fakeroot debian/rules clean test -x debian/rules test "`id -u`" = 0 for i in ./config.guess ./config.sub ; do \ if test -e $i.cdbs-orig ; then \ mv $i.cdbs-orig $i ; \ fi ; \ done /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' for i in ./config.guess ./config.sub ; do \ if test -e $i.cdbs-orig ; then \ mv $i.cdbs-orig $i ; \ fi ; \ done make[1]: Leaving directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' if [ -d "." ] ; then \ cd . && QUILT_PATCHES=patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \ fi Kein Patch entfernt if [ -n "patches" ] ; then \ if [ -L ./patches ] ; then \ rm ./patches ; \ fi ; \ fi rm -rf ./.pc rm -f debian/stamp-patch* dh_clean /usr/bin/make -C . -k distclean make[1]: Entering directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' make[1]: *** Keine Regel, um »distclean« zu erstellen. make[1]: Leaving directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' make: [makefile-clean] Fehler 2 (ignoriert) rm -f debian/stamp-makefile-build rm -f debian/stamp-autotools-files dpkg-source -b libMems-1.5.0 dpkg-source: Warnung: source directory './libMems-1.5.0' is not - 'libmems-1.5.0' dpkg-source: Warnung: .orig directory name libMems-1.5.0.orig is not - (wanted libmems-1.5.0.orig) dpkg-source: building libmems using existing libmems_1.5.0.orig.tar.gz dpkg-source: baue libmems in libmems_1.5.0-1.diff.gz dpkg-source: baue libmems in libmems_1.5.0-1.dsc debian/rules build test -x debian/rules mkdir -p "." /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' for i in ./config.guess ./config.sub ; do \ if test -e $i.cdbs-orig ; then \ mv $i.cdbs-orig $i ; \ fi ; \ done make[1]: Leaving directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' if [ -n "patches" ] ; then \ if [ -L ./patches ] ; then : ; else \ (cd .; ln -s /home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0/debian/patches patches) ; \ fi ; \ fi cd . && QUILT_PATCHES=patches quilt --quiltrc /dev/null push -a || test $? = 2 Wende Patch 01_libMems_Makefile_am.patch an patching file libMems/Makefile.am Wende Patch 02_autoreconf.patch an patching file Makefile.in patching file aclocal.m4 patching file configure patching file doc/Makefile.in patching file libMems/Makefile.in patching file libMems/dmSML/Makefile.in Wende Patch 03_libtool.patch an patching file ltmain.sh Jetzt in Patch 03_libtool.patch touch debian/stamp-patched /usr/bin/make -f debian/rules update-config make[1]: Entering directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' if test -e /usr/share/misc/config.guess ; then \ for i in ./config.guess ; do \ if ! test -e $i.cdbs-orig ; then \ mv $i $i.cdbs-orig ; \ cp --remove-destination /usr/share/misc/config.guess $i ; \ fi ; \ done ; \ fi if test -e /usr/share/misc/config.sub ; then \ for i in ./config.sub ; do \ if ! test -e $i.cdbs-orig ; then \ mv $i $i.cdbs-orig ; \ cp --remove-destination /usr/share/misc/config.sub $i ; \ fi ; \ done ; \ fi make[1]: Leaving directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' if test -e /usr/share/misc/config.guess ; then \ for i in ./config.guess ; do \ if ! test -e $i.cdbs-orig ; then \ mv $i $i.cdbs-orig ; \ cp --remove-destination /usr/share/misc/config.guess $i ; \ fi ; \ done ; \ fi if test -e /usr/share/misc/config.sub ; then \ for i in ./config.sub ; do \ if ! test -e $i.cdbs-orig ; then \ mv $i $i.cdbs-orig ; \ cp --remove-destination /usr/share/misc/config.sub $i ; \ fi ; \ done ; \ fi touch debian/stamp-autotools-files chmod a+x /home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0/./configure cd . && CC="cc" CXX="g++" CFLAGS="-g -Wall -O2" CXXFLAGS="-g -Wall -O2" CPPFLAGS="" LDFLAGS="" /home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0/./configure --build=i486-linux-gnu --prefix=/usr --includedir="\${prefix}/include" --mandir="\${prefix}/share/man" --infodir="\${prefix}/share/info" --sysconfdir=/etc --localstatedir=/var --libexecdir="\${prefix}/lib/libmems" --disable-maintainer-mode --disable-dependency-tracking --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... none checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking build system type... i486-pc-linux-gnu checking host system type... i486-pc-linux-gnu checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognize dependent libraries... pass_all checking how to run the C preprocessor... cc -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 dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking how to run the C++ preprocessor... g++ -E checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... yes checking whether g77 accepts -g... yes checking the maximum length of command line arguments... 98304 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) 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 configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC checking if g++ PIC flag -fPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so (cached) (cached) checking how to hardcode library paths into programs... immediate appending configuration tag "F77" to libtool checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g77 option to produce PIC... -fPIC checking if g77 PIC flag -fPIC works... yes checking if g77 static flag -static works... yes checking if g77 supports -c -o file.o... yes checking whether the g77 linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so (cached) (cached) checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for ANSI C header files... (cached) yes checking whether the compiler implements namespaces... yes checking whether the Boost::Filesystem library is available... yes checking for main in -lboost_filesystem... yes checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for DEPS... yes checking for sys/types.h... (cached) yes checking sys/aio.h usability... no checking sys/aio.h presence... no checking for sys/aio.h... no checking aio.h usability... yes checking aio.h presence... yes checking for aio.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking for pthread_mutex_unlock in -lpthread... yes checking for aio_write in -lrt... