* Package: sci-biology/mira-3.4.0.2  * Repository: gentoo  * Maintainer: weaver@gentoo.org sci-biology@gentoo.org  * USE: amd64 elibc_glibc kernel_linux multilib userland_GNU  * FEATURES: nostrip sandbox splitdebug >>> Unpacking source... >>> Unpacking mira-3.4.0.2.tar.bz2 to /var/tmp/portage/sci-biology/mira-3.4.0.2/work >>> Unpacking mira_3rdparty_06-07-2012.tar.bz2 to /var/tmp/portage/sci-biology/mira-3.4.0.2/work >>> Source unpacked in /var/tmp/portage/sci-biology/mira-3.4.0.2/work >>> Preparing source in /var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2 ... * Applying mira-3.4.0.2-boost-1.50.patch ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2' ... * Running libtoolize --install --copy --force --automake ...  [ ok ] * Running aclocal -I config/m4 ...  [ ok ] * Running autoconf -I config/m4 ...  [ ok ] * Running automake --add-missing --copy ...  [ ok ] * Running elibtoolize in: mira-3.4.0.2/ * Applying portage/1.2.0 patch ... * Applying sed/1.5.6 patch ... * Applying as-needed/2.2.6 patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2 ... * econf: updating mira-3.4.0.2/config.guess with /usr/share/gnuconfig/config.guess * econf: updating mira-3.4.0.2/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --disable-dependency-tracking --with-boost=/usr/lib64 --with-boost-libdir=/usr/lib64 --with-boost-thread=boost_thread-mt configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux 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 how to create a ustar tar archive... gnutar checking whether to add --prefix as include path... yes +++++++++++++++++++++++++++++++++++++ systemuname: Linux CFLAGS now: -O2 -pipe -march=nocona -I/usr/include CXXFLAGS now: -O2 -pipe -march=nocona -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking dependency style of x86_64-pc-linux-gnu-g++... none +++++++++++++++++++++++++++++++++++++ systemuname: Linux CFLAGS now: -O2 -pipe -march=nocona -I/usr/include CXXFLAGS now: -O2 -pipe -march=nocona -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int64_t... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -march=nocona -I/usr/include CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether long has 64bit... yes checking whether enabling 64bit compilation support... yes checking build system type... x86_64-pc-linux-gnu checking for compiler optimisation settings... -O2 +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking for sysroot... no checking for x86_64-pc-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether make sets $(MAKE)... (cached) yes checking whether ln -s works... yes checking for a sed that does not truncate output... (cached) /bin/sed checking for flex... no checking for flex... flex checking lex output file root... lex.yy checking lex library... -lfl checking whether yytext is a pointer... yes checking for flex... yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for C/C++ restrict keyword... __restrict checking whether struct tm is in sys/time.h or time.h... time.h checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for strftime... yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for isblank... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether the compiler implements namespaces... yes checking whether the compiler supports ISO C++ standard library... yes checking whether the compiler supports Standard Template Library... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether perl executable path has been provided... no checking for perl... /usr/bin/perl checking for Expat XML Parser headers in /usr/include... found checking for Expat XML Parser libraries... found checking for Expat XML Parser... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking if zlib is wanted... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for boostlib >= 1.35.0... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/usr/lib64/include BOOST LDFLAGS: -L/usr/lib64 CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/usr/lib64/include BOOST LDFLAGS: -L/usr/lib64 CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread-mt... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/lib64/include BOOST LDFLAGS: -L/usr/lib64 ac_boost_path: /usr/lib64 ac_boost_lib_path: /usr/lib64 BOOST_THREAD_LIB: -lboost_thread-mt CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/lib64/include BOOST LDFLAGS: -L/usr/lib64 ac_boost_path: /usr/lib64 ac_boost_lib_path: /usr/lib64 BOOST_THREAD_LIB: -lboost_thread-mt CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64 -lboost_thread-mt +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex-mt... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/lib64/include BOOST LDFLAGS: -L/usr/lib64 ac_boost_path: /usr/lib64 ac_boost_lib_path: /usr/lib64 BOOST_REGEX_LIB: -lboost_regex-mt -lboost_system CFLAGS now: -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64 -lboost_thread-mt -lboost_regex-mt -lboost_system +++++++++++++++++++++++++++++++++++++ checking for flex version compatible with MIRA... yes checking for purify... no checking whether linking with tcmalloc works... yes checking whether mira should compile in public quiet mode... yes checking whether mira should compile a development version... no checking whether mira should compile with bound tracking... yes checking whether mira should compile with bug tracking... yes checking whether mira should compile with extended bug tracking... no checking whether mira should compile with function trace... