.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple.cpp nwdasimple2.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore.cpp objscore2.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy.cpp phy2.cpp phy3.cpp phy4.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoredist.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp tomhydro.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp RMuscle.cpp
make[2]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/Muscle'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:186:17: warning: unused variable ‘uLengthA’ [-Wunused-variable]
  186 |  const unsigned uLengthA = msaA.GetColCount();
      |                 ^~~~~~~~
aligngivenpath.cpp:187:17: warning: unused variable ‘uLengthB’ [-Wunused-variable]
  187 |  const unsigned uLengthB = msaB.GetColCount();
      |                 ^~~~~~~~
aligngivenpath.cpp: In function ‘void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpath.cpp:335:19: warning: unused variable ‘uColA’ [-Wunused-variable]
  335 |    const unsigned uColA = uPrefixLengthA - 1;
      |                   ^~~~~
aligngivenpath.cpp:336:19: warning: unused variable ‘uColB’ [-Wunused-variable]
  336 |    const unsigned uColB = uPrefixLengthB - 1;
      |                   ^~~~~
aligngivenpath.cpp:346:19: warning: unused variable ‘uColA’ [-Wunused-variable]
  346 |    const unsigned uColA = uPrefixLengthA - 1;
      |                   ^~~~~
aligngivenpath.cpp:354:19: warning: unused variable ‘uColB’ [-Wunused-variable]
  354 |    const unsigned uColB = uPrefixLengthB - 1;
      |                   ^~~~~
In file included from muscle.h:38,
                 from aligngivenpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:58:17: warning: unused variable ‘uLengthA’ [-Wunused-variable]
   58 |  const unsigned uLengthA = msaA.GetColCount();
      |                 ^~~~~~~~
aligngivenpathsw.cpp:59:17: warning: unused variable ‘uLengthB’ [-Wunused-variable]
   59 |  const unsigned uLengthB = msaB.GetColCount();
      |                 ^~~~~~~~
aligngivenpathsw.cpp: In function ‘void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpathsw.cpp:204:19: warning: unused variable ‘uColA’ [-Wunused-variable]
  204 |    const unsigned uColA = uPrefixLengthA - 1;
      |                   ^~~~~
aligngivenpathsw.cpp:205:19: warning: unused variable ‘uColB’ [-Wunused-variable]
  205 |    const unsigned uColB = uPrefixLengthB - 1;
      |                   ^~~~~
aligngivenpathsw.cpp:215:19: warning: unused variable ‘uColA’ [-Wunused-variable]
  215 |    const unsigned uColA = uPrefixLengthA - 1;
      |                   ^~~~~
aligngivenpathsw.cpp:223:19: warning: unused variable ‘uColB’ [-Wunused-variable]
  223 |    const unsigned uColB = uPrefixLengthB - 1;
      |                   ^~~~~
In file included from muscle.h:38,
                 from aligngivenpathsw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c aligntwomsas.cpp -o aligntwomsas.o
In file included from muscle.h:38,
                 from aligntwomsas.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c aligntwoprofs.cpp -o aligntwoprofs.o
In file included from muscle.h:38,
                 from aligntwoprofs.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c aln.cpp -o aln.o
In file included from muscle.h:38,
                 from aln.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c alpha.cpp -o alpha.o
alpha.cpp: In function ‘unsigned int GetAlphaSize(ALPHA)’:
alpha.cpp:84:9: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch]
   84 |  switch (Alpha)
      |         ^
In file included from muscle.h:38,
                 from alpha.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:162:13: warning: unused variable ‘uWindowCenter’ [-Wunused-variable]
  162 |    unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
      |             ^~~~~~~~~~~~~
anchors.cpp: At global scope:
anchors.cpp:105:13: warning: ‘void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)’ defined but not used [-Wunused-function]
  105 | static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
      |             ^~~~~~~~~~~~
anchors.cpp:53:13: warning: ‘void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)’ defined but not used [-Wunused-function]
   53 | static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
      |             ^~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from anchors.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp: In function ‘void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)’:
bittraceback.cpp:146:7: warning: unused variable ‘Bits’ [-Wunused-variable]
  146 |  char Bits = TraceBack[uLengthA][uLengthB];
      |       ^~~~
bittraceback.cpp: At global scope:
bittraceback.cpp:15:20: warning: ‘const char* BitsToStr(char)’ defined but not used [-Wunused-function]
   15 | static const char *BitsToStr(char Bits)
      |                    ^~~~~~~~~
In file included from muscle.h:38,
                 from bittraceback.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c blosum62.cpp -o blosum62.o
In file included from muscle.h:38,
                 from blosum62.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c blosumla.cpp -o blosumla.o
blosumla.cpp:7:14: warning: ‘Blosum62LA’ defined but not used [-Wunused-variable]
    7 | static float Blosum62LA[20][20] =
      |              ^~~~~~~~~~
In file included from muscle.h:38,
                 from blosumla.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:167:9: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch]
  167 |  switch (m_JoinStyle)
      |         ^
clust.cpp: In member function ‘void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:184:17: warning: unused variable ‘uClusterCount’ [-Wunused-variable]
  184 |  const unsigned uClusterCount = GetClusterCount();
      |                 ^~~~~~~~~~~~~
clust.cpp: In member function ‘void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:204:17: warning: unused variable ‘uClusterCount’ [-Wunused-variable]
  204 |  const unsigned uClusterCount = GetClusterCount();
      |                 ^~~~~~~~~~~~~
clust.cpp: In member function ‘float Clust::ComputeDist(unsigned int, unsigned int)’:
clust.cpp:295:9: warning: enumeration value ‘LINKAGE_Undefined’ not handled in switch [-Wswitch]
  295 |  switch (m_CentroidStyle)
      |         ^
clust.cpp: In member function ‘float Clust::ComputeDistMAFFT(unsigned int, unsigned int)’:
clust.cpp:360:14: warning: unused variable ‘dDistLR’ [-Wunused-variable]
  360 |  const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
      |              ^~~~~~~
clust.cpp: In member function ‘float Clust::ComputeMetric(unsigned int, unsigned int) const’:
clust.cpp:611:9: warning: enumeration value ‘JOIN_Undefined’ not handled in switch [-Wswitch]
  611 |  switch (m_JoinStyle)
      |         ^
In file included from muscle.h:38,
                 from clust.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cluster.cpp -o cluster.o
cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’:
cluster.cpp:284:8: warning: variable ‘bFound’ set but not used [-Wunused-but-set-variable]
  284 |   bool bFound = false;
      |        ^~~~~~
cluster.cpp:267:9: warning: unused variable ‘dMaxDist’ [-Wunused-variable]
  267 |  double dMaxDist = 0.0;
      |         ^~~~~~~~
In file included from muscle.h:38,
                 from cluster.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’:
cluster.cpp:308:33: warning: ‘uIndexClosest2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  308 |   ClusterNode &Child2 = m_Nodes[uIndexClosest2];
      |                                 ^~~~~~~~~~~~~~
cluster.cpp:307:33: warning: ‘uIndexClosest1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  307 |   ClusterNode &Child1 = m_Nodes[uIndexClosest1];
      |                                 ^~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c clwwt.cpp -o clwwt.o
In file included from muscle.h:38,
                 from clwwt.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c color.cpp -o color.o
color.cpp:72:12: warning: ‘int BlosumScore(char, char)’ defined but not used [-Wunused-function]
   72 | static int BlosumScore(char c1, char c2)
      |            ^~~~~~~~~~~
In file included from muscle.h:38,
                 from color.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cons.cpp -o cons.o
In file included from muscle.h:38,
                 from cons.cpp:7:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c diaglist.cpp -o diaglist.o
In file included from muscle.h:38,
                 from diaglist.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
diaglist.cpp: In member function ‘void DiagList::FromPath(const PWPath&)’:
diaglist.cpp:77:6: warning: ‘uStartPosB’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   77 |   Add(uStartPosA, uStartPosB, uLength);
      |   ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diaglist.cpp:77:6: warning: ‘uStartPosA’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp: In function ‘SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)’:
diffobjscore.cpp:76:17: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
   76 |  const unsigned uSeqCount = msa.GetSeqCount();
      |                 ^~~~~~~~~
diffobjscore.cpp:77:17: warning: unused variable ‘uColCount’ [-Wunused-variable]
   77 |  const unsigned uColCount = msa.GetColCount();
      |                 ^~~~~~~~~
In file included from muscle.h:38,
                 from diffobjscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c diffpaths.cpp -o diffpaths.o
In file included from muscle.h:38,
                 from diffpaths.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c difftrees.cpp -o difftrees.o
difftrees.cpp: In function ‘void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)’:
difftrees.cpp:161:17: warning: unused variable ‘uLeafCount2’ [-Wunused-variable]
  161 |  const unsigned uLeafCount2 = Tree2.GetLeafCount();
      |                 ^~~~~~~~~~~
In file included from muscle.h:38,
                 from difftrees.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c difftreese.cpp -o difftreese.o
In file included from muscle.h:38,
                 from difftreese.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c distcalc.cpp -o distcalc.o
In file included from muscle.h:38,
                 from distcalc.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c distfunc.cpp -o distfunc.o
In file included from muscle.h:38,
                 from distfunc.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c distpwkimura.cpp -o distpwkimura.o
In file included from muscle.h:38,
                 from distpwkimura.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c domuscle.cpp -o domuscle.o
domuscle.cpp: In function ‘void DoMuscle(MuscleInput*, MuscleOutput*)’:
domuscle.cpp:169:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  169 |   if (g_bClusterOnly)
      |   ^~
domuscle.cpp:172:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  172 |    return;
      |    ^~~~~~
domuscle.cpp:180:6: warning: unused variable ‘PNlength’ [-Wunused-variable]
  180 |  int PNlength = (msaInput->inputSeqs).Length();
      |      ^~~~~~~~
In file included from muscle.h:38,
                 from RMuscle.h:4,
                 from domuscle.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c dosp.cpp -o dosp.o
In file included from muscle.h:38,
                 from dosp.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp: In function ‘void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)’:
dpreglist.cpp:82:19: warning: unused variable ‘uDiagLengthMinusCaps’ [-Wunused-variable]
   82 |    const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
      |                   ^~~~~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from dpreglist.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c drawtree.cpp -o drawtree.o
In file included from muscle.h:38,
                 from drawtree.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c edgelist.cpp -o edgelist.o
In file included from muscle.h:38,
                 from edgelist.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c enumopts.cpp -o enumopts.o
In file included from muscle.h:38,
                 from enumopts.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c enumtostr.cpp -o enumtostr.o
In file included from muscle.h:38,
                 from enumtostr.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c estring.cpp -o estring.o
estring.cpp:464:13: warning: ‘bool CanMultiplyEstrings(const short int*, const short int*)’ defined but not used [-Wunused-function]
  464 | static bool CanMultiplyEstrings(const short es1[], const short es2[])
      |             ^~~~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from estring.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
estring.cpp: In function ‘void EstringsToPath(const short int*, const short int*, PWPath&)’:
estring.cpp:409:3: warning: ‘cType’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  409 |   switch (cType)
      |   ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fasta.cpp -o fasta.o
fasta.cpp: In member function ‘void MSA::FromFASTAFile(TextFile&)’:
fasta.cpp:15:11: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
   15 |  unsigned uSeqCount = 0;
      |           ^~~~~~~~~
fasta.cpp:16:11: warning: unused variable ‘uColCount’ [-Wunused-variable]
   16 |  unsigned uColCount = uInsane;
      |           ^~~~~~~~~
In file included from muscle.h:38,
                 from fasta.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fasta2.cpp -o fasta2.o
