* Package: sci-biology/mira-3.2.0 * Repository: gentoo * Maintainer: weaver@gentoo.org sci-biology@gentoo.org * USE: elibc_glibc kernel_linux test userland_GNU x86 * FEATURES: sandbox test userpriv usersandbox >>> Unpacking source... >>> Unpacking mira-3.2.0.tar.bz2 to /var/tmp/portage/sci-biology/mira-3.2.0/work >>> Unpacking mira_3rdparty_17-04-2010.tar.bz2 to /var/tmp/portage/sci-biology/mira-3.2.0/work >>> Source unpacked in /var/tmp/portage/sci-biology/mira-3.2.0/work >>> Preparing source in /var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0 ... * Applying mira-3.0.0-asneeded.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0' ... * Running aclocal -I config/m4 ... [ ok ] * Running libtoolize --copy --force --install --automake ... [ ok ] * Running aclocal -I config/m4 ... [ ok ] * Running autoconf -I config/m4 ... [ ok ] * Running automake --add-missing --copy ... [ ok ] * Running elibtoolize in: mira-3.2.0/ * Applying portage-1.2.0.patch ... * Applying sed-1.5.6.patch ... * Applying as-needed-2.2.6.patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0 ... * econf: updating mira-3.2.0/config.sub with /usr/share/gnuconfig/config.sub * econf: updating mira-3.2.0/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --with-boost=/usr/lib --with-boost-libdir=/usr/lib --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 build system type... i686-pc-linux-gnu checking whether to add --prefix as include path... yes +++++++++++++++++++++++++++++++++++++ systemuname: CFLAGS now: -O2 -pipe -I/usr/include CXXFLAGS now: -O2 -pipe -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for i686-pc-linux-gnu-gcc... i686-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 i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether i686-pc-linux-gnu-g++ accepts -g... yes checking dependency style of i686-pc-linux-gnu-g++... gcc3 +++++++++++++++++++++++++++++++++++++ systemuname: Linux CFLAGS now: -O2 -pipe -I/usr/include CXXFLAGS now: -O2 -pipe -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking how to run the C preprocessor... i686-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 -I/usr/include CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether long long has 64bit... no checking whether enabling 64bit compilation support... no checking for compiler optimisation settings... -O2 +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking host system type... i686-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 i686-pc-linux-gnu-gcc... /usr/i686-pc-linux-gnu/bin/ld checking if the linker (/usr/i686-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 i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/i686-pc-linux-gnu/bin/ld option to reload object files... -r checking for i686-pc-linux-gnu-objdump... i686-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for i686-pc-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar checking for archiver @FILE support... @ checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-strip checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok checking for sysroot... no checking for i686-pc-linux-gnu-mt... no checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if i686-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for i686-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if i686-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if i686-pc-linux-gnu-gcc static flag -static works... yes checking if i686-pc-linux-gnu-gcc supports -c -o file.o... yes checking if i686-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes checking whether the i686-pc-linux-gnu-gcc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E checking for ld used by i686-pc-linux-gnu-g++... /usr/i686-pc-linux-gnu/bin/ld checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking for i686-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC checking if i686-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes checking if i686-pc-linux-gnu-g++ static flag -static works... yes checking if i686-pc-linux-gnu-g++ supports -c -o file.o... yes checking if i686-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) 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 isblank... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -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 -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -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 -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok +++++++++++++++++++++++++++++++++++++ CFLAGS now: -O2 -pipe -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for boostlib >= 1.35.0... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/usr/lib/include BOOST LDFLAGS: -L/usr/lib CFLAGS now: -O2 -pipe -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/usr/lib/include BOOST LDFLAGS: -L/usr/lib CFLAGS now: -O2 -pipe -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib -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/lib/include BOOST LDFLAGS: -L/usr/lib ac_boost_path: /usr/lib ac_boost_lib_path: /usr/lib BOOST_THREAD_LIB: -lboost_thread-mt CFLAGS now: -O2 -pipe -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/lib/include BOOST LDFLAGS: -L/usr/lib ac_boost_path: /usr/lib ac_boost_lib_path: /usr/lib BOOST_THREAD_LIB: -lboost_thread-mt CFLAGS now: -O2 -pipe -I/usr/include -O2 CXXFLAGS now: -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include LDFLAGS now: -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib -L/usr/lib -L/usr/lib -lboost_thread-mt +++++++++++++++++++++++++++++++++++++ checking for flex version compatible with MIRA... yes checking for purify... no checking whether linking with tcmalloc works... no 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 -------------------------------------------------------------------------------- Could not find the tcmalloc library. It is part of the Google perftools library at http://code.google.com/p/google-perftools/downloads/list Please consult the INSTALL file of MIRA for more help on installing it. Linking to this library is *HIGHLY* recommended as without this library the memory requirements for MIRA may be 100% higher! Building version ................................. 3.2.0_prod_linux-gnu_i686_32_dynamic Production or development version?................ production We are building on ............................... Linux CPU supports 64 bit? ......... ................... no Compiler ......................................... i686-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 Building completely static? ...................... no BOOST expected to compile and link?............... yes Linking with TCmalloc library?.................... no Can MIRA be built on this system? ................ yes Using CFLAGS : -O2 -pipe -I/usr/include -O2 Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include Using LDFLAGS : -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -L/usr/lib -L/usr/lib -L/usr/lib -lboost_thread-mt System: Linux tinderbox.home.flameeyes.eu 2.6.38.3 #46 SMP PREEMPT Fri Apr 15 00:45:36 CEST 2011 i686 Quad-Core AMD Opteron(tm) Processor 2350 AuthenticAMD GNU/Linux Compiler: 'i686-pc-linux-gnu-gcc -v' output: Using built-in specs. Reading specs from /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/asneeded.specs COLLECT_GCC=/usr/i686-pc-linux-gnu/gcc-bin/4.6.0/i686-pc-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-pc-linux-gnu/4.6.0/lto-wrapper Target: i686-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-4.6.0/work/gcc-4.6.0/configure --prefix=/usr --bindir=/usr/i686-pc-linux-gnu/gcc-bin/4.6.0 --includedir=/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include --datadir=/usr/share/gcc-data/i686-pc-linux-gnu/4.6.0 --mandir=/usr/share/gcc-data/i686-pc-linux-gnu/4.6.0/man --infodir=/usr/share/gcc-data/i686-pc-linux-gnu/4.6.0/info --with-gxx-include-dir=/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4 --host=i686-pc-linux-gnu --build=i686-pc-linux-gnu --disable-altivec --disable-fixed-point --without-ppl --without-cloog --enable-lto --enable-nls --without-included-gettext --with-system-zlib --disable-werror --enable-secureplt --disable-multilib --enable-libmudflap --disable-libssp --enable-libgomp --enable-cld --with-python-dir=/share/gcc-data/i686-pc-linux-gnu/4.6.0/python --enable-checking=release --with-arch=i686 --enable-languages=c,c++,java,objc,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --with-bugurl=http://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.6.0 p1.0, pie-0.4.5' Thread model: posix gcc driver version 4.6.0 (Gentoo 4.6.0 p1.0, pie-0.4.5) executing gcc version 4.5.2 -------------------------------------------------------------------------------- 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-3.2.0/work/mira-3.2.0 ... make -j14 Making all in src make[1]: Entering directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src' Making all in lec make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/lec' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/lec' Making all in io make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/io' i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT gbf.o -MD -MP -MF .deps/gbf.Tpo -c -o gbf.o gbf.