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Gentoo's Bugzilla – Attachment 334472 Details for
Bug 450322
sci-biology/mira-3.4.0.2 - libtool: Version mismatch error. This is libtool 2.4, but the definition of this LT_INIT comes from libtool 2.4.2.
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build.log
build.log (text/plain), 103.22 KB, created by
Martin Mokrejš
on 2013-01-05 01:48:58 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Martin Mokrejš
Created:
2013-01-05 01:48:58 UTC
Size:
103.22 KB
patch
obsolete
>[32;01m * [39;49;00mPackage: sci-biology/mira-3.4.0.2 >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: weaver@gentoo.org sci-biology@gentoo.org >[32;01m * [39;49;00mUSE: amd64 elibc_glibc kernel_linux multilib userland_GNU >[32;01m * [39;49;00mFEATURES: 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 ... > [32;01m*[0m Applying mira-3.4.0.2-boost-1.50.patch ... >[A[262C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2' ... > [32;01m*[0m Running libtoolize --install --copy --force --automake ... >[A[262C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running aclocal -I config/m4 ... >[A[262C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running autoconf -I config/m4 ... >[A[262C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running automake --add-missing --copy ... >[A[262C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running elibtoolize in: mira-3.4.0.2/ > [32;01m*[0m Applying portage/1.2.0 patch ... > [32;01m*[0m Applying sed/1.5.6 patch ... > [32;01m*[0m 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 > [31;01m*[0m ERROR: sci-biology/mira-3.4.0.2 failed (compile phase): > [31;01m*[0m emake failed > [31;01m*[0m > [31;01m*[0m If you need support, post the output of `emerge --info '=sci-biology/mira-3.4.0.2'`, > [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-biology/mira-3.4.0.2'`. > [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/mira-3.4.0.2/temp/build.log'. > [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/mira-3.4.0.2/temp/environment'. > [31;01m*[0m Working directory: '/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2' > [31;01m*[0m S: '/var/tmp/portage/sci-biology/mira-3.4.0.2/work/mira-3.4.0.2'
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