In file included from muscle.h:38,
                 from fasta2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastclust.cpp -o fastclust.o
In file included from muscle.h:38,
                 from fastclust.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastdist.cpp -o fastdist.o
In file included from muscle.h:38,
                 from fastdist.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastdistjones.cpp -o fastdistjones.o
In file included from muscle.h:38,
                 from fastdistjones.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastdistkbit.cpp -o fastdistkbit.o
In file included from muscle.h:38,
                 from fastdistkbit.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function ‘void FastDistKmer(const SeqVect&, DistFunc&)’:
fastdistkmer.cpp:235:11: warning: unused variable ‘KD’ [-Wunused-variable]
  235 |    double KD = KimuraDist(EstimatedPctId);
      |           ^~
In file included from muscle.h:38,
                 from fastdistkmer.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function ‘void DistKmer6_6(const SeqVect&, DistFunc&)’:
fastdistmafft.cpp:239:15: warning: unused variable ‘pName1’ [-Wunused-variable]
  239 |   const char *pName1 = s1.GetName();
      |               ^~~~~~
fastdistmafft.cpp: At global scope:
fastdistmafft.cpp:104:13: warning: ‘void ListCount(const unsigned char*)’ defined but not used [-Wunused-function]
  104 | static void ListCount(const unsigned char Count[])
      |             ^~~~~~~~~
In file included from muscle.h:38,
                 from fastdistmafft.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function ‘void DistKmer4_6(const SeqVect&, DistFunc&)’:
fastdistnuc.cpp:223:15: warning: unused variable ‘pName1’ [-Wunused-variable]
  223 |   const char *pName1 = s1.GetName();
      |               ^~~~~~
fastdistnuc.cpp: At global scope:
fastdistnuc.cpp:85:13: warning: ‘void ListCount(const unsigned char*)’ defined but not used [-Wunused-function]
   85 | static void ListCount(const unsigned char Count[])
      |             ^~~~~~~~~
fastdistnuc.cpp:33:17: warning: ‘uResidueGroupCount’ defined but not used [-Wunused-variable]
   33 | static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
      |                 ^~~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from fastdistnuc.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastscorepath2.cpp -o fastscorepath2.o
In file included from muscle.h:38,
                 from fastscorepath2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c finddiags.cpp -o finddiags.o
finddiags.cpp:11:14: warning: ‘char* TupleToStr(int)’ defined but not used [-Wunused-function]
   11 | static char *TupleToStr(int t)
      |              ^~~~~~~~~~
In file included from muscle.h:38,
                 from finddiags.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function ‘char* TupleToStr(int)’:
finddiagsn.cpp:16:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   16 |  for (int i = 0; i < K; ++i)
      |                  ~~^~~
finddiagsn.cpp: At global scope:
finddiagsn.cpp:12:14: warning: ‘char* TupleToStr(int)’ defined but not used [-Wunused-function]
   12 | static char *TupleToStr(int t)
      |              ^~~~~~~~~~
In file included from muscle.h:38,
                 from finddiagsn.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c glbalign.cpp -o glbalign.o
In file included from muscle.h:38,
                 from glbalign.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c glbalign352.cpp -o glbalign352.o
In file included from muscle.h:38,
                 from glbalign352.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c glbaligndiag.cpp -o glbaligndiag.o
In file included from muscle.h:38,
                 from glbaligndiag.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c glbalignle.cpp -o glbalignle.o
In file included from muscle.h:38,
                 from glbalignle.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
glbalignle.cpp: In function ‘SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignle.cpp:431:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  431 |   iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                ^~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c glbalignsimple.cpp -o glbalignsimple.o
glbalignsimple.cpp:52:13: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
   52 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
glbalignsimple.cpp:28:13: warning: ‘void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
   28 | static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
In file included from muscle.h:38,
                 from glbalignsimple.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c glbalignsp.cpp -o glbalignsp.o
In file included from muscle.h:38,
                 from glbalignsp.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
glbalignsp.cpp: In function ‘SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignsp.cpp:366:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  366 |   iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                ^~~~~~~~~~~~~~~~
glbalignsp.cpp:305:24: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  305 |     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                        ^~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c glbalignspn.cpp -o glbalignspn.o
In file included from muscle.h:38,
                 from glbalignspn.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
glbalignspn.cpp: In function ‘SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)’:
glbalignspn.cpp:401:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  401 |   iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                ^~~~~~~~~~~~~~~~
glbalignspn.cpp:340:24: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  340 |     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                        ^~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’:
glbalignss.cpp:177:16: warning: unused variable ‘ptrRowA’ [-Wunused-variable]
  177 |   const SCORE *ptrRowA = MxRowA[i];
      |                ^~~~~~~
glbalignss.cpp:119:17: warning: unused variable ‘uPrefixCountA’ [-Wunused-variable]
  119 |  const unsigned uPrefixCountA = uLengthA + 1;
      |                 ^~~~~~~~~~~~~
glbalignss.cpp:120:17: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable]
  120 |  const unsigned uPrefixCountB = uLengthB + 1;
      |                 ^~~~~~~~~~~~~
glbalignss.cpp: At global scope:
glbalignss.cpp:11:14: warning: ‘SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
   11 | static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
      |              ^~~~~
In file included from muscle.h:38,
                 from glbalignss.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’:
glbalignss.cpp:310:16: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  310 |   iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                ^~~~~~~~~~~~~~~~
glbalignss.cpp:252:24: warning: ‘uInsertPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  252 |     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                        ^~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function ‘SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)’:
glbalndimer.cpp:123:9: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch]
  123 |  switch (g_PPScore)
      |         ^
glbalndimer.cpp:123:9: warning: enumeration value ‘PPSCORE_SPN’ not handled in switch [-Wswitch]
glbalndimer.cpp: At global scope:
glbalndimer.cpp:14:20: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used [-Wunused-function]
   14 | static const char *LocalScoreToStr(SCORE s)
      |                    ^~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from glbalndimer.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c globals.cpp -o globals.o
In file included from muscle.h:38,
                 from globals.cpp:6:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c globalslinux.cpp -o globalslinux.o
globalslinux.cpp: In function ‘double GetNAN()’:
globalslinux.cpp:17:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   17 |  double dNAN = *( double* )nan;
      |                 ^~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from globalslinux.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c globalsosx.cpp -o globalsosx.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c globalsother.cpp -o globalsother.o
In file included from muscle.h:38,
                 from globalsother.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c globalswin32.cpp -o globalswin32.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c gonnet.cpp -o gonnet.o
gonnet.cpp:137:14: warning: ‘Gonnet160’ defined but not used [-Wunused-variable]
  137 | static SCORE Gonnet160[20][20] =
      |              ^~~~~~~~~
In file included from muscle.h:38,
                 from gonnet.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c henikoffweight.cpp -o henikoffweight.o
In file included from muscle.h:38,
                 from henikoffweight.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c henikoffweightpb.cpp -o henikoffweightpb.o
In file included from muscle.h:38,
                 from henikoffweightpb.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c html.cpp -o html.o
In file included from muscle.h:38,
                 from html.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c hydro.cpp -o hydro.o
In file included from muscle.h:38,
                 from hydro.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c intmath.cpp -o intmath.o
In file included from muscle.h:38,
                 from intmath.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c local.cpp -o local.o
In file included from muscle.h:38,
                 from local.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c main.cpp -o main.o
In file included from muscle.h:38,
                 from main.cpp:3:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp: In function ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’:
makerootmsa.cpp:18:17: warning: unused variable ‘uSeqLength’ [-Wunused-variable]
   18 |  const unsigned uSeqLength = s.Length();
      |                 ^~~~~~~~~~
makerootmsa.cpp: In function ‘short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)’:
makerootmsa.cpp:94:17: warning: unused variable ‘Path’ [-Wunused-variable]
   94 |   const PWPath &Path = Nodes[uNodeIndex].m_Path;
      |                 ^~~~
makerootmsa.cpp: In function ‘void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)’:
makerootmsa.cpp:168:17: warning: unused variable ‘uTreeNodeCount’ [-Wunused-variable]
  168 |  const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
      |                 ^~~~~~~~~~~~~~
makerootmsa.cpp: At global scope:
makerootmsa.cpp:12:13: warning: ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’ defined but not used [-Wunused-function]
   12 | static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
      |             ^~~~~~~
In file included from muscle.h:38,
                 from makerootmsa.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c makerootmsab.cpp -o makerootmsab.o
In file included from muscle.h:38,
                 from makerootmsab.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c maketree.cpp -o maketree.o
In file included from muscle.h:38,
                 from maketree.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mhack.cpp -o mhack.o
In file included from muscle.h:38,
                 from mhack.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mpam200.cpp -o mpam200.o
In file included from muscle.h:38,
                 from mpam200.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msa.cpp -o msa.o
msa.cpp:419:13: warning: ‘void FmtPad(unsigned int)’ defined but not used [-Wunused-function]
  419 | static void FmtPad(unsigned n)
      |             ^~~~~~
msa.cpp:407:13: warning: ‘void FmtInt0(unsigned int, unsigned int)’ defined but not used [-Wunused-function]
  407 | static void FmtInt0(unsigned u, unsigned uWidth)
      |             ^~~~~~~
msa.cpp:392:13: warning: ‘void FmtInt(unsigned int, unsigned int)’ defined but not used [-Wunused-function]
  392 | static void FmtInt(unsigned u, unsigned uWidth)
      |             ^~~~~~
msa.cpp:385:13: warning: ‘void FmtChar(char, unsigned int)’ defined but not used [-Wunused-function]
  385 | static void FmtChar(char c, unsigned uWidth)
      |             ^~~~~~~
In file included from muscle.h:38,
                 from msa.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msa2.cpp -o msa2.o
msa2.cpp: In function ‘void SetMSAWeightsMuscle(MSA&)’:
msa2.cpp:357:9: warning: enumeration value ‘SEQWEIGHT_Undefined’ not handled in switch [-Wswitch]
  357 |  switch (Method)
      |         ^
msa2.cpp: In function ‘void MSAAppend(MSA&, const MSA&)’:
msa2.cpp:476:17: warning: unused variable ‘uColCountCat’ [-Wunused-variable]
  476 |  const unsigned uColCountCat = uColCount1 + uColCount2;
      |                 ^~~~~~~~~~~~
In file included from muscle.h:38,
                 from msa2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msadistkimura.cpp -o msadistkimura.o
In file included from muscle.h:38,
                 from msadistkimura.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msf.cpp -o msf.o
msf.cpp:24:20: warning: ‘const char* strfind(const char*, const char*)’ defined but not used [-Wunused-function]
   24 | static const char *strfind(const char *s, const char *t)
      |                    ^~~~~~~