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT generalio.o -MD -MP -MF .deps/generalio.Tpo -c -o generalio.o generalio.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT fasta.o -MD -MP -MF .deps/fasta.Tpo -c -o fasta.o fasta.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT phd.o -MD -MP -MF .deps/phd.Tpo -c -o phd.o phd.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT scf.o -MD -MP -MF .deps/scf.Tpo -c -o scf.o scf.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT exp.o -MD -MP -MF .deps/exp.Tpo -c -o exp.o exp.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT ncbiinfoxml.o -MD -MP -MF .deps/ncbiinfoxml.Tpo -c -o ncbiinfoxml.o ncbiinfoxml.C Flexing exp_flexer.flex.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT exp_flexer.flex.o -MD -MP -MF .deps/exp_flexer.flex.Tpo -c -o exp_flexer.flex.o exp_flexer.flex.C In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/misc.H:47, from ../errorhandling/errorhandling.H:44, from scf.H:67, from scf.C:34: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../io/phd.H:34, from phd.C:31: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/misc.H:47, from ../errorhandling/errorhandling.H:44, from ../io/gbf.H:36, from gbf.C:28: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../io/fasta.H:40, from fasta.C:27: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from generalio.H:32, from generalio.C:29: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ncbiinfoxml.H:35, from ncbiinfoxml.C:37: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from exp.H:39, from exp.C:41: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] mv -f .deps/exp_flexer.flex.Tpo .deps/exp_flexer.flex.Po mv -f .deps/generalio.Tpo .deps/generalio.Po mv -f .deps/phd.Tpo .deps/phd.Po mv -f .deps/ncbiinfoxml.Tpo .deps/ncbiinfoxml.Po mv -f .deps/fasta.Tpo .deps/fasta.Po mv -f .deps/exp.Tpo .deps/exp.Po mv -f .deps/scf.Tpo .deps/scf.Po mv -f .deps/gbf.Tpo .deps/gbf.Po rm -f libmirafio.a i686-pc-linux-gnu-ar cru libmirafio.a gbf.o generalio.o fasta.o phd.o scf.o exp.o ncbiinfoxml.o exp_flexer.flex.o i686-pc-linux-gnu-ranlib libmirafio.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/io' Making all in stdinc make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/stdinc' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/stdinc' Making all in errorhandling make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/errorhandling' i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT errorhandling.o -MD -MP -MF .deps/errorhandling.Tpo -c -o errorhandling.o errorhandling.C In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/misc.H:47, from errorhandling.H:44, from errorhandling.C:34: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] mv -f .deps/errorhandling.Tpo .deps/errorhandling.Po rm -f libmiraerrorhandling.a i686-pc-linux-gnu-ar cru libmiraerrorhandling.a errorhandling.o i686-pc-linux-gnu-ranlib libmiraerrorhandling.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/errorhandling' Making all in util make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/util' i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT misc.o -MD -MP -MF .deps/misc.Tpo -c -o misc.o misc.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT dptools.o -MD -MP -MF .deps/dptools.Tpo -c -o dptools.o dptools.C In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/dptools.H:37, from dptools.C:27: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/misc.H:47, from misc.C:25: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] mv -f .deps/misc.Tpo .deps/misc.Po rm -f libmirautil.a i686-pc-linux-gnu-ar cru libmirautil.a misc.o i686-pc-linux-gnu-ranlib libmirautil.a mv -f .deps/dptools.Tpo .deps/dptools.Po rm -f libmiradptools.a i686-pc-linux-gnu-ar cru libmiradptools.a dptools.o i686-pc-linux-gnu-ranlib libmiradptools.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/util' Making all in mira make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/mira' i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT estassembly.o -MD -MP -MF .deps/estassembly.Tpo -c -o estassembly.o estassembly.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT multitag.o -MD -MP -MF .deps/multitag.Tpo -c -o multitag.o multitag.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT maf_parse.o -MD -MP -MF .deps/maf_parse.Tpo -c -o maf_parse.o maf_parse.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT contig.o -MD -MP -MF .deps/contig.Tpo -c -o contig.o contig.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT adsfacts.o -MD -MP -MF .deps/adsfacts.Tpo -c -o adsfacts.o adsfacts.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT ads.o -MD -MP -MF .deps/ads.Tpo -c -o ads.o ads.