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking whether cc needs -traditional... no configure: creating ./config.status config.status: creating Makefile config.status: creating libMems/Makefile config.status: creating libMems/dmSML/Makefile config.status: creating doc/Makefile config.status: creating libMems-1.5.pc config.status: creating config.h config.status: executing depfiles commands /usr/bin/make -C . make[1]: Entering directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' cd . && /bin/bash /home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0/missing --run autoheader rm -f stamp-h1 touch config.h.in cd . && /bin/bash ./config.status config.h config.status: creating config.h config.status: config.h is unchanged /usr/bin/make all-recursive make[2]: Entering directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0' Making all in libMems make[3]: Entering directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0/libMems' Making all in dmSML make[4]: Entering directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0/libMems/dmSML' /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o asyncio.lo asyncio.c mkdir .libs cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c asyncio.c -fPIC -DPIC -o .libs/asyncio.o cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c asyncio.c -o asyncio.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o alinuxaio.lo alinuxaio.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c alinuxaio.c -o alinuxaio.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o aPOSIXaio.lo aPOSIXaio.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o aPOSIXaio.c: In function 'QueryLastCompletePAIO': aPOSIXaio.c:115: warning: passing argument 1 of 'aio_suspend' from incompatible pointer type cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o alibc.lo alibc.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c alibc.c -fPIC -DPIC -o .libs/alibc.o cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c alibc.c -o alibc.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o awin32aio.lo awin32aio.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c awin32aio.c -o awin32aio.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o buffer.lo buffer.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c buffer.c -fPIC -DPIC -o .libs/buffer.o cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c buffer.c -o buffer.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o util.lo util.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c util.c -fPIC -DPIC -o .libs/util.o util.c: In function 'removeFile': util.c:126: warning: assignment discards qualifiers from pointer target type util.c:128: warning: assignment discards qualifiers from pointer target type util.c:129: warning: implicit declaration of function 'system' cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c util.c -o util.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o sorting.lo sorting.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c sorting.c -fPIC -DPIC -o .libs/sorting.o cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c sorting.c -o sorting.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o dmsort.lo dmsort.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c dmsort.c -fPIC -DPIC -o .libs/dmsort.o dmsort.c: In function 'Translate32': dmsort.c:498: warning: array subscript has type 'char' dmsort.c: In function 'RestructureReadSMLBins': dmsort.c:617: warning: array subscript has type 'char' dmsort.c:662: warning: array subscript has type 'char' dmsort.c:544: warning: unused variable 'config_value' dmsort.c: In function 'dmSML': dmsort.c:1849: warning: unused variable 'buffer_size' dmsort.c:1848: warning: unused variable 'working_mb' dmsort.c: At top level: dmsort.c:212: warning: 'ComputeNNNNNBinNumber' defined but not used dmsort.c:239: warning: 'ComputeAsciiBinNumber' defined but not used dmsort.c: In function 'InitdmSML': dmsort.c:778: warning: 'desired_ws_size' may be used uninitialized in this function cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c dmsort.c -o dmsort.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o timing.lo timing.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c timing.c -fPIC -DPIC -o .libs/timing.o cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c timing.c -o timing.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c -o sml.lo sml.c cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c sml.c -fPIC -DPIC -o .libs/sml.o ../../libMems/dmSML/sml.h:41: warning: 'DNA_TABLE' defined but not used ../../libMems/dmSML/sml.h:45: warning: 'seed_mask' defined but not used ../../libMems/dmSML/sml.h:46: warning: 'mask_length' defined but not used ../../libMems/dmSML/sml.h:47: warning: 'mask_weight' defined but not used cc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -DUSE_POSIX_AIO -g -Wall -O2 -c sml.c -o sml.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=link cc -DUSE_POSIX_AIO -g -Wall -O2 -o libdmSML.la asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lrt -lpthread ar cru .libs/libdmSML.a .libs/asyncio.o .libs/alinuxaio.o .libs/aPOSIXaio.o .libs/alibc.o .libs/awin32aio.o .libs/buffer.o .libs/util.o .libs/sorting.o .libs/dmsort.o .libs/timing.o .libs/sml.o ranlib .libs/libdmSML.a creating libdmSML.la (cd .libs && rm -f libdmSML.la && ln -s ../libdmSML.la libdmSML.la) make[4]: Leaving directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0/libMems/dmSML' make[4]: Entering directory `/home/tillea/debian-maintain/todo/mauve/libmems/libMems-1.5.0/libMems' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o MemScorer.lo MemScorer.cpp mkdir .libs g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MemScorer.cpp -fPIC -DPIC -o .libs/MemScorer.o In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/MemScorer.h:16, from MemScorer.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/MemScorer.h:16, from MemScorer.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': MemScorer.cpp:247: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MemScorer.cpp:247: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions MemScorer.cpp:247: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MemScorer.cpp:247: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions MemScorer.cpp:247: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MemScorer.cpp:247: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions MemScorer.cpp:247: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MemScorer.cpp -o MemScorer.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o RepeatHash.lo RepeatHash.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': RepeatHash.cpp:63: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': RepeatHash.cpp:63: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions RepeatHash.cpp:63: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': RepeatHash.cpp:63: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions RepeatHash.cpp:63: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': RepeatHash.cpp:63: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions RepeatHash.cpp:63: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o ClustalInterface.lo ClustalInterface.