In file included from muscle.h:38,
                 from msf.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c muscle.cpp -o muscle.o
In file included from muscle.h:38,
                 from muscle.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c muscleout.cpp -o muscleout.o
In file included from muscle.h:38,
                 from muscleout.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c nucmx.cpp -o nucmx.o
In file included from muscle.h:38,
                 from nucmx.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c nwdasimple.cpp -o nwdasimple.o
In file included from muscle.h:38,
                 from nwdasimple.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c nwdasimple2.cpp -o nwdasimple2.o
In file included from muscle.h:38,
                 from nwdasimple2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c nwdasmall.cpp -o nwdasmall.o
In file included from muscle.h:38,
                 from nwdasmall.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c nwrec.cpp -o nwrec.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c nwsmall.cpp -o nwsmall.o
In file included from muscle.h:38,
                 from nwsmall.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:31:9: warning: enumeration value ‘OBJSCORE_Undefined’ not handled in switch [-Wswitch]
   31 |  switch (OS)
      |         ^
objscore.cpp:31:9: warning: enumeration value ‘OBJSCORE_SPM’ not handled in switch [-Wswitch]
In file included from muscle.h:38,
                 from objscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c objscore2.cpp -o objscore2.o
objscore2.cpp: In function ‘SCORE TermGapScore(bool)’:
objscore2.cpp:22:9: warning: enumeration value ‘TERMGAPS_Undefined’ not handled in switch [-Wswitch]
   22 |  switch (g_TermGaps)
      |         ^
objscore2.cpp: In function ‘SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)’:
objscore2.cpp:62:8: warning: unused variable ‘scoreGaps’ [-Wunused-variable]
   62 |  SCORE scoreGaps = 0;
      |        ^~~~~~~~~
objscore2.cpp:63:7: warning: unused variable ‘bGapping1’ [-Wunused-variable]
   63 |  bool bGapping1 = false;
      |       ^~~~~~~~~
objscore2.cpp:64:7: warning: unused variable ‘bGapping2’ [-Wunused-variable]
   64 |  bool bGapping2 = false;
      |       ^~~~~~~~~
objscore2.cpp:67:7: warning: variable ‘bLeftTermGap’ set but not used [-Wunused-but-set-variable]
   67 |  bool bLeftTermGap = false;
      |       ^~~~~~~~~~~~
objscore2.cpp:82:7: warning: variable ‘bRightTermGap’ set but not used [-Wunused-but-set-variable]
   82 |  bool bRightTermGap = false;
      |       ^~~~~~~~~~~~~
objscore2.cpp: In function ‘SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)’:
objscore2.cpp:140:7: warning: variable ‘bLeftTermGap’ set but not used [-Wunused-but-set-variable]
  140 |  bool bLeftTermGap = false;
      |       ^~~~~~~~~~~~
objscore2.cpp:155:7: warning: variable ‘bRightTermGap’ set but not used [-Wunused-but-set-variable]
  155 |  bool bRightTermGap = false;
      |       ^~~~~~~~~~~~~
objscore2.cpp: In function ‘SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)’:
objscore2.cpp:314:17: warning: unused variable ‘uColCount2’ [-Wunused-variable]
  314 |  const unsigned uColCount2 = msa2.GetColCount();
      |                 ^~~~~~~~~~
objscore2.cpp: In function ‘SCORE ObjScoreXP(const MSA&, const MSA&)’:
objscore2.cpp:493:17: warning: unused variable ‘w’ [-Wunused-variable]
  493 |    const WEIGHT w = w1*w2;
      |                 ^
In file included from muscle.h:38,
                 from objscore2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c objscoreda.cpp -o objscoreda.o
In file included from muscle.h:38,
                 from objscoreda.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c onexception.cpp -o onexception.o
In file included from muscle.h:38,
                 from onexception.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c options.cpp -o options.o
In file included from muscle.h:38,
                 from options.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c outweights.cpp -o outweights.o
In file included from muscle.h:38,
                 from outweights.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:6:14: warning: ‘PAM200’ defined but not used [-Wunused-variable]
    6 | static float PAM200[23][23] =
      |              ^~~~~~
In file included from muscle.h:38,
                 from pam200mafft.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c params.cpp -o params.o
params.cpp: In function ‘void SetPPScore(bool)’:
params.cpp:441:9: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch [-Wswitch]
  441 |  switch (g_PPScore)
      |         ^
In file included from muscle.h:38,
                 from params.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c phy.cpp -o phy.o
phy.cpp: In member function ‘void Tree::RootUnrootedTree(ROOT)’:
phy.cpp:665:9: warning: unused variable ‘dEdgeLength’ [-Wunused-variable]
  665 |  double dEdgeLength = GetEdgeLength(uNode1, uNode2);
      |         ^~~~~~~~~~~
In file included from muscle.h:38,
                 from phy.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c phy2.cpp -o phy2.o
In file included from muscle.h:38,
                 from phy2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c phy3.cpp -o phy3.o
phy3.cpp: In function ‘void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)’:
phy3.cpp:125:15: warning: unused variable ‘dThisDist’ [-Wunused-variable]
  125 |  const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
      |               ^~~~~~~~~
phy3.cpp: In function ‘void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)’:
phy3.cpp:167:17: warning: unused variable ‘uLeafCount’ [-Wunused-variable]
  167 |  const unsigned uLeafCount = tree.GetLeafCount();
      |                 ^~~~~~~~~~
phy3.cpp:190:9: warning: unused variable ‘dAllMaxDist’ [-Wunused-variable]
  190 |  double dAllMaxDist = -1e20;
      |         ^~~~~~~~~~~
phy3.cpp:191:11: warning: unused variable ‘uMaxFrom’ [-Wunused-variable]
  191 |  unsigned uMaxFrom = NULL_NEIGHBOR;
      |           ^~~~~~~~
phy3.cpp:192:11: warning: unused variable ‘uMaxTo’ [-Wunused-variable]
  192 |  unsigned uMaxTo = NULL_NEIGHBOR;
      |           ^~~~~~
phy3.cpp: In function ‘void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)’:
phy3.cpp:263:11: warning: variable ‘uMostDistantLeaf’ set but not used [-Wunused-but-set-variable]
  263 |  unsigned uMostDistantLeaf = NULL_NEIGHBOR;
      |           ^~~~~~~~~~~~~~~~
phy3.cpp: At global scope:
phy3.cpp:45:13: warning: ‘void ListEIs(EdgeInfo**, unsigned int)’ defined but not used [-Wunused-function]
   45 | static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
      |             ^~~~~~~
In file included from muscle.h:38,
                 from phy3.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c phy4.cpp -o phy4.o
In file included from muscle.h:38,
                 from phy4.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c phyfromclust.cpp -o phyfromclust.o
In file included from muscle.h:38,
                 from phyfromclust.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c phyfromfile.cpp -o phyfromfile.o
In file included from muscle.h:38,
                 from phyfromfile.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c physeq.cpp -o physeq.o
physeq.cpp: In member function ‘void MSA::ToPhySequentialFile(TextFile&) const’:
physeq.cpp:60:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   60 |     if (Col == ColCount)
      |         ~~~~^~~~~~~~~~~
physeq.cpp:71:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   71 |    if (Col == ColCount)
      |        ~~~~^~~~~~~~~~~
physeq.cpp: In member function ‘void MSA::ToPhyInterleavedFile(TextFile&) const’:
physeq.cpp:112:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  112 |     if (Col == ColCount)
      |         ~~~~^~~~~~~~~~~
physeq.cpp:124:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  124 |   if (Col == ColCount)
      |       ~~~~^~~~~~~~~~~
In file included from muscle.h:38,
                 from physeq.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c phytofile.cpp -o phytofile.o
In file included from muscle.h:38,
                 from phytofile.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c posgap.cpp -o posgap.o
In file included from muscle.h:38,
                 from posgap.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ppscore.cpp -o ppscore.o
In file included from muscle.h:38,
                 from ppscore.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:22:9: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
   22 |   switch(m_Distance)
      |         ^
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
In file included from muscle.h:38,
                 from profdb.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c profile.cpp -o profile.o
In file included from muscle.h:38,
                 from profile.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp: In function ‘void ListProfile(const ProfPos*, unsigned int, const MSA*)’:
profilefrommsa.cpp:131:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  131 |   if (-1 == PP.m_uResidueGroup)
      |       ~~~^~~~~~~~~~~~~~~~~~~~~
profilefrommsa.cpp: In function ‘unsigned int ResidueGroupFromFCounts(const FCOUNT*)’:
profilefrommsa.cpp:230:9: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch [-Wswitch]
  230 |  switch (g_Alpha)
      |         ^
profilefrommsa.cpp: In function ‘ProfPos* ProfileFromMSA(const MSA&)’:
profilefrommsa.cpp:245:17: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
  245 |  const unsigned uSeqCount = a.GetSeqCount();
      |                 ^~~~~~~~~
profilefrommsa.cpp:253:11: warning: unused variable ‘uHydrophobicRunLength’ [-Wunused-variable]
  253 |  unsigned uHydrophobicRunLength = 0;
      |           ^~~~~~~~~~~~~~~~~~~~~
profilefrommsa.cpp: At global scope:
profilefrommsa.cpp:15:20: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used [-Wunused-function]
   15 | static const char *LocalScoreToStr(SCORE s)
      |                    ^~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from profilefrommsa.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c progalign.cpp -o progalign.o
progalign.cpp: In function ‘ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)’:
progalign.cpp:41:17: warning: unused variable ‘uIterCount’ [-Wunused-variable]
   41 |  const unsigned uIterCount = uSeqCount - 1;
      |                 ^~~~~~~~~~
In file included from muscle.h:38,
                 from progalign.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c progress.cpp -o progress.o
In file included from muscle.h:38,
                 from progress.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c progressivealign.cpp -o progressivealign.o
In file included from muscle.h:38,
                 from progressivealign.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function ‘void PWPath::Validate() const’:
pwpath.cpp:80:16: warning: unused variable ‘LastEdge’ [-Wunused-variable]
   80 |  const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
      |                ^~~~~~~~
pwpath.cpp: In member function ‘void PWPath::FromFile(TextFile&)’:
pwpath.cpp:213:11: warning: unused variable ‘uEdgeIndex’ [-Wunused-variable]
  213 |  unsigned uEdgeIndex = 0;
      |           ^~~~~~~~~~
In file included from muscle.h:38,
                 from pwpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c readmx.cpp -o readmx.o
readmx.cpp: In function ‘float (* ReadMx(TextFile&))[32][32]’:
readmx.cpp:83:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   83 |  for (int i = 0; i < MAX_ALPHA; ++i)
      |                  ~~^~~~~~~~~~~
readmx.cpp:84:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   84 |   for (int j = 0; j < MAX_ALPHA; ++j)
      |                   ~~^~~~~~~~~~~
readmx.cpp: In function ‘float (* ReadMxFromR(std::vector<std::__cxx11::basic_string<char> >, float (*)[32]))[32][32]’:
readmx.cpp:184:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  184 |  for (int i = 0; i < MAX_ALPHA; ++i)
      |                  ~~^~~~~~~~~~~
readmx.cpp:185:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  185 |   for (int j = 0; j < MAX_ALPHA; ++j)
      |                   ~~^~~~~~~~~~~
readmx.cpp: At global scope:
readmx.cpp:30:17: warning: ‘unsigned int MxCharToLetter(char)’ defined but not used [-Wunused-function]
   30 | static unsigned MxCharToLetter(char c)
      |                 ^~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from readmx.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c realigndiffs.cpp -o realigndiffs.o
In file included from muscle.h:38,
                 from realigndiffs.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:77:13: warning: unused variable ‘uNewRight’ [-Wunused-variable]
   77 |    unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
      |             ^~~~~~~~~
realigndiffse.cpp:80:13: warning: unused variable ‘uOldRight’ [-Wunused-variable]
   80 |    unsigned uOldRight = OldTree.GetRight(uOld);
      |             ^~~~~~~~~
In file included from muscle.h:38,
                 from realigndiffse.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:22:9: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
   22 |   switch(m_Distance)
      |         ^
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
In file included from muscle.h:38,
                 from refine.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c refinehoriz.cpp -o refinehoriz.o
In file included from muscle.h:38,