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/stdinc/Makefile config.status: creating src/lec/Makefile config.status: creating src/errorhandling/Makefile config.status: creating src/util/Makefile config.status: creating src/io/Makefile config.status: creating src/mira/Makefile config.status: creating src/EdIt/Makefile config.status: creating src/caf/Makefile config.status: creating src/examine/Makefile config.status: creating src/knn_abi373/Makefile config.status: creating src/knn_alf/Makefile config.status: creating src/support/Makefile config.status: creating src/scripts/Makefile config.status: creating src/test/Makefile config.status: creating src/test/io/Makefile config.status: creating src/test/io/scf/Makefile config.status: creating src/test/io/fasta/Makefile config.status: creating src/test/io/generalio/Makefile config.status: creating src/test/mira/Makefile config.status: creating src/test/mira/align/Makefile config.status: creating src/test/mira/read/Makefile config.status: creating src/test/mira/readpool/Makefile config.status: creating src/examples_programming/Makefile config.status: creating src/progs/Makefile config.status: creating doc/Makefile config.status: creating doc/docbook/Makefile config.status: creating distribution/Makefile config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------------------------------------- Summary of MIRA configuration -------------------------------------------------------------------------------- Building version ................................. 3.4.0.2_prod_linux-gnu_x86_64_dynamic Production or development version?................ production We are building on ............................... Linux CPU supports 64 bit? ......... ................... yes Compiler ......................................... x86_64-pc-linux-gnu-gcc Compiler is not GCC. This *MIGHT* be a problem! (more compilation tests needed, please report succes or failure) Compiler optimisation flags used ................. -O2 Do we compile in 64 bit? ......................... yes Building completely static? ...................... no BOOST expected to compile and link?............... yes Linking with TCmalloc library?.................... yes Can MIRA be built on this system? ................ yes Using CFLAGS : -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include Using LDFLAGS : -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64 -lboost_thread-mt -lboost_regex-mt -lboost_system System: Linux fold 2.6.35.9-default #5 SMP Tue Nov 22 10:50:21 MET 2011 x86_64 Intel(R) Core(TM)2 Quad CPU Q9650 @ 3.00GHz GenuineIntel GNU/Linux Compiler: 'x86_64-pc-linux-gnu-gcc -v' output: Using built-in specs. COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.5.2/x86_64-pc-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.5.2/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-4.5.2/work/gcc-4.5.2/configure --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.5.2 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.2/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.5.2 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.5.2/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.5.2/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.2/include/g++-v4 --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --disable-altivec --disable-fixed-point --without-ppl --without-cloog --disable-ppl-version-check --disable-lto --enable-nls --without-included-gettext --with-system-zlib --disable-werror --enable-secureplt --enable-multilib --disable-libmudflap --disable-libssp --enable-libgomp --enable-cld --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.5.2/python --enable-checking=release --disable-libgcj --enable-languages=c,c++,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --with-bugurl=http://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.5.2 p1.0, pie-0.4.5' Thread model: posix gcc version 4.5.2 (Gentoo 4.5.2 p1.0, pie-0.4.5) -------------------------------------------------------------------------------- Ooops, we might encounter some problems in compilation/linking. Please give it a try and report success or failure. Type 'make' to make the binaries and if no error occured, then 'make install' to install them. In case of failure, please help to fix if you can. >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2 ... make -j5 Making all in src make[1]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src' Making all in lec make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/lec' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/lec' Making all in io make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/io' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o gbf.o gbf.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o generalio.o generalio.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o fasta.o fasta.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o fastq-mira.o fastq-mira.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o phd.o phd.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o scf.o scf.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o exp.o exp.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o ncbiinfoxml.o ncbiinfoxml.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o exp_flexer.o exp_flexer.cc rm -f libmirafio.a x86_64-pc-linux-gnu-ar cru libmirafio.a gbf.o generalio.o fasta.o fastq-mira.o phd.o scf.o exp.o ncbiinfoxml.o exp_flexer.o x86_64-pc-linux-gnu-ranlib libmirafio.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/io' Making all in stdinc make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/stdinc' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/stdinc' Making all in errorhandling make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/errorhandling' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o errorhandling.o errorhandling.C rm -f libmiraerrorhandling.a x86_64-pc-linux-gnu-ar cru libmiraerrorhandling.a errorhandling.o x86_64-pc-linux-gnu-ranlib libmiraerrorhandling.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/errorhandling' Making all in util make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/util' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o misc.o misc.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o dptools.o dptools.C rm -f libmiradptools.a x86_64-pc-linux-gnu-ar cru libmiradptools.a dptools.o rm -f libmirautil.a x86_64-pc-linux-gnu-ar cru libmirautil.a misc.o x86_64-pc-linux-gnu-ranlib libmiradptools.a x86_64-pc-linux-gnu-ranlib libmirautil.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/util' Making all in mira make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/mira' Making .H out of .xxd adaptorsforclip.454.xxd.H Making .H out of .xxd adaptorsforclip.solexa.xxd.H Making .H out of .xxd adaptorsforclip.iontor.xxd.H Making .H out of .xxd adaptorsregex.solexa.xxd.H Making .H out of .xxd adaptorsregex.iontor.xxd.H make all-am make[3]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/mira' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o estassembly.o estassembly.