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c ClustalInterface.cpp -fPIC -DPIC -o .libs/ClustalInterface.o In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/ClustalInterface.h:18, from ClustalInterface.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' In file included from ../libMems/ClustalInterface.h:20, from ClustalInterface.cpp:13: ../libMems/GappedAligner.h: In function 'boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)': ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp: In member function 'void mems::ClustalInterface::SetDistanceMatrix(NumericMatrix&, std::string&, boolean)': ClustalInterface.cpp:172: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:180: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:181: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:193: warning: unused variable 'status' ClustalInterface.cpp: In member function 'void mems::ClustalInterface::setGuideTree(std::string&, NumericMatrix&, uint)': ClustalInterface.cpp:230: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:235: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:236: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp: In member function 'virtual boolean mems::ClustalInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, std::vector >&)': ClustalInterface.cpp:266: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:266: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:275: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:279: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:307: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:308: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:320: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:401: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:349: warning: unused variable 'flankI' ClustalInterface.cpp:250: warning: unused variable 'flank' ClustalInterface.cpp: In member function 'boolean mems::ClustalInterface::CallClustal(std::vector, std::allocator >, std::allocator, std::allocator > > >&)': ClustalInterface.cpp:428: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp:429: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]': ../libMems/GappedAlignment.h:94: instantiated from here ../libMems/SparseAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ClustalInterface.cpp: In member function 'boolean mems::ClustalInterface::CallClustal(std::vector, std::allocator >, std::allocator, std::allocator > > >&)': ClustalInterface.cpp:419: warning: 'phylip_name' may be used uninitialized in this function ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c ClustalInterface.cpp -o ClustalInterface.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o DNAFileSML.lo DNAFileSML.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.o In file included from ../libMems/DNAFileSML.h:16, from DNAFileSML.cpp:15: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from DNAFileSML.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o MatchFinder.lo MatchFinder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from MatchFinder.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from MatchFinder.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' MatchFinder.cpp: In member function 'virtual boolean mems::MatchFinder::SearchRange(std::vector >&, std::vector >&)': MatchFinder.cpp:270: warning: comparison between signed and unsigned integer expressions MatchFinder.cpp:273: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': MatchFinder.cpp:438: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MatchFinder.cpp:438: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions MatchFinder.cpp:438: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MatchFinder.cpp:438: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions MatchFinder.cpp:438: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MatchFinder.cpp:438: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions MatchFinder.cpp:438: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o MemSubsets.lo MemSubsets.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MemSubsets.cpp -fPIC -DPIC -o .libs/MemSubsets.o ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MemSubsets.cpp:255: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions MemSubsets.cpp:255: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions MemSubsets.cpp:255: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MemSubsets.cpp:265: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions MemSubsets.cpp:265: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions MemSubsets.cpp:265: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': ../libMems/Match.h:156: instantiated from 'void mems::GenericMatch::UpdateSupersets() [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]' MemSubsets.cpp:258: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:156: instantiated from 'void mems::GenericMatch::UpdateSupersets() [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]' MemSubsets.cpp:258: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': MemSubsets.cpp:346: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions MemSubsets.cpp:346: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions MemSubsets.cpp:346: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': MemSubsets.cpp:346: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MemSubsets.cpp -o MemSubsets.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o DNAMemorySML.lo DNAMemorySML.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from DNAMemorySML.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o MemorySML.lo MemorySML.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/MemorySML.h:16, from MemorySML.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o SortedMerList.lo SortedMerList.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.o In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::FindAll(const std::string&, std::vector >)': SortedMerList.cpp:227: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::translate(uint8*, const gnSeqC*, gnSeqI) const': SortedMerList.cpp:408: warning: array subscript has type 'char' SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::translate32(uint32*, const gnSeqC*, gnSeqI) const': SortedMerList.cpp:437: warning: array subscript has type 'char' SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector >&)': SortedMerList.cpp:547: warning: array subscript has type 'char' SortedMerList.cpp:559: warning: array subscript has type 'char' SortedMerList.cpp: In member function 'virtual uint64 mems::SortedMerList::GetSeedMer(gnSeqI) const': SortedMerList.cpp:742: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::Create(const genome::gnSequence&, uint64)': SortedMerList.cpp:795: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function 'virtual gnSeqI mems::SortedMerList::UniqueMerCount()': SortedMerList.cpp:471: warning: 'prev_mer.mems::bmer::mer' may be used uninitialized in this function g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o FileSML.lo FileSML.