                 from refinehoriz.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp: In function ‘bool RefineSubfams(MSA&, const Tree&, unsigned int)’:
refinesubfams.cpp:63:17: warning: unused variable ‘uNodeCount’ [-Wunused-variable]
   63 |  const unsigned uNodeCount = tree.GetNodeCount();
      |                 ^~~~~~~~~~
In file included from muscle.h:38,
                 from refinesubfams.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c refinetree.cpp -o refinetree.o
In file included from muscle.h:38,
                 from refinetree.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c refinetreee.cpp -o refinetreee.o
In file included from muscle.h:38,
                 from refinetreee.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c refinevert.cpp -o refinevert.o
In file included from muscle.h:38,
                 from refinevert.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c refinew.cpp -o refinew.o
refinew.cpp: In function ‘void AppendMSA(MSA&, const MSA&)’:
refinew.cpp:22:17: warning: unused variable ‘uColCountCat’ [-Wunused-variable]
   22 |  const unsigned uColCountCat = uColCount1 + uColCount2;
      |                 ^~~~~~~~~~~~
refinew.cpp: In function ‘void RefineW(const MSA&, MSA&)’:
refinew.cpp:125:13: warning: unused variable ‘uOutCols’ [-Wunused-variable]
  125 |    unsigned uOutCols = msaOut.GetColCount();
      |             ^~~~~~~~
In file included from muscle.h:38,
                 from refinew.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c savebest.cpp -o savebest.o
In file included from muscle.h:38,
                 from savebest.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c scoredist.cpp -o scoredist.o
In file included from muscle.h:38,
                 from scoredist.cpp:3:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c scoregaps.cpp -o scoregaps.o
scoregaps.cpp:80:14: warning: ‘SCORE Penalty(unsigned int, bool)’ defined but not used [-Wunused-function]
   80 | static SCORE Penalty(unsigned Length, bool Term)
      |              ^~~~~~~
scoregaps.cpp:37:13: warning: ‘void FreeGapInfo(GAPINFO*)’ defined but not used [-Wunused-function]
   37 | static void FreeGapInfo(GAPINFO *GI)
      |             ^~~~~~~~~~~
In file included from muscle.h:38,
                 from scoregaps.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c scorehistory.cpp -o scorehistory.o
In file included from muscle.h:38,
                 from scorehistory.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c scorepp.cpp -o scorepp.o
In file included from muscle.h:38,
                 from scorepp.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c seq.cpp -o seq.o
In file included from muscle.h:38,
                 from seq.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c seqvect.cpp -o seqvect.o
In file included from muscle.h:38,
                 from seqvect.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c setblosumweights.cpp -o setblosumweights.o
In file included from muscle.h:38,
                 from setblosumweights.cpp:42:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c setgscweights.cpp -o setgscweights.o
In file included from muscle.h:38,
                 from setgscweights.cpp:104:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c setnewhandler.cpp -o setnewhandler.o
In file included from muscle.h:38,
                 from setnewhandler.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c spfast.cpp -o spfast.o
spfast.cpp: In function ‘SCORE ObjScoreSPDimer(const MSA&)’:
spfast.cpp:252:17: warning: unused variable ‘uSeqCount’ [-Wunused-variable]
  252 |  const unsigned uSeqCount = msa.GetSeqCount();
      |                 ^~~~~~~~~
spfast.cpp: At global scope:
spfast.cpp:59:14: warning: ‘SCORE SPColBrute(const MSA&, unsigned int)’ defined but not used [-Wunused-function]
   59 | static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
      |              ^~~~~~~~~~
spfast.cpp:14:20: warning: ‘const char* GapTypeToStr(int)’ defined but not used [-Wunused-function]
   14 | static const char *GapTypeToStr(int GapType)
      |                    ^~~~~~~~~~~~
In file included from muscle.h:38,
                 from spfast.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sptest.cpp -o sptest.o
In file included from muscle.h:38,
                 from sptest.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c stabilize.cpp -o stabilize.o
In file included from muscle.h:38,
                 from stabilize.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c subfam.cpp -o subfam.o
subfam.cpp: In function ‘void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)’:
subfam.cpp:173:6: warning: unused variable ‘NotUsed’ [-Wunused-variable]
  173 |  int NotUsed = system(CmdLine);
      |      ^~~~~~~
In file included from muscle.h:38,
                 from subfam.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c subfams.cpp -o subfams.o
subfams.cpp:52:13: warning: ‘void Relax(DistFunc&, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
   52 | static void Relax(DistFunc &DF, unsigned u, unsigned v)
      |             ^~~~~
subfams.cpp:40:13: warning: ‘void InitializeSingleSource(DistFunc&, unsigned int)’ defined but not used [-Wunused-function]
   40 | static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
      |             ^~~~~~~~~~~~~~~~~~~~~~
subfams.cpp:10:13: warning: ‘void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)’ defined but not used [-Wunused-function]
   10 | static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
      |             ^~~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from subfams.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sw.cpp -o sw.o
sw.cpp:20:13: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used [-Wunused-function]
   20 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
In file included from muscle.h:38,
                 from sw.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c termgaps.cpp -o termgaps.o
In file included from muscle.h:38,
                 from termgaps.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c textfile.cpp -o textfile.o
textfile.cpp: In member function ‘void TextFile::PutChar(char)’:
textfile.cpp:111:6: warning: unused variable ‘i’ [-Wunused-variable]
  111 |  int i = fputc(c, m_ptrFile);
      |      ^
textfile.cpp: In member function ‘void TextFile::PutString(const char*)’:
textfile.cpp:124:6: warning: unused variable ‘iError’ [-Wunused-variable]
  124 |  int iError = fputs(szLine, m_ptrFile);
      |      ^~~~~~
In file included from muscle.h:38,
                 from textfile.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c threewaywt.cpp -o threewaywt.o
In file included from muscle.h:38,
                 from threewaywt.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tomhydro.cpp -o tomhydro.o
In file included from muscle.h:38,
                 from tomhydro.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:21:17: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable]
   21 |  const unsigned uPrefixCountB = uLengthB + 1;
      |                 ^~~~~~~~~~~~~
In file included from muscle.h:38,
                 from traceback.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
traceback.cpp: In function ‘SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)’:
traceback.cpp:72:3: warning: ‘cPrevEdgeType’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   72 |   switch (cEdgeType)
      |   ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tracebackopt.cpp -o tracebackopt.o
In file included from muscle.h:38,
                 from tracebackopt.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:22:17: warning: unused variable ‘uPrefixCountB’ [-Wunused-variable]
   22 |  const unsigned uPrefixCountB = uLengthB + 1;
      |                 ^~~~~~~~~~~~~
tracebacksw.cpp:29:8: warning: unused variable ‘scoreMax’ [-Wunused-variable]
   29 |  SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
      |        ^~~~~~~~
In file included from muscle.h:38,
                 from tracebacksw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
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:47:3: warning: ‘cPrevEdgeType’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   47 |   switch (cEdgeType)
      |   ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -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:22:9: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch [-Wswitch]
   22 |   switch(m_Distance)
      |         ^
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch [-Wswitch]
In file included from muscle.h:38,
                 from treefrommsa.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c typetostr.cpp -o typetostr.o
In file included from muscle.h:38,
                 from typetostr.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
typetostr.cpp: In function ‘const char* SecsToStr(long unsigned int)’:
typetostr.cpp:13:21: warning: ‘:’ directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=]
   13 |  sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss);
      |                     ^
typetostr.cpp:13:15: note: directive argument in the range [0, 59]
   13 |  sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss);
      |               ^~~~~~~~~~~~~~~~~~~
typetostr.cpp:13:15: note: directive argument in the range [0, 59]
In file included from /usr/include/stdio.h:867,
                 from /usr/include/c++/9/cstdio:42,
                 from /usr/include/c++/9/ext/string_conversions.h:43,
                 from /usr/include/c++/9/bits/basic_string.h:6493,
                 from /usr/include/c++/9/string:55,
                 from muscle.h:2,
                 from typetostr.cpp:1:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 9 and 23 bytes into a destination of size 16
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c upgma2.cpp -o upgma2.o
upgma2.cpp:68:13: warning: ‘void ListState()’ defined but not used [-Wunused-function]
   68 | static void ListState()
      |             ^~~~~~~~~
In file included from muscle.h:38,
                 from upgma2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
upgma2.cpp: In function ‘void UPGMA2(const DistCalc&, Tree&, LINKAGE)’:
upgma2.cpp:292:15: warning: ‘dtNewDist’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  292 |    g_Dist[vL] = dtNewDist;
      |    ~~~~~~~~~~~^~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c usage.cpp -o usage.o
In file included from muscle.h:38,
                 from usage.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c validateids.cpp -o validateids.o
In file included from muscle.h:38,
                 from validateids.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c vtml2.cpp -o vtml2.o
In file included from muscle.h:38,
                 from vtml2.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c writescorefile.cpp -o writescorefile.o
In file included from muscle.h:38,
                 from writescorefile.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
writescorefile.cpp: In function ‘void WriteScoreFile(const MSA&)’:
writescorefile.cpp:40:9: warning: ‘Score’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   40 |    dSum += Score;
      |    ~~~~~^~~~~~~~
writescorefile.cpp:27:11: note: ‘Score’ was declared here
   27 |    double Score;
      |           ^~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RMuscle.cpp -o RMuscle.o
In file included from muscle.h:38,
                 from RMuscle.h:4,
                 from RMuscle.cpp:1:
intmath.h:59:15: warning: ‘double ScoreToDouble(SCORE)’ defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/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 -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
make[2]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/Muscle'
ar rcs libMuscle.a aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o
cp libMuscle.a ../
make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalW
make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalW'
./configure; \
cd src; \
export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. "; \
/home/biocbuild/bbs-3.13-bioc/R/bin/R CMD SHLIB -o libClustalW.so pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp && \
ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \
cp libClustalW.a ../../
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
building for linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make sets $(MAKE)... (cached) yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for ranlib... ranlib
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating m4/Makefile
config.status: creating src/Makefile
config.status: creating src/clustalw_version.h
config.status: creating src/config.h
config.status: executing depfiles commands
make[2]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalW/src'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/FileReader.cpp -o fileInput/FileReader.o
In file included from fileInput/FileReader.cpp:29:
fileInput/FileReader.h:43:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   43 |         void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from fileInput/FileReader.h:11,
                 from fileInput/FileReader.cpp:29:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
fileInput/FileReader.cpp: In member function ‘int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)’:
fileInput/FileReader.cpp:155:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  155 |     auto_ptr<FileParser> fileParser; // Means we dont need to delete it!