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o contig.o contig.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o gff_parse.o gff_parse.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o parameters_flexer.o parameters_flexer.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o multitag.o multitag.C contig.C:185:13: warning: multi-character character constant contig.C:3293:17: warning: multi-character character constant x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o maf_parse.o maf_parse.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o adsfacts.o adsfacts.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o ads.o ads.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o assembly_output.o assembly_output.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o assembly_info.o assembly_info.C assembly_info.C:100:80: warning: trigraph ??) ignored, use -trigraphs to enable x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o readpool.o readpool.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o contig_output.o contig_output.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o contig_analysis.o contig_analysis.C contig_output.C:221:21: warning: multi-character character constant x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o contig_edit.o contig_edit.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o read.o read.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o align.o align.C read.C: In member function 'void Read::dumpAsFASTA(std::ostream&, bool, bool, bool)': read.C:1039:33: warning: format '%x' expects type 'unsigned int', but argument 3 has type 'Read*' read.C: In member function 'void Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)': read.C:1121:33: warning: format '%x' expects type 'unsigned int', but argument 3 has type 'Read*' read.C: In member function 'void Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)': read.C:1215:33: warning: format '%x' expects type 'unsigned int', but argument 3 has type 'Read*' read.C: In member function 'void Read::dumpAsCAF(std::ostream&)': read.C:1287:33: warning: format '%x' expects type 'unsigned int', but argument 3 has type 'Read*' read.C: In member function 'void Read::dumpAsMAF(std::ostream&)': read.C:1714:33: warning: format '%x' expects type 'unsigned int', but argument 3 has type 'Read*' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o dynamic.o dynamic.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o parameters.o parameters.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o assembly.o assembly.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o scaffolder.o scaffolder.C assembly.C:1563:0: warning: "CEBUG" redefined ../../src/stdinc/defines.H:60:0: note: this is the location of the previous definition assembly.C:2954:0: warning: "CEBUG" redefined assembly.C:1563:0: note: this is the location of the previous definition x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o skim.o skim.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o dataprocessing.o dataprocessing.C dataprocessing.C:3077:0: warning: "CEBUG" redefined dataprocessing.C:44:0: note: this is the location of the previous definition dataprocessing.C:3111:0: warning: "CEBUG" redefined dataprocessing.C:3077:0: note: this is the location of the previous definition assembly.C: In member function 'bool Assembly::checkTerminationRequest()': assembly.C:985:28: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o assembly_io.o assembly_io.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o assembly_repeatresolve.o assembly_repeatresolve.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o assembly_reduceskimhits.o assembly_reduceskimhits.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o assembly_swalign.o assembly_swalign.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o newpathfinder.o newpathfinder.C assembly_reduceskimhits.C:716:0: warning: "CEBUG" redefined assembly_reduceskimhits.C:604:0: note: this is the location of the previous definition assembly_reduceskimhits.C:789:0: warning: "CEBUG" redefined assembly_reduceskimhits.C:716:0: note: this is the location of the previous definition assembly_reduceskimhits.C:1025:0: warning: "CEBUG" redefined assembly_reduceskimhits.C:789:0: note: this is the location of the previous definition assembly_reduceskimhits.C:1065:0: warning: "CEBUG" redefined assembly_reduceskimhits.C:1025:0: note: this is the location of the previous definition assembly_reduceskimhits.C:2476:0: warning: "CEBUG" redefined assembly_reduceskimhits.C:1065:0: note: this is the location of the previous definition assembly_reduceskimhits.C:2505:0: warning: "CEBUG" redefined assembly_reduceskimhits.C:2476:0: note: this is the location of the previous definition assembly_reduceskimhits.C:2510:0: warning: "CEBUG" redefined assembly_reduceskimhits.C:2505:0: note: this is the location of the previous definition assembly_reduceskimhits.C:2580:0: warning: "CEBUG" redefined assembly_reduceskimhits.C:2510:0: note: this is the location of the previous definition newpathfinder.C:4357:0: warning: "CEBUG" redefined ../../src/stdinc/defines.H:60:0: note: this is the location of the previous definition newpathfinder.C:4363:0: warning: "CEBUG" redefined newpathfinder.C:4357:0: note: this is the location of the previous definition rm -f libmiraestass.a x86_64-pc-linux-gnu-ar cru libmiraestass.a estassembly.o x86_64-pc-linux-gnu-ranlib libmiraestass.a rm -f libmirasupport.a x86_64-pc-linux-gnu-ar cru libmirasupport.a contig.o gff_parse.o parameters_flexer.o multitag.o maf_parse.o adsfacts.o ads.o assembly_output.o assembly_info.o readpool.o contig_output.o contig_analysis.o contig_edit.o read.o align.o dynamic.o parameters.o x86_64-pc-linux-gnu-ranlib libmirasupport.a assembly_reduceskimhits.C: In member function 'void Assembly::rsh4_filterSkimHits(const std::string&, const std::string&, size_t&)': assembly_reduceskimhits.C:682:44: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result rm -f libmira.a x86_64-pc-linux-gnu-ar cru libmira.a assembly.o scaffolder.o skim.o dataprocessing.o assembly_io.o assembly_repeatresolve.o assembly_reduceskimhits.o assembly_swalign.o newpathfinder.o x86_64-pc-linux-gnu-ranlib libmira.a make[3]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/mira' make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/mira' Making all in EdIt make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/EdIt' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o hypothesen.o hypothesen.