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o In file included from FileSML.cpp:10: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' In file included from ../libMems/Aligner.h:18, from FileSML.cpp:12: ../libMems/GappedAligner.h: In function 'boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)': ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from FileSML.cpp:12: ../libMems/Aligner.h: In member function 'boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const': ../libMems/Aligner.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:56: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function 'boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const': ../libMems/Aligner.h:102: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:102: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function 'bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const': ../libMems/Aligner.h:293: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:293: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:294: warning: comparison between signed and unsigned integer expressions FileSML.cpp: In member function 'virtual boolean mems::FileSML::WriteHeader()': FileSML.cpp:131: warning: deprecated conversion from string constant to 'char*' FileSML.cpp:136: warning: deprecated conversion from string constant to 'char*' FileSML.cpp:144: warning: deprecated conversion from string constant to 'char*' FileSML.cpp: In function 'void mems::maskNNNNN(const genome::gnSequence&, genome::gnSequence&, std::vector >&, int)': FileSML.cpp:250: warning: comparison between signed and unsigned integer expressions FileSML.cpp: In member function 'void mems::FileSML::dmCreate(const genome::gnSequence&, uint64)': FileSML.cpp:294: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]': ../libMems/GappedAlignment.h:94: instantiated from here ../libMems/SparseAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::GenericMatch, std::allocator > > >]': ../libMems/Aligner.h:336: instantiated from here ../libMems/AbstractMatch.h:302: warning: unused variable 'diff' ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': FileSML.cpp:702: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': FileSML.cpp:702: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions FileSML.cpp:702: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': FileSML.cpp:702: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions FileSML.cpp:702: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': FileSML.cpp:702: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions FileSML.cpp:702: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used ../libMems/dmSML/sml.h:21: warning: 'uint8* mems::CreateBasicDNATable()' defined but not used ../libMems/dmSML/sml.h:41: warning: 'mems::DNA_TABLE' defined but not used ../libMems/dmSML/sml.h:45: warning: 'mems::seed_mask' defined but not used ../libMems/dmSML/sml.h:46: warning: 'mems::mask_length' defined but not used ../libMems/dmSML/sml.h:47: warning: 'mems::mask_weight' defined but not used ../libMems/dmSML/dmsort.h:107: warning: 'mems::buffer_t* mems::AllocateFree()' declared 'static' but never defined ../libMems/dmSML/dmsort.h:109: warning: 'int mems::ComputeBinNumber(const unsigned char*)' declared 'static' but never defined ../libMems/dmSML/dmsort.h:112: warning: 'int mems::ComputeNNNNNBinNumber(const unsigned char*)' declared 'static' but never defined ../libMems/dmSML/dmsort.h:114: warning: 'int mems::ComputeAsciiBinNumber(const unsigned char*)' declared 'static' but never defined ../libMems/dmSML/dmsort.h:116: warning: 'void mems::DoBinning()' declared 'static' but never defined ../libMems/dmSML/dmsort.h:122: warning: 'void mems::DoReading()' declared 'static' but never defined ../libMems/dmSML/dmsort.h:124: warning: 'void mems::HandleBinWriteCompletions()' declared 'static' but never defined ../libMems/dmSML/dmsort.h:126: warning: 'void mems::HandleSeqbufWriteCompletions()' declared 'static' but never defined ../libMems/dmSML/dmsort.h:130: warning: 'void mems::Translate32(uint32*, const char*, unsigned int)' declared 'static' but never defined ../libMems/dmSML/dmsort.h:134: warning: 'void mems::HandleReadingCompletions()' declared 'static' but never defined g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c FileSML.cpp -o FileSML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o MemHash.lo MemHash.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from MemHash.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from MemHash.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' MemHash.cpp: In member function 'virtual void mems::MemHash::SetDirection(mems::MatchHashEntry&)': MemHash.cpp:245: warning: comparison between signed and unsigned integer expressions MemHash.cpp:251: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/MatchFinder.h: In member function 'void mems::MatchFinder::ExtendMatch(UngappedMatchType&, std::vector >&, gnSeqI, gnSeqI) [with UngappedMatchType = mems::MatchHashEntry]': MemHash.cpp:276: instantiated from here ../libMems/MatchFinder.h:227: warning: comparison between signed and unsigned integer expressions ../libMems/MatchFinder.h:250: warning: comparison between signed and unsigned integer expressions ../libMems/MatchFinder.h:332: warning: comparison between signed and unsigned integer expressions ../libMems/MatchFinder.h:338: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': MemHash.cpp:377: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MemHash.cpp:377: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions MemHash.cpp:377: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MemHash.cpp:377: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions MemHash.cpp:377: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MemHash.cpp:377: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions MemHash.cpp:377: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o MatchHashEntry.lo MatchHashEntry.