      |     ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from fileInput/FileReader.h:11,
                 from fileInput/FileReader.cpp:29:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
fileInput/FileReader.cpp: In member function ‘int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)’:
fileInput/FileReader.cpp:321:6: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  321 |      auto_ptr<FileParser> fileParser; // Means we dont need to delete it!
      |      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from fileInput/FileReader.h:11,
                 from fileInput/FileReader.cpp:29:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
fileInput/FileReader.cpp:421:10: warning: variable ‘maxAlnLength’ set but not used [-Wunused-but-set-variable]
  421 |      int maxAlnLength; // Get values from the Alignment object.
      |          ^~~~~~~~~~~~
fileInput/FileReader.cpp: At global scope:
fileInput/FileReader.cpp:563:42: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  563 | void FileReader::checkInfile(int *nseqs, auto_ptr<FileParser>& fileParser)
      |                                          ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from fileInput/FileReader.h:11,
                 from fileInput/FileReader.cpp:29:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
fileInput/FileReader.cpp: In member function ‘void clustalw::FileReader::checkInfile(int*, std::auto_ptr<clustalw::FileParser>&)’:
fileInput/FileReader.cpp:692:21: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
  692 |     catch(exception ex)
      |                     ^~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/FileParser.cpp -o fileInput/FileParser.o
fileInput/FileParser.cpp: In member function ‘std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)’:
fileInput/FileParser.cpp:38:7: warning: unused variable ‘n’ [-Wunused-variable]
   38 |   int n = (*input).inputSeqs.size();
      |       ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
In file included from tree/UPGMA/../ClusterTree.h:23,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
tree/UPGMA/../../general/OutputFile.h:26:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   26 |         std::auto_ptr<std::ofstream> file;
      |              ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/UPGMA/../ClusterTree.h:16,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
tree/UPGMA/../ClusterTree.h:70:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   70 |         auto_ptr<clustalw::DistMatrix> quickDistMat;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/UPGMA/../ClusterTree.h:16,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/UPGMA/RootedClusterTree.cpp:9:
tree/UPGMA/RootedClusterTree.h:22:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   22 |         auto_ptr<AlignmentSteps> treeFromDistMatrix(RootedGuideTree* phyloTree,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/UPGMA/../ClusterTree.h:16,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/UPGMA/RootedClusterTree.cpp:11:
tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   23 |         auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/UPGMA/../ClusterTree.h:16,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/UPGMA/RootedClusterTree.cpp:11:
tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   51 |         auto_ptr<AlignmentSteps> progSteps;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/UPGMA/../ClusterTree.h:16,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/UPGMA/RootedClusterTree.cpp:17:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   17 | auto_ptr<AlignmentSteps> RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr,
      | ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/UPGMA/../ClusterTree.h:16,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/UPGMA/RootedClusterTree.cpp: In member function ‘std::auto_ptr<clustalw::AlignmentSteps> clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)’:
tree/UPGMA/RootedClusterTree.cpp:21:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   21 |     auto_ptr<AlignmentSteps> progSteps;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/UPGMA/../ClusterTree.h:16,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
In file included from tree/UPGMA/UPGMAAlgorithm.cpp:4:
tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   23 |         auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from tree/UPGMA/../../general/SquareMat.h:9,
                 from tree/UPGMA/../../general/clustalw.h:43,
                 from tree/UPGMA/UPGMAAlgorithm.h:6,
                 from tree/UPGMA/UPGMAAlgorithm.cpp:4:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/UPGMA/UPGMAAlgorithm.cpp:4:
tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   51 |         auto_ptr<AlignmentSteps> progSteps;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from tree/UPGMA/../../general/SquareMat.h:9,
                 from tree/UPGMA/../../general/clustalw.h:43,
                 from tree/UPGMA/UPGMAAlgorithm.h:6,
                 from tree/UPGMA/UPGMAAlgorithm.cpp:4:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   27 | auto_ptr<AlignmentSteps> UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree,
      | ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from tree/UPGMA/../../general/SquareMat.h:9,
                 from tree/UPGMA/../../general/clustalw.h:43,
                 from tree/UPGMA/UPGMAAlgorithm.h:6,
                 from tree/UPGMA/UPGMAAlgorithm.cpp:4:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/Tree.cpp -o tree/Tree.o
In file included from tree/Tree.cpp:10:
tree/Tree.h:26:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   26 |         auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from tree/../alignment/Alignment.h:38,
                 from tree/Tree.h:13,
                 from tree/Tree.cpp:10:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/Tree.cpp:281:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  281 | auto_ptr<AlignmentSteps> Tree::createSets(int firstSeq, int lastSeq)
      | ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from tree/../alignment/Alignment.h:38,
                 from tree/Tree.h:13,
                 from tree/Tree.cpp:10:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/Tree.cpp: In member function ‘std::auto_ptr<clustalw::AlignmentSteps> clustalw::Tree::createSets(int, int)’:
tree/Tree.cpp:283:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  283 |     auto_ptr<AlignmentSteps> progAlignSteps;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from tree/../alignment/Alignment.h:38,
                 from tree/Tree.h:13,
                 from tree/Tree.cpp:10:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/ClusterTree.cpp -o tree/ClusterTree.o
In file included from tree/ClusterTree.h:23,
                 from tree/ClusterTree.cpp:9:
tree/../general/OutputFile.h:26:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   26 |         std::auto_ptr<std::ofstream> file;
      |              ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/ClusterTree.h:16,
                 from tree/ClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/ClusterTree.cpp:9:
tree/ClusterTree.h:70:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   70 |         auto_ptr<clustalw::DistMatrix> quickDistMat;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/ClusterTree.h:16,
                 from tree/ClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/ClusterTree.cpp: In member function ‘void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)’:
tree/ClusterTree.cpp:580:9: warning: variable ‘rs’ set but not used [-Wunused-but-set-variable]
  580 |     int rs = 0, rl = 0;
      |         ^~
tree/ClusterTree.cpp:580:17: warning: variable ‘rl’ set but not used [-Wunused-but-set-variable]
  580 |     int rs = 0, rl = 0;
      |                 ^~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/TreeInterface.cpp -o tree/TreeInterface.o
In file included from tree/TreeInterface.cpp:15:
tree/TreeInterface.h:38:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   38 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/TreeInterface.cpp:15:
tree/TreeInterface.h:57:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   57 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/TreeInterface.cpp:15:
tree/TreeInterface.h:102:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  102 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/TreeInterface.cpp:15:
tree/TreeInterface.h:108:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  108 |         auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/TreeInterface.cpp:15:
tree/TreeInterface.h:133:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  133 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/TreeInterface.cpp:15:
tree/TreeInterface.h:138:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  138 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/TreeInterface.cpp:15:
tree/TreeInterface.h:142:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  142 |         auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/ClusterTree.h:23,
                 from tree/UnRootedClusterTree.h:8,
                 from tree/TreeInterface.cpp:17:
tree/../general/OutputFile.h:26:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   26 |         std::auto_ptr<std::ofstream> file;
      |              ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/UnRootedClusterTree.h:8,
                 from tree/TreeInterface.cpp:17:
tree/ClusterTree.h:70:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   70 |         auto_ptr<clustalw::DistMatrix> quickDistMat;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/TreeInterface.cpp:18:
tree/Tree.h:26:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   26 |         auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/TreeInterface.cpp:23:
tree/UPGMA/RootedClusterTree.h:22:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   22 |         auto_ptr<AlignmentSteps> treeFromDistMatrix(RootedGuideTree* phyloTree,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp:31:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   31 | auto_ptr<AlignmentSteps>
      | ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp:103:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  103 | auto_ptr<AlignmentSteps>
      | ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp:195:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  195 | auto_ptr<AlignmentSteps>
      | ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp: In member function ‘std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsFromDistMatNJ(std::vector<int>*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)’:
tree/TreeInterface.cpp:200:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  200 |     auto_ptr<AlignmentSteps> progSteps;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp: At global scope:
tree/TreeInterface.cpp:208:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  208 | auto_ptr<AlignmentSteps>
      | ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp: In member function ‘std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::string*, std::vector<int>*, int, int, bool*)’:
tree/TreeInterface.cpp:214:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  214 |     auto_ptr<AlignmentSteps> progSteps;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp: At global scope:
tree/TreeInterface.cpp:440:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  440 | auto_ptr<AlignmentSteps>
      | ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp: In member function ‘std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::string*, std::vector<int>*, int, int, bool*)’:
tree/TreeInterface.cpp:446:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  446 |     auto_ptr<AlignmentSteps> progSteps;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp: At global scope:
tree/TreeInterface.cpp:486:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  486 | auto_ptr<AlignmentSteps>
      | ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp: In member function ‘std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsFromDistMatUPGMA(std::vector<int>*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)’:
tree/TreeInterface.cpp:491:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  491 |     auto_ptr<AlignmentSteps> progSteps;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp: At global scope:
tree/TreeInterface.cpp:504:1: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  504 | auto_ptr<AlignmentSteps> TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs,
      | ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
tree/TreeInterface.cpp: In member function ‘std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::generateTreeFromDistMatUPGMA(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)’:
tree/TreeInterface.cpp:507:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  507 |     auto_ptr<AlignmentSteps> progSteps;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/TreeInterface.h:17,
                 from tree/TreeInterface.cpp:15:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
In file included from tree/ClusterTree.h:23,
                 from tree/UnRootedClusterTree.h:8,
                 from tree/UnRootedClusterTree.cpp:9:
tree/../general/OutputFile.h:26:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   26 |         std::auto_ptr<std::ofstream> file;
      |              ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/ClusterTree.h:16,
                 from tree/UnRootedClusterTree.h:8,
                 from tree/UnRootedClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from tree/UnRootedClusterTree.h:8,
                 from tree/UnRootedClusterTree.cpp:9:
tree/ClusterTree.h:70:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   70 |         auto_ptr<clustalw::DistMatrix> quickDistMat;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from tree/ClusterTree.h:16,
                 from tree/UnRootedClusterTree.h:8,
                 from tree/UnRootedClusterTree.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/NJTree.cpp -o tree/NJTree.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
In file included from interface/../Clustal.h:18,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../fileInput/FileReader.h:43:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   43 |         void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../alignment/AlignmentOutput.h:70:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   70 |         bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../alignment/AlignmentOutput.h:71:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   71 |         string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../alignment/AlignmentOutput.h:77:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   77 |         auto_ptr<ofstream> clustalOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../alignment/AlignmentOutput.h:78:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   78 |         auto_ptr<ofstream> gcgOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../alignment/AlignmentOutput.h:79:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   79 |         auto_ptr<ofstream> nbrfOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../alignment/AlignmentOutput.h:80:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   80 |         auto_ptr<ofstream> phylipOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../alignment/AlignmentOutput.h:81:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   81 |         auto_ptr<ofstream> gdeOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../alignment/AlignmentOutput.h:82:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   82 |         auto_ptr<ofstream> nexusOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../alignment/AlignmentOutput.h:83:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   83 |         auto_ptr<ofstream> fastaOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from interface/../general/SquareMat.h:9,