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o parameters.o parameters.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o faultRegion.o faultRegion.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o parameters_flexer.o parameters_flexer.cc rm -f libmiraEdIt.a x86_64-pc-linux-gnu-ar cru libmiraEdIt.a hypothesen.o parameters.o faultRegion.o parameters_flexer.o x86_64-pc-linux-gnu-ranlib libmiraEdIt.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/EdIt' Making all in caf make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/caf' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o caf.o caf.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o caf_flexer.o caf_flexer.cc rm -f libmiracaf.a x86_64-pc-linux-gnu-ar cru libmiracaf.a caf.o caf_flexer.o x86_64-pc-linux-gnu-ranlib libmiracaf.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/caf' Making all in examine make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/examine' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o scf_look.o scf_look.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o ranges.o ranges.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o afh_info.o afh_info.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o cfh.o cfh.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o calc.o calc.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o prescan.o prescan.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o misc.o misc.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o buffer.o buffer.C prescan.C: In member function 'int32 prescan::initialize()': prescan.C:67:30: warning: deprecated conversion from string constant to 'char*' rm -f libmiraExamine.a x86_64-pc-linux-gnu-ar cru libmiraExamine.a scf_look.o ranges.o afh_info.o cfh.o calc.o prescan.o misc.o buffer.o x86_64-pc-linux-gnu-ranlib libmiraExamine.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/examine' Making all in knn_abi373 make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/knn_abi373' x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c wrong.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c under.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c add.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c over.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c nplus.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c missing.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c ncall.c rm -f libmiraKNN_abi373.a x86_64-pc-linux-gnu-ar cru libmiraKNN_abi373.a wrong.o under.o add.o over.o nplus.o missing.o ncall.o x86_64-pc-linux-gnu-ranlib libmiraKNN_abi373.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/knn_abi373' Making all in knn_alf make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/knn_alf' x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c wrong.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c under.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c add.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c over.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c nplus.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c missing.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -c ncall.c rm -f libmiraKNN_alf.a x86_64-pc-linux-gnu-ar cru libmiraKNN_alf.a wrong.o under.o add.o over.o nplus.o missing.o ncall.o x86_64-pc-linux-gnu-ranlib libmiraKNN_alf.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/knn_alf' Making all in examples_programming make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/examples_programming' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -pthread -I/usr/lib64/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o mira_101.o mira_101.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -pthread -I/usr/lib64/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o read_101.o read_101.C x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.2\" -DPACKAGE_STRING=\"mira\ 3.4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -pthread -I/usr/lib64/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -c -o readpool_101.o readpool_101.C /bin/sh ../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -pthread -I/usr/lib64/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -march=nocona -I/usr/include -O2 -I/usr/include -pthread -I/usr/lib64/include -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/ -L../EdIt/ -L../caf/ -L../knn_abi373 -L../knn_alf -L/usr/lib64 -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64 -lboost_thread-mt -lboost_regex-mt -lboost_system -o read_101 read_101.o -lmirasupport -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lm -lz -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib -lexpat -ltcmalloc_minimal libtool: Version mismatch error. This is libtool 2.4, but the libtool: definition of this LT_INIT comes from libtool 2.4.2. libtool: You should recreate aclocal.m4 with macros from libtool 2.4 libtool: and run autoconf again. make[2]: *** [read_101] Error 63 make[2]: *** Waiting for unfinished jobs.... make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src/examples_programming' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2/src' make: *** [all-recursive] Error 1 * ERROR: sci-biology/mira-3.4.0.2 failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/mira-3.4.0.2'`, * the complete build log and the output of `emerge -pqv '=sci-biology/mira-3.4.0.2'`. * The complete build log is located at '/var/tmp/portage/sci-biology/mira-3.4.0.2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mira-3.4.0.2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2' * S: '/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2'