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o MatchHashEntry.cpp: In static member function 'static boolean mems::MatchHashEntry::start_lessthan_ptr(const mems::MatchHashEntry*, const mems::MatchHashEntry*)': MatchHashEntry.cpp:37: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:37: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp: In static member function 'static int64 mems::MatchHashEntry::start_compare(const mems::MatchHashEntry&, const mems::MatchHashEntry&)': MatchHashEntry.cpp:81: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:81: warning: comparison between signed and unsigned integer expressions ../libMems/MatchHashEntry.h: In constructor 'mems::MatchHashEntry::MatchHashEntry(uint32, gnSeqI, mems::MatchHashEntry::MemType)': ../libMems/MatchHashEntry.h:110: warning: 'mems::MatchHashEntry::m_offsets' will be initialized after ../libMems/MatchHashEntry.h:108: warning: 'gnSeqI mems::MatchHashEntry::m_mersize' MatchHashEntry.cpp:106: warning: when initialized here MatchHashEntry.cpp: In member function 'virtual void mems::MatchHashEntry::CalculateOffset()': MatchHashEntry.cpp:159: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp: In member function 'boolean mems::MatchHashEntry::Contains(const mems::MatchHashEntry&) const': MatchHashEntry.cpp:182: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:197: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:197: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': MatchHashEntry.cpp:208: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:208: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:208: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': MatchHashEntry.cpp:208: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MatchHashEntry.cpp:208: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:208: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MatchHashEntry.cpp:208: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:208: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MatchHashEntry.cpp:208: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:208: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o Interval.lo Interval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c Interval.cpp -fPIC -DPIC -o .libs/Interval.o In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/gnAlignedSequences.h:32, from ../libMems/Interval.h:19, from Interval.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' ../libMems/SparseAbstractMatch.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]': ../libMems/GappedAlignment.h:94: instantiated from here ../libMems/SparseAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c Interval.cpp -o Interval.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o IntervalList.lo IntervalList.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.o In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/IntervalList.h:23, from IntervalList.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/SortedMerList.h:19, from ../libMems/IntervalList.h:20, from IntervalList.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' ../libMems/SparseAbstractMatch.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]': ../libMems/GappedAlignment.h:94: instantiated from here ../libMems/SparseAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': IntervalList.cpp:24: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': IntervalList.cpp:24: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions IntervalList.cpp:24: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': IntervalList.cpp:24: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions IntervalList.cpp:24: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': IntervalList.cpp:24: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions IntervalList.cpp:24: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o twister.lo twister.c cc -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c twister.c -fPIC -DPIC -o .libs/twister.o cc -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c twister.c -o twister.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o gnAlignedSequences.lo gnAlignedSequences.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/gnAlignedSequences.h:32, from gnAlignedSequences.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' gnAlignedSequences.cpp: In member function 'void mems::gnAlignedSequences::constructFromClustalW(std::string)': gnAlignedSequences.cpp:47: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'void mems::gnAlignedSequences::constructFromPhylip(std::string)': gnAlignedSequences.cpp:60: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'void mems::gnAlignedSequences::constructFromMSF(std::string)': gnAlignedSequences.cpp:73: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'void mems::gnAlignedSequences::constructFromNexus(std::string)': gnAlignedSequences.cpp:95: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'void mems::gnAlignedSequences::constructFromMega(std::string)': gnAlignedSequences.cpp:108: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In static member function 'static boolean mems::gnAlignedSequences::isSupportedFormat(const std::string&)': gnAlignedSequences.cpp:129: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::outputPhylip(std::ostream&) const': gnAlignedSequences.cpp:179: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::outputClustalW(std::ostream&) const': gnAlignedSequences.cpp:221: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:227: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:245: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::outputMSF(std::ostream&) const': gnAlignedSequences.cpp:275: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:280: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:313: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:320: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:333: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::outputNexus(std::ostream&) const': gnAlignedSequences.cpp:366: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:367: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:372: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:384: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:400: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:409: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:414: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::outputMega(std::ostream&) const': gnAlignedSequences.cpp:521: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:530: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:541: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::outputCodon(std::ostream&) const': gnAlignedSequences.cpp:566: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:582: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:596: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::outputWithConsensus(std::ostream&)': gnAlignedSequences.cpp:618: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:634: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:648: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:657: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:671: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'mems::gnAlignedSequences