                 from interface/../general/clustalw.h:43,
                 from interface/../Clustal.h:15,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -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:1305:10: warning: unused variable ‘inline1’ [-Wunused-variable]
 1305 |     char inline1[1024];
      |          ^~~~~~~
substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable ‘nmat’ [-Wunused-variable]
 1307 |     int nmat;
      |         ^~~~
substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable ‘n’ [-Wunused-variable]
 1308 |     int n, llimit, ulimit;
      |         ^
substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable ‘llimit’ [-Wunused-variable]
 1308 |     int n, llimit, ulimit;
      |            ^~~~~~
substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable ‘ulimit’ [-Wunused-variable]
 1308 |     int n, llimit, ulimit;
      |                    ^~~~~~
substitutionMatrix/SubMatrix.cpp: In member function ‘int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)’:
substitutionMatrix/SubMatrix.cpp:1361:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1361 |   for (j = 0; j < curline.length(); j++) {
      |               ~~^~~~~~~~~~~~~~~~~~
substitutionMatrix/SubMatrix.cpp: In member function ‘void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])’:
substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable ‘maxRes’ set but not used [-Wunused-but-set-variable]
 1845 |     int maxRes;
      |         ^~~~~~
substitutionMatrix/SubMatrix.cpp: In member function ‘void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])’:
substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable ‘maxRes’ set but not used [-Wunused-but-set-variable]
 1905 |     int maxRes;
      |         ^~~~~~
substitutionMatrix/SubMatrix.cpp: In member function ‘int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)’:
substitutionMatrix/SubMatrix.cpp:1128:19: warning: ‘n’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1128 |     return (maxRes);
      |                   ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
In file included from multipleAlign/Iteration.cpp:17:
multipleAlign/../tree/TreeInterface.h:38:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   38 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from multipleAlign/../alignment/Alignment.h:38,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from multipleAlign/Iteration.cpp:17:
multipleAlign/../tree/TreeInterface.h:57:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   57 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from multipleAlign/../alignment/Alignment.h:38,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from multipleAlign/Iteration.cpp:17:
multipleAlign/../tree/TreeInterface.h:102:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  102 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from multipleAlign/../alignment/Alignment.h:38,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from multipleAlign/Iteration.cpp:17:
multipleAlign/../tree/TreeInterface.h:108:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  108 |         auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from multipleAlign/../alignment/Alignment.h:38,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from multipleAlign/Iteration.cpp:17:
multipleAlign/../tree/TreeInterface.h:133:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  133 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from multipleAlign/../alignment/Alignment.h:38,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from multipleAlign/Iteration.cpp:17:
multipleAlign/../tree/TreeInterface.h:138:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  138 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from multipleAlign/../alignment/Alignment.h:38,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from multipleAlign/Iteration.cpp:17:
multipleAlign/../tree/TreeInterface.h:142:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  142 |         auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from multipleAlign/../alignment/Alignment.h:38,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
multipleAlign/Iteration.cpp: In member function ‘bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)’:
multipleAlign/Iteration.cpp:170:9: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
  170 |     int count;
      |         ^~~~~
multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result]
  231 |                 tmpnam (buffer);
      |                 ~~~~~~~^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -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>*, clustalw::AlignmentSteps*, int)’:
multipleAlign/MSA.cpp:340:11: warning: unused variable ‘alignmentScore’ [-Wunused-variable]
  340 |       int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
      |           ^~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c general/OutputFile.cpp -o general/OutputFile.o
In file included from general/OutputFile.cpp:9:
general/OutputFile.h:26:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   26 |         std::auto_ptr<std::ofstream> file;
      |              ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from general/OutputFile.h:8,
                 from general/OutputFile.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c general/UserParameters.cpp -o general/UserParameters.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c general/Utility.cpp -o general/Utility.o
general/Utility.cpp: In member function ‘bool clustalw::Utility::lineType(char*, const char*)’:
general/Utility.cpp:251:8: warning: variable ‘n’ set but not used [-Wunused-but-set-variable]
  251 |    int n;
      |        ^
general/Utility.cpp: In member function ‘double clustalw::Utility::getReal(const char*, double, double, double)’:
general/Utility.cpp:183:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  183 |         fgets(line, MAXLINE, stdin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~
general/Utility.cpp: In member function ‘int clustalw::Utility::getInt(const char*, int, int, int)’:
general/Utility.cpp:221:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  221 |         fgets(line, MAXLINE, stdin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c general/InvalidCombination.cpp -o general/InvalidCombination.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c general/DebugLog.cpp -o general/DebugLog.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c general/ClustalWResources.cpp -o general/ClustalWResources.o
general/ClustalWResources.cpp: In member function ‘std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const’:
general/ClustalWResources.cpp:106:12: warning: array subscript 1 is above array bounds of ‘char [1]’ [-Warray-bounds]
  106 |     delim[1] = 0;
      |     ~~~~~~~^
general/ClustalWResources.cpp:104:10: note: while referencing ‘delim’
  104 |     char delim[1];
      |          ^~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c general/SymMatrix.cpp -o general/SymMatrix.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c general/Stats.cpp -o general/Stats.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c Help.cpp -o Help.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c alignment/Alignment.cpp -o alignment/Alignment.o
alignment/Alignment.cpp: In member function ‘bool clustalw::Alignment::keepPortionOfSeqArray(int, int)’:
alignment/Alignment.cpp:1715:24: warning: variable ‘posToAddTo’ set but not used [-Wunused-but-set-variable]
 1715 |     SeqArray::iterator posToAddTo = sectionToRealign.begin();
      |                        ^~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
In file included from alignment/AlignmentOutput.cpp:27:
alignment/AlignmentOutput.h:70:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   70 |         bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from alignment/AlignmentOutput.cpp:27:
alignment/AlignmentOutput.h:71:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   71 |         string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from alignment/AlignmentOutput.cpp:27:
alignment/AlignmentOutput.h:77:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   77 |         auto_ptr<ofstream> clustalOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from alignment/AlignmentOutput.cpp:27:
alignment/AlignmentOutput.h:78:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   78 |         auto_ptr<ofstream> gcgOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from alignment/AlignmentOutput.cpp:27:
alignment/AlignmentOutput.h:79:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   79 |         auto_ptr<ofstream> nbrfOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from alignment/AlignmentOutput.cpp:27:
alignment/AlignmentOutput.h:80:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   80 |         auto_ptr<ofstream> phylipOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from alignment/AlignmentOutput.cpp:27:
alignment/AlignmentOutput.h:81:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   81 |         auto_ptr<ofstream> gdeOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from alignment/AlignmentOutput.cpp:27:
alignment/AlignmentOutput.h:82:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   82 |         auto_ptr<ofstream> nexusOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from alignment/AlignmentOutput.cpp:27:
alignment/AlignmentOutput.h:83:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   83 |         auto_ptr<ofstream> fastaOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
alignment/AlignmentOutput.cpp:514:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  514 | bool AlignmentOutput::openExplicitFile(auto_ptr<ofstream>& outFile, string fileName)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
alignment/AlignmentOutput.cpp:537:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  537 | string AlignmentOutput::openOutputFile(auto_ptr<ofstream>& outFile, string prompt,
      |                                        ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from alignment/AlignmentOutput.h:20,
                 from alignment/AlignmentOutput.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion, ClustalWOutput*)’:
alignment/AlignmentOutput.cpp:683:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=]
  683 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)’:
alignment/AlignmentOutput.cpp:878:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=]
  878 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::phylipOut(clustalw::Alignment*, clustalw::outputRegion)’:
alignment/AlignmentOutput.cpp:1037:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=]
 1037 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)’:
alignment/AlignmentOutput.cpp:1166:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=]
 1166 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)’:
alignment/AlignmentOutput.cpp:1455:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=]
 1455 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)’:
alignment/AlignmentOutput.cpp:1570:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=]
 1570 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion, ClustalWOutput*)’:
alignment/AlignmentOutput.cpp:2153:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=]
 2153 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp:2160:21: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
 2160 |     catch(exception e)
      |                     ^
alignment/AlignmentOutput.cpp: In member function ‘void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)’:
alignment/AlignmentOutput.cpp:2410:28: warning: catching polymorphic type ‘class clustalw::VectorOutOfRange’ by value [-Wcatch-value=]
 2410 |     catch(VectorOutOfRange e)
      |                            ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c alignment/Sequence.cpp -o alignment/Sequence.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c Clustal.cpp -o Clustal.o
In file included from Clustal.h:18,
                 from Clustal.cpp:27:
fileInput/FileReader.h:43:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   43 |         void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.h:20,
                 from Clustal.cpp:27:
alignment/AlignmentOutput.h:70:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   70 |         bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.h:20,
                 from Clustal.cpp:27:
alignment/AlignmentOutput.h:71:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   71 |         string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.h:20,
                 from Clustal.cpp:27:
alignment/AlignmentOutput.h:77:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   77 |         auto_ptr<ofstream> clustalOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.h:20,
                 from Clustal.cpp:27:
alignment/AlignmentOutput.h:78:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   78 |         auto_ptr<ofstream> gcgOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.h:20,
                 from Clustal.cpp:27:
alignment/AlignmentOutput.h:79:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   79 |         auto_ptr<ofstream> nbrfOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.h:20,
                 from Clustal.cpp:27:
alignment/AlignmentOutput.h:80:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   80 |         auto_ptr<ofstream> phylipOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.h:20,
                 from Clustal.cpp:27:
alignment/AlignmentOutput.h:81:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   81 |         auto_ptr<ofstream> gdeOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.h:20,
                 from Clustal.cpp:27:
alignment/AlignmentOutput.h:82:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   82 |         auto_ptr<ofstream> nexusOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.h:20,
                 from Clustal.cpp:27:
alignment/AlignmentOutput.h:83:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   83 |         auto_ptr<ofstream> fastaOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.cpp:33:
tree/TreeInterface.h:38:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   38 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.cpp:33:
tree/TreeInterface.h:57:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   57 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.cpp:33:
tree/TreeInterface.h:102:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  102 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.cpp:33:
tree/TreeInterface.h:108:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  108 |         auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.cpp:33:
tree/TreeInterface.h:133:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  133 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.cpp:33:
tree/TreeInterface.h:138:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  138 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from Clustal.cpp:33:
tree/TreeInterface.h:142:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  142 |         auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
Clustal.cpp: In member function ‘void clustalw::Clustal::align(std::string*, ClustalWOutput*, bool)’:
Clustal.cpp:162:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  162 |     auto_ptr<AlignmentSteps> progSteps;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
Clustal.cpp: In member function ‘void clustalw::Clustal::doAlignUseOldTree(std::string*, ClustalWOutput*)’:
Clustal.cpp:846:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  846 |     auto_ptr<AlignmentSteps> progSteps;
      |     ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from general/SquareMat.h:9,
                 from general/clustalw.h:43,
                 from Clustal.h:15,
                 from Clustal.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c RClustalWMain.cpp -o RClustalWMain.o
In file included from RClustalWMain.cpp:11:
fileInput/FileReader.h:43:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   43 |         void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from RClustalWMain.cpp:12:
interface/../alignment/AlignmentOutput.h:70:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   70 |         bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from RClustalWMain.cpp:12:
interface/../alignment/AlignmentOutput.h:71:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   71 |         string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from RClustalWMain.cpp:12:
interface/../alignment/AlignmentOutput.h:77:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   77 |         auto_ptr<ofstream> clustalOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from RClustalWMain.cpp:12:
interface/../alignment/AlignmentOutput.h:78:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   78 |         auto_ptr<ofstream> gcgOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from RClustalWMain.cpp:12:
interface/../alignment/AlignmentOutput.h:79:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   79 |         auto_ptr<ofstream> nbrfOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from RClustalWMain.cpp:12:
interface/../alignment/AlignmentOutput.h:80:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   80 |         auto_ptr<ofstream> phylipOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from RClustalWMain.cpp:12:
interface/../alignment/AlignmentOutput.h:81:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   81 |         auto_ptr<ofstream> gdeOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from RClustalWMain.cpp:12:
interface/../alignment/AlignmentOutput.h:82:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   82 |         auto_ptr<ofstream> nexusOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from interface/../Clustal.h:20,
                 from interface/CommandLineParser.h:18,
                 from RClustalWMain.cpp:12:
interface/../alignment/AlignmentOutput.h:83:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   83 |         auto_ptr<ofstream> fastaOutFile;
      |         ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from alignment/Alignment.h:38,
                 from RClustalWMain.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include  -DHAVE_CONFIG_H -I.  -fpic  -g -O2  -Wall -c RClustalW.cpp -o RClustalW.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/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 -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
/usr/bin/ld: multipleAlign/Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalW/src/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
make[2]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalW/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalW'
----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalOmega
make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalOmega'
./configure `/home/biocbuild/bbs-3.13-bioc/R/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`; \
export PKG_LIBS=" "; \
export PKG_CXXFLAGS="  `/home/biocbuild/bbs-3.13-bioc/R/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"` -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
export PKG_CFLAGS="  -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
cd src; \
/home/biocbuild/bbs-3.13-bioc/R/bin/R CMD SHLIB -o libClustalOmega.so exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \
ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \
cp libClustalOmega.a ../../
configure:

    Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo)

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

              
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configure: creating ./config.status
config.status: creating Makefile
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config.status: creating Doxyfile
config.status: creating src/exceptions4c/Makefile
config.status: creating src/clustal/Makefile
config.status: creating src/hhalign/Makefile
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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
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make[2]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalOmega/src'
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c argtable2/argtable2.c -o argtable2/argtable2.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c argtable2/arg_end.c -o argtable2/arg_end.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c argtable2/arg_rem.c -o argtable2/arg_rem.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c argtable2/arg_lit.c -o argtable2/arg_lit.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c argtable2/arg_int.c -o argtable2/arg_int.o
argtable2/arg_int.c: In function ‘strtol0X’:
argtable2/arg_int.c:60:12: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration]
   60 |     while (isspace(*ptr))
      |            ^~~~~~~
argtable2/arg_int.c:89:8: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration]
   89 |    if (toupper(*ptr++)!=toupper(X))
      |        ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c argtable2/arg_str.c -o argtable2/arg_str.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c argtable2/arg_file.c -o argtable2/arg_file.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include     -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c kmpp/KMeans.cpp -o kmpp/KMeans.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include     -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c kmpp/KmTree.cpp -o kmpp/KmTree.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include     -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/hhalign_wrapper.c: In function ‘SanitiseUnknown’:
clustal/hhalign_wrapper.c:85:9: warning: unused variable ‘iLen’ [-Wunused-variable]
   85 |     int iLen; /* length of sequence */
      |         ^~~~
clustal/hhalign_wrapper.c:84:9: warning: unused variable ‘iR’ [-Wunused-variable]
   84 |     int iR; /* iterator for residue */
      |         ^~
clustal/hhalign_wrapper.c: In function ‘ReAttachLeadingGaps’:
clustal/hhalign_wrapper.c:239:9: warning: variable ‘iSize2’ set but not used [-Wunused-but-set-variable]
  239 |     int iSize2 = 0; /* #seqs in 2nd profile */
      |         ^~~~~~
clustal/hhalign_wrapper.c:238:9: warning: variable ‘iSize1’ set but not used [-Wunused-but-set-variable]
  238 |     int iSize1 = 0; /* #seqs in 1st profile */
      |         ^~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/ktuple_pair.c: In function ‘KTuplePairDist’:
clustal/ktuple_pair.c:758: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  758 |         #pragma omp critical(ktuple)
      | 
clustal/ktuple_pair.c:801: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  801 |             #pragma omp critical(ktuple)
      | 
clustal/ktuple_pair.c:822: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  822 |     #pragma omp critical(ktuple)
      | 
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/list.c -o clustal/list.o
In file included from clustal/list.c:32:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/log.c -o clustal/log.o
In file included from clustal/log.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/muscle_tree.c -o clustal/muscle_tree.o
clustal/muscle_tree.c:519:1: warning: ‘IsEdge’ defined but not used [-Wunused-function]
  519 | IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree)
      | ^~~~~~
clustal/muscle_tree.c:42:21: warning: ‘VERY_NEGATIVE_DOUBLE’ defined but not used [-Wunused-const-variable=]
   42 | static const double VERY_NEGATIVE_DOUBLE = -9e29;
      |                     ^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/mbed.c -o clustal/mbed.o
In file included from clustal/mbed.c:28:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/mbed.c: In function ‘BisectingKmeans’:
clustal/mbed.c:786:16: warning: variable ‘dCost’ set but not used [-Wunused-but-set-variable]
  786 |         double dCost = -1.0;
      |                ^~~~~
At top level:
clustal/mbed.c:69:18: warning: ‘MAX_ALLOWED_SEQ_PER_PRECLUSTER’ defined but not used [-Wunused-const-variable=]
   69 | static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100;
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/pair_dist.c: In function ‘SquidIdPairDist’:
clustal/pair_dist.c:206: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  206 |         #pragma omp critical(squidid)
      | 
clustal/pair_dist.c:218: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
  218 |         #pragma omp atomic
      | 
clustal/pair_dist.c:228: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  228 |             #pragma omp critical(squidid)
      | 
clustal/pair_dist.c:177:10: warning: unused variable ‘bPrintCR’ [-Wunused-variable]
  177 |     bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
      |          ^~~~~~~~
clustal/pair_dist.c: In function ‘PairDistances’:
clustal/pair_dist.c:336: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  336 |             #pragma omp parallel for private(iChunk) schedule(dynamic)
      | 
clustal/pair_dist.c:359: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  359 |             #pragma omp parallel for private(iChunk) schedule(dynamic)
      | 
clustal/pair_dist.c:376: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  376 |             #pragma omp parallel for private(iChunk) schedule(dynamic)
      | 
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/progress.c -o clustal/progress.o
In file included from clustal/progress.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/seq.c -o clustal/seq.o
In file included from clustal/seq.c:30:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/seq.c: In function ‘AliStat’:
clustal/seq.c:68:9: warning: unused variable ‘iAux’ [-Wunused-variable]
   68 |     int iAux;
      |         ^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/symmatrix.c -o clustal/symmatrix.o
In file included from clustal/symmatrix.c:30:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/tree.c -o clustal/tree.o
In file included from clustal/tree.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/util.c -o clustal/util.o
In file included from clustal/util.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal/weights.c -o clustal/weights.o
In file included from clustal/weights.c:72:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
squid/clustal.c: In function ‘WriteClustal’:
squid/clustal.c:214:7: warning: unused variable ‘cons’ [-Wunused-variable]
  214 |   int cons;
      |       ^~~~
squid/clustal.c: In function ‘WriteClustalForR’:
squid/clustal.c:438:6: warning: unused variable ‘cons’ [-Wunused-variable]
  438 |  int cons;
      |      ^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c squid/gsi64.c -o squid/gsi64.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
squid/hsregex.c: In function ‘regbranch’:
squid/hsregex.c:499:6: warning: ‘flags’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  499 |  int flags;
      |      ^~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
squid/msf.c: In function ‘ReadMSF’:
squid/msf.c:87:11: warning: variable ‘alleged_checksum’ set but not used [-Wunused-but-set-variable]
   87 |   int     alleged_checksum;
      |           ^~~~~~~~~~~~~~~~
squid/msf.c:85:11: warning: variable ‘alleged_alen’ set but not used [-Wunused-but-set-variable]
   85 |   int     alleged_alen;
      |           ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
squid/phylip.c: In function ‘ReadPhylip’:
squid/phylip.c:80:15: warning: variable ‘alen’ set but not used [-Wunused-but-set-variable]
   80 |   int   nseq, alen;
      |               ^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c squid/sqerror.c -o squid/sqerror.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c squid/squidcore.c -o squid/squidcore.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c squid/sre_random.c -o squid/sre_random.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
squid/ssi.c: In function ‘SSIAddPrimaryKeyToIndex’:
squid/ssi.c:751:26: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=]
  751 |         fprintf(g->ptmp, "%s\t%d\t%" PRIu64 "\t%" PRIu64 "\t%lu\n",
      |                          ^~~~~~~~~~~
  752 |                 key, fh, (unsigned long long)r_off->off.i64,
      |                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                          |
      |                          long long unsigned int
In file included from squid/ssi.c:20:
/usr/include/inttypes.h:105:34: note: format string is defined here
  105 | # define PRIu64  __PRI64_PREFIX "u"
squid/ssi.c:751:26: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’ [-Wformat=]
  751 |         fprintf(g->ptmp, "%s\t%d\t%" PRIu64 "\t%" PRIu64 "\t%lu\n",
      |                          ^~~~~~~~~~~
  752 |                 key, fh, (unsigned long long)r_off->off.i64,
  753 |                 d_off == NULL ? 0 : (unsigned long long) d_off->off.i64,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   long long unsigned int
In file included from squid/ssi.c:20:
/usr/include/inttypes.h:105:34: note: format string is defined here
  105 | # define PRIu64  __PRI64_PREFIX "u"
squid/ssi.c: In function ‘activate_external_sort’:
squid/ssi.c:1407:24: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=]
 1407 |       fprintf(g->ptmp, "%s\t%u\t%" PRIu64 "\t%" PRIu64 "\t%lu\n",
      |                        ^~~~~~~~~~~
 1408 |        g->pkeys[i].key, g->pkeys[i].fnum,
 1409 |        (unsigned long long) g->pkeys[i].r_off.off.i64,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |        |
      |        long long unsigned int
In file included from squid/ssi.c:20:
/usr/include/inttypes.h:105:34: note: format string is defined here
  105 | # define PRIu64  __PRI64_PREFIX "u"
squid/ssi.c:1407:24: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’ [-Wformat=]
 1407 |       fprintf(g->ptmp, "%s\t%u\t%" PRIu64 "\t%" PRIu64 "\t%lu\n",
      |                        ^~~~~~~~~~~
......