mems::gnAlignedSequences::getCodons(int, int, int)': gnAlignedSequences.cpp:696: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::removeAlignedSeq(unsigned int)': gnAlignedSequences.cpp:737: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::constructClustalWAlignedSequenceList(std::ifstream&)': gnAlignedSequences.cpp:1101: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::constructPhylipAlignedSequenceList(std::ifstream&)': gnAlignedSequences.cpp:1147: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1170: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::constructMSFAlignedSequenceList(std::ifstream&)': gnAlignedSequences.cpp:1211: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::constructNexusAlignedSequenceList(std::ifstream&)': gnAlignedSequences.cpp:1259: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1257: warning: unused variable 'newFilter' gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::constructMegaAlignedSequenceList(std::ifstream&)': gnAlignedSequences.cpp:1315: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::buildConsensus()': gnAlignedSequences.cpp:1384: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1390: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1409: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'void mems::gnAlignedSequences::addSequence(genome::gnSequence, std::string, int, std::string)': gnAlignedSequences.cpp:1477: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1492: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::coordinates(std::string)': gnAlignedSequences.cpp:1558: warning: comparison between signed and unsigned integer expressions g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o MatchList.lo MatchList.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from MatchList.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/SortedMerList.h:19, from ../libMems/MatchList.h:18, from MatchList.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': MatchList.cpp:25: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MatchList.cpp:25: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions MatchList.cpp:25: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MatchList.cpp:25: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions MatchList.cpp:25: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MatchList.cpp:25: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions MatchList.cpp:25: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o Aligner.lo Aligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/Aligner.h:19, from Aligner.cpp:9: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' In file included from ../libMems/Aligner.h:18, from Aligner.cpp:9: ../libMems/GappedAligner.h: In function 'boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)': ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from Aligner.cpp:9: ../libMems/Aligner.h: In member function 'boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const': ../libMems/Aligner.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:56: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function 'boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const': ../libMems/Aligner.h:102: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:102: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function 'bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const': ../libMems/Aligner.h:293: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:293: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:294: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function 'boolean mems::validateLCB(mems::MatchList&)': Aligner.cpp:58: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function 'bool mems::SimpleBreakpointScorer::isValid(size_t, double)': Aligner.cpp:398: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function 'void mems::SimpleBreakpointScorer::remove(uint, std::vector, std::allocator > >&)': Aligner.cpp:426: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function 'int64 mems::greedyBreakpointElimination_v4(std::vector >&, std::vector >&, mems::SimpleBreakpointScorer&, std::ostream*, bool)': Aligner.cpp:453: warning: unused variable 'seq_count' Aligner.cpp: In function 'void mems::EliminateOverlaps(mems::MatchList&)': Aligner.cpp:618: warning: comparison between signed and unsigned integer expressions Aligner.cpp:668: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function 'boolean mems::checkCollinearity(mems::Match*, mems::Match*)': Aligner.cpp:799: warning: comparison between signed and unsigned integer expressions Aligner.cpp:800: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function 'void mems::scanFit(std::list >&, std::_List_iterator&, mems::Match*, uint)': Aligner.cpp:822: warning: comparison between signed and unsigned integer expressions Aligner.cpp:848: warning: comparison between signed and unsigned integer expressions Aligner.cpp:850: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function 'void mems::AaronsLCB(mems::MatchList&, std::set, std::allocator >&)': Aligner.cpp:915: warning: comparison between signed and unsigned integer expressions Aligner.cpp:945: warning: comparison between signed and unsigned integer expressions Aligner.cpp:960: warning: comparison between signed and unsigned integer expressions Aligner.cpp:964: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1040: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function 'void mems::GetLCBCoverage(mems::MatchList&, uint64&)': Aligner.cpp:1132: warning: unused variable 'debug' Aligner.cpp: In function 'void mems::computeLCBAdjacencies_v2(mems::IntervalList&, std::vector >&, std::vector >&)': Aligner.cpp:1192: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function 'void mems::Aligner::CreateGapSearchList(std::vector >&, mems::MatchList&, std::vector >, std::allocator > > >&, boolean)': Aligner.cpp:1390: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1391: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function 'void mems::Aligner::SearchLCBGaps(std::vector >&, mems::MatchList&, const std::vector >, std::allocator > > >&, boolean)': Aligner.cpp:1576: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1446: warning: unused variable 'lcbI' Aligner.cpp: In function 'void mems::transposeMatches(mems::MatchList&, uint, const std::vector >&)': Aligner.cpp:1638: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1659: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function 'void mems::Aligner::Recursion(mems::MatchList&, mems::Match*, mems::Match*, boolean)': Aligner.cpp:1746: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1747: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1765: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1773: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1909: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function 'void mems::Aligner::AlignLCB(mems::MatchList&, mems::Interval&)': Aligner.cpp:1996: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1994: warning: unused variable 'matchI' Aligner.cpp: In member function 'void mems::Aligner::SearchWithinLCB(mems::MatchList&, std::vector, std::allocator > >&)': Aligner.cpp:2086: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2069: warning: unused variable 'config_value' Aligner.cpp: In function 'int64 mems::greedyBreakpointElimination(gnSeqI, std::vector >&, std::vector >&, std::ostream*)': Aligner.cpp:2233: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2237: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2281: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2281: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2285: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2290: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2293: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2295: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2306: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2306: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2313: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2314: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2321: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2321: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2364: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2371: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function 'void mems::filterMatches(std::vector >&, std::vector, std::allocator > >&, std::vector >&)': Aligner.cpp:2413: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2429: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2432: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2432: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2442: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2442: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function 'void mems::Aligner::WritePermutation(std::vector >&, std::string)': Aligner.cpp:2485: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2489: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2492: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2498: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function 'void mems::Aligner::RecursiveAnchorSearch(mems::MatchList&, gnSeqI, std::vector, std::allocator > >&, boolean, std::ostream*)': Aligner.cpp:2634: warning: unused variable 'prev_size' Aligner.cpp:2709: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2724: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]': ../libMems/GappedAlignment.h:94: instantiated from here ../libMems/SparseAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::GenericMatch, std::allocator > > >]': ../libMems/Aligner.h:336: instantiated from here ../libMems/AbstractMatch.h:302: warning: unused variable 'diff' Aligner.cpp: In function 'uint mems::RemoveLCBandCoalesce(size_t, LcbVector&, std::vector >&, std::vector, std::allocator > >&, std::vector >&) [with LcbVector = std::vector >]': Aligner.cpp:409: instantiated from here Aligner.cpp:185: warning: comparison between signed and unsigned integer expressions Aligner.cpp:187: warning: comparison between signed and unsigned integer expressions Aligner.cpp:198: warning: comparison between signed and unsigned integer expressions Aligner.cpp:203: warning: comparison between signed and unsigned integer expressions Aligner.cpp:409: instantiated from here Aligner.cpp:220: warning: comparison between signed and unsigned integer expressions Aligner.cpp:220: warning: comparison between signed and unsigned integer expressions Aligner.cpp:222: warning: comparison between signed and unsigned integer expressions Aligner.cpp:222: warning: comparison between signed and unsigned integer expressions Aligner.cpp:224: warning: comparison between signed and unsigned integer expressions Aligner.cpp:224: warning: comparison between signed and unsigned integer expressions Aligner.cpp:226: warning: comparison between signed and unsigned integer expressions Aligner.cpp:226: warning: comparison between signed and unsigned integer expressions Aligner.cpp:409: instantiated from here Aligner.cpp:269: warning: comparison between signed and unsigned integer expressions Aligner.cpp:274: warning: comparison between signed and unsigned integer expressions Aligner.cpp:277: warning: comparison between signed and unsigned integer expressions Aligner.cpp:280: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function 'void mems::undoLcbRemoval(LcbVector&, std::vector, std::allocator > >&) [with LcbVector = std::vector >]': Aligner.cpp:410: instantiated from here Aligner.cpp:308: warning: comparison between signed and unsigned integer expressions Aligner.cpp:318: warning: comparison between signed and unsigned integer expressions Aligner.cpp:320: warning: comparison between signed and unsigned integer expressions Aligner.cpp:341: warning: comparison between signed and unsigned integer expressions Aligner.cpp:347: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function 'boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]': Aligner.cpp:2395: instantiated from here ../libMems/AbstractMatch.h:335: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:335: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:336: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]': /usr/include/c++/4.2/bits/stl_algo.h:125: instantiated from 'const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::GenericMatch, std::allocator > > >*, _Compare = mems::MatchStartComparator]' /usr/include/c++/4.2/bits/stl_algo.h:2795: instantiated from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator > > >**, std::vector, std::allocator > > >*> > >, _Size = int, _Compare = mems::MatchStartComparator]' /usr/include/c++/4.2/bits/stl_algo.h:2866: instantiated from 'void std::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator > > >**, std::vector, std::allocator > > >*> > >, _Compare = mems::MatchStartComparator]' Aligner.cpp:2464: instantiated from here ../libMems/AbstractMatch.h:302: warning: unused variable 'diff' ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': Aligner.cpp:2868: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': Aligner.cpp:2868: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2868: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': Aligner.cpp:2868: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2868: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': Aligner.cpp:2868: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2868: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used ../libMems/SubstitutionMatrix.h:67: warning: 'mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c Aligner.cpp -o Aligner.