 1410 |        (unsigned long long) g->pkeys[i].d_off.off.i64,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |        |
      |        long long unsigned int
In file included from squid/ssi.c:20:
/usr/include/inttypes.h:105:34: note: format string is defined here
  105 | # define PRIu64  __PRI64_PREFIX "u"
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c squid/stopwatch.c -o squid/stopwatch.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c squid/vectorops.c -o squid/vectorops.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -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: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include     -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c hhalign/hhalign.cpp -o hhalign/hhalign.o
In file included from hhalign/hhalign.cpp:62:
hhalign/util-C.h: In function ‘float fast_log2(float)’:
hhalign/util-C.h:94:16: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   94 |   int a = (((*((int *)&x)) & 0x7F800000) >>23 )-0x7f;
      |               ~^~~~~~~~~~
hhalign/util-C.h:95:16: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   95 |   int b =  ((*((int *)&x)) & 0x007FE000) >>13;
      |               ~^~~~~~~~~~
hhalign/util-C.h:96:16: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   96 |   int c =  ((*((int *)&x)) & 0x00001FFF);
      |               ~^~~~~~~~~~
hhalign/util-C.h: In function ‘float fpow2(float)’:
hhalign/util-C.h:111:14: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  111 |   int lx = *((int*)&tx) - 0x4b400000;   // integer value of x
      |             ~^~~~~~~~~~
hhalign/util-C.h: In function ‘float fast_pow2(float)’:
hhalign/util-C.h:158:15: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  158 |    pow2[b]=(*((unsigned int *)(&f)) & 0x7FFFFF); // store the mantisse of 2^(1+b/1024)
      |              ~^~~~~~~~~~~~~~~~~~~~~
hhalign/util-C.h:202:12: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  202 |   return *((float*)&y);
      |           ~^~~~~~~~~~~
In file included from hhalign/hhalign.cpp:76:
hhalign/hhhmm-C.h: In member function ‘int HMM::ReadHMMer3(FILE*, char*)’:
hhalign/hhhmm-C.h:1141:12: warning: variable ‘dAlphaInv’ set but not used [-Wunused-but-set-variable]
 1141 |     double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */
      |            ^~~~~~~~~
hhalign/hhhmm-C.h: In member function ‘void HMM::WriteToFileHMMER(char*)’:
hhalign/hhhmm-C.h:2206:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2206 |   for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n");
      |   ^~~
hhalign/hhhmm-C.h:2206:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2206 |   for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n");
      |                                                                  ^~~~~~~
In file included from hhalign/hhalign.cpp:77:
hhalign/hhalignment-C.h: In member function ‘void Alignment::Read(FILE*, char*, char*)’:
hhalign/hhalignment-C.h:245:32: warning: variable ‘ptr2’ set but not used [-Wunused-but-set-variable]
  245 |                   char *ptr1, *ptr2;
      |                                ^~~~
hhalign/hhalignment-C.h: In member function ‘int Alignment::FilterWithCoreHMM(char*, float, HMM&)’:
hhalign/hhalignment-C.h:1429:19: warning: variable ‘score_M’ set but not used [-Wunused-but-set-variable]
 1429 |             float score_M=0.0;
      |                   ^~~~~~~
hhalign/hhalignment-C.h:1430:19: warning: variable ‘score_prev’ set but not used [-Wunused-but-set-variable]
 1430 |             float score_prev=0.0;
      |                   ^~~~~~~~~~
hhalign/hhalignment-C.h: In member function ‘void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)’:
hhalign/hhalignment-C.h:1905:11: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
 1905 |        if (ncol<NCOLMIN)
      |           ^
hhalign/hhalignment-C.h: In member function ‘void Alignment::Transitions_from_I_state(HMM&, char*)’:
hhalign/hhalignment-C.h:2137:28: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
 2137 |                         if (ncol>=NCOLMIN)
      |                            ^
hhalign/hhalignment-C.h: In member function ‘void Alignment::Transitions_from_D_state(HMM&, char*)’:
hhalign/hhalignment-C.h:2344:32: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
 2344 |                             if (ncol<NCOLMIN)
      |                                ^
In file included from hhalign/hhalign.cpp:81:
hhalign/hhhitlist-C.h: In member function ‘void HitList::TransitiveScoring()’:
hhalign/hhhitlist-C.h:1259:10: warning: variable ‘unused’ set but not used [-Wunused-but-set-variable]
 1259 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhalign/hhhitlist-C.h: In member function ‘void HitList::TransitiveScoring2()’:
hhalign/hhhitlist-C.h:1624:10: warning: variable ‘unused’ set but not used [-Wunused-but-set-variable]
 1624 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhalign/hhhitlist-C.h: In member function ‘void HitList::TransitiveScoring3()’:
hhalign/hhhitlist-C.h:1994:10: warning: variable ‘unused’ set but not used [-Wunused-but-set-variable]
 1994 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhalign/hhhitlist-C.h: In member function ‘void HitList::TransitiveScoring4()’:
hhalign/hhhitlist-C.h:2359:10: warning: variable ‘unused’ set but not used [-Wunused-but-set-variable]
 2359 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
In file included from hhalign/hhalign.cpp:82:
hhalign/hhfunc-C.h: In function ‘void AddBackgroundFrequencies(float**, float**, float**, int, hmm_light*, char**, char*, int, char*)’:
hhalign/hhfunc-C.h:74:9: warning: unused variable ‘iT’ [-Wunused-variable]
   74 |     int iT; /* transition state iterator */
      |         ^~
In file included from hhalign/hhalign.cpp:82:
hhalign/hhfunc-C.h:80:11: warning: unused variable ‘fGThgiew’ [-Wunused-variable]
   80 |     float fGThgiew = UNITY - fGWeight; /* weight of 'true' transitions */
      |           ^~~~~~~~
hhalign/hhfunc-C.h:85:11: warning: unused variable ‘zf1SeqTrans’ [-Wunused-variable]
   85 |     float zf1SeqTrans[] = {0.98, 0.01, 0.01, 0.25, 0.75, 0.25, 0.75};
      |           ^~~~~~~~~~~
hhalign/hhfunc-C.h:86:11: warning: unused variable ‘zf1SeqInit’ [-Wunused-variable]
   86 |     float zf1SeqInit[]  = {0.98, 0.01, 0.01, 0.99, 0.01, 0.99, 0.01};
      |           ^~~~~~~~~~
hhalign/hhfunc-C.h:87:11: warning: unused variable ‘zf1SeqDel’ [-Wunused-variable]
   87 |     float zf1SeqDel[]   = {0.24, 0.01, 0.75, 0.01, 0.01, 0.01, 0.01};
      |           ^~~~~~~~~
hhalign/hhfunc-C.h:88:11: warning: unused variable ‘zf1SeqRevrt’ [-Wunused-variable]
   88 |     float zf1SeqRevrt[] = {0.98, 0.01, 0.01, 0.01, 0.01, 0.99, 0.01};
      |           ^~~~~~~~~~~
hhalign/hhfunc-C.h: In function ‘int ReadAndPrepare(int, char**, int, hmm_light*, char*, char*, double*, char*, HMM&, Alignment*)’:
hhalign/hhfunc-C.h:328:17: warning: unused variable ‘NEFF_SCORE’ [-Wunused-variable]
  328 |       const int NEFF_SCORE = 10; /* FIXME: Magic Number */
      |                 ^~~~~~~~~~
hhalign/hhfunc-C.h:511:17: warning: unused variable ‘NEFF_SCORE’ [-Wunused-variable]
  511 |       const int NEFF_SCORE = 10; /* FIXME: Magic Number */
      |                 ^~~~~~~~~~
hhalign/hhalign.cpp: In function ‘int hhalign(char**, int, double*, char**, int, double*, double*, hmm_light*, char*, char*, char*, char*, hhalign_para, hhalign_scores*, int, int, char*, char*)’:
hhalign/hhalign.cpp:721:9: warning: variable ‘Nali’ set but not used [-Wunused-but-set-variable]
  721 |     int Nali;                    /* number of normally backtraced alignments
      |         ^~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include     -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c RClustalOmega.cpp -o RClustalOmega.o
In file included from RClustalOmega.cpp:27:
config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c mymain.c -o mymain.o
In file included from mymain.c:22:
config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2  -Wall -c clustal-omega.c -o clustal-omega.o
In file included from clustal-omega.c:22:
config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal-omega.c:134:18: warning: ‘ITERATION_SCORE_IMPROVEMENT_THRESHOLD’ defined but not used [-Wunused-const-variable=]
  134 | static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01;
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/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 -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
/usr/bin/ld: clustal-omega.o: in function `AlnToHHMFile':
/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalOmega/src/clustal-omega.c:389: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
make[2]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalOmega/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalOmega'
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o msa.so R_init_msa.o SplitCharVector2List.o SplitCharVector2Matrix.o -Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a -Wl,--no-whole-archive -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
/usr/bin/ld: ./libClustalW.a(Iteration.o): in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalW/src/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/bin/ld: ./libClustalOmega.a(clustal-omega.o): in function `AlnToHHMFile':
/home/biocbuild/bbs-3.13-bioc/meat/msa/src/ClustalOmega/src/clustal-omega.c:389: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-msa/00new/msa/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (msa)
name	user	system	elapsed
MsaMetaData-class	0.521	0.159	0.682
MsaMultipleAlignmentClasses	0.211	0.039	0.250
msa-package	0.149	0.004	0.154
msa	0.482	0.012	0.493
msaCheckNames	0.033	0.004	0.038
msaClustalOmega	0.336	0.040	0.375
msaClustalW	0.287	0.004	0.290
msaConsensusSequence-methods	0.099	0.000	0.099
msaConservationScore-methods	0.919	0.040	0.959
msaConvert	0.143	0.024	0.168
msaMuscle	0.36	0.00	0.36
msaPrettyPrint	3.096	0.091	3.188
CHECK results for msa on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings