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o Islands.lo Islands.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/IntervalList.h:23, from ../libMems/Islands.h:18, from Islands.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/Islands.h:16, from Islands.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' In file included from ../libMems/Aligner.h:18, from ../libMems/Islands.h:23, from Islands.cpp:13: ../libMems/GappedAligner.h: In function 'boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)': ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Islands.h:23, from Islands.cpp:13: ../libMems/Aligner.h: In member function 'boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const': ../libMems/Aligner.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:56: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function 'boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const': ../libMems/Aligner.h:102: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:102: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function 'bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const': ../libMems/Aligner.h:293: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:293: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:294: warning: comparison between signed and unsigned integer expressions Islands.cpp: In function 'void mems::addUnalignedIntervals(mems::IntervalList&, std::set, std::allocator >, std::vector >)': Islands.cpp:451: warning: comparison between signed and unsigned integer expressions Islands.cpp: In function 'void mems::findIslandsBetweenLCBs(mems::IntervalList&, uint, std::ostream&)': Islands.cpp:479: warning: comparison between signed and unsigned integer expressions Islands.cpp: In function 'void mems::TransformDistanceIdentity(NumericMatrix&)': Islands.cpp:611: warning: comparison between signed and unsigned integer expressions Islands.cpp:612: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]': ../libMems/GappedAlignment.h:94: instantiated from here ../libMems/SparseAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::GenericMatch, std::allocator > > >]': ../libMems/Aligner.h:336: instantiated from here ../libMems/AbstractMatch.h:302: warning: unused variable 'diff' ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': Islands.cpp:698: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': Islands.cpp:698: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions Islands.cpp:698: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': Islands.cpp:698: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions Islands.cpp:698: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': Islands.cpp:698: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions Islands.cpp:698: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/SubstitutionMatrix.h: At global scope: ../libMems/SubstitutionMatrix.h:67: warning: 'mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()' defined but not used ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c Islands.cpp -o Islands.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o MaskedMemHash.lo MaskedMemHash.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' MaskedMemHash.cpp: In member function 'virtual boolean mems::MaskedMemHash::HashMatch(std::list >&)': MaskedMemHash.cpp:56: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]': ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:139: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:152: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:505: instantiated from here ../libMems/HybridAbstractMatch.h:161: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': MaskedMemHash.cpp:64: instantiated from here ../libMems/UngappedLocalAlignment.h:128: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::EvenlyOverlaps(const mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MaskedMemHash.cpp:64: instantiated from here ../libMems/Match.h:356: warning: comparison between signed and unsigned integer expressions MaskedMemHash.cpp:64: instantiated from here ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:365: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:376: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueStart(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MaskedMemHash.cpp:64: instantiated from here ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:221: warning: comparison between signed and unsigned integer expressions MaskedMemHash.cpp:64: instantiated from here ../libMems/Match.h:235: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:245: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: In member function 'boolean mems::GenericMatch::GetUniqueEnd(const mems::GenericMatch&, mems::GenericMatch&) const [with BaseType = mems::UngappedLocalAlignment, std::allocator > >]': MaskedMemHash.cpp:64: instantiated from here ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:278: warning: comparison between signed and unsigned integer expressions MaskedMemHash.cpp:64: instantiated from here ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h:302: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:390: warning: 'mems::seq_compare_start' defined but not used g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o GappedAlignment.lo GappedAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' ../libMems/SparseAbstractMatch.h: In member function 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]': ../libMems/GappedAlignment.h:94: instantiated from here ../libMems/SparseAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c -o MuscleInterface.lo MuscleInterface.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include/libGenome-1.3 -I/usr/include/libClustalW-1.0 -g -Wall -O2 -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o In file included from /usr/include/libGenome-1.3/libGenome/gnSequence.h:30, from ../libMems/MuscleInterface.h:18, from MuscleInterface.cpp:13: /usr/include/libGenome-1.3/libGenome/gnCompare.h: In member function 'boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const': /usr/include/libGenome-1.3/libGenome/gnCompare.h:141: warning: array subscript has type 'char' In file included from ../libMems/MuscleInterface.h:20, from MuscleInterface.cpp:13: ../libMem