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT assembly_output.o -MD -MP -MF .deps/assembly_output.Tpo -c -o assembly_output.o assembly_output.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT assembly_info.o -MD -MP -MF .deps/assembly_info.Tpo -c -o assembly_info.o assembly_info.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT readpool.o -MD -MP -MF .deps/readpool.Tpo -c -o readpool.o readpool.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT parameters.o -MD -MP -MF .deps/parameters.Tpo -c -o parameters.o parameters.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT contig_output.o -MD -MP -MF .deps/contig_output.Tpo -c -o contig_output.o contig_output.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT contig_analysis.o -MD -MP -MF .deps/contig_analysis.Tpo -c -o contig_analysis.o contig_analysis.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT read.o -MD -MP -MF .deps/read.Tpo -c -o read.o read.C i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT align.o -MD -MP -MF .deps/align.Tpo -c -o align.o align.C In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/misc.H:47, from ../errorhandling/errorhandling.H:44, from ../mira/assembly_info.H:31, from assembly_info.C:31: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/misc.H:47, from ../errorhandling/errorhandling.H:44, from ../mira/assembly_info.H:31, from assembly_output.H:39, from assembly_output.C:40: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ads.H:36, from ads.C:43: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../mira/read.H:40, from read.C:37: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/misc.H:47, from ../errorhandling/errorhandling.H:44, from adsfacts.H:32, from adsfacts.C:43: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from align.H:35, from align.C:33: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../mira/multitag.H:35, from multitag.C:36: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../mira/read.H:40, from maf_parse.H:37, from maf_parse.C:27: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from contig.H:41, from contig_analysis.C:33: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from readpool.H:37, from readpool.C:36: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from contig.H:41, from contig.C:33: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from contig.H:41, from contig_output.C:34: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] read.C:48:28: error: uninitialized const ‘Read::REA_bposhashstat_default’ [-fpermissive] ../mira/read.H:158:10: note: ‘const struct Read::bposhashstat_t’ has no user-provided default constructor In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/misc.H:47, from ../errorhandling/errorhandling.H:44, from ../mira/parameters.H:43, from parameters.C:35: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] mv -f .deps/adsfacts.Tpo .deps/adsfacts.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.2.0\" -DPACKAGE_STRING=\"mira\ 3.2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.2.0\" -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 -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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe -I/usr/include -O2 -pthread -I/usr/lib/include -MT dynamic.o -MD -MP -MF .deps/dynamic.Tpo -c -o dynamic.o dynamic.C assembly_info.C:97:80: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs] contig.C:204:13: warning: multi-character character constant [-Wmultichar] contig.C:2878:17: warning: multi-character character constant [-Wmultichar] contig_output.C:222:21: warning: multi-character character constant [-Wmultichar] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from assembly.H:63, from estassembly.C:31: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/ext/hash_map:61:0, from ../stdinc/stlincludes.H:72, from ../util/misc.H:47, from ../errorhandling/errorhandling.H:44, from dynamic.H:63, from dynamic.C:34: /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] make[2]: *** [read.o] Error 1 make[2]: *** Waiting for unfinished jobs.... mv -f .deps/align.Tpo .deps/align.Po mv -f .deps/dynamic.Tpo .deps/dynamic.Po mv -f .deps/assembly_info.Tpo .deps/assembly_info.Po mv -f .deps/multitag.Tpo .deps/multitag.Po mv -f .deps/maf_parse.Tpo .deps/maf_parse.Po mv -f .deps/estassembly.Tpo .deps/estassembly.Po mv -f .deps/ads.Tpo .deps/ads.Po mv -f .deps/contig_output.Tpo .deps/contig_output.Po mv -f .deps/readpool.Tpo .deps/readpool.Po mv -f .deps/assembly_output.Tpo .deps/assembly_output.Po mv -f .deps/contig_analysis.Tpo .deps/contig_analysis.Po mv -f .deps/parameters.Tpo .deps/parameters.Po mv -f .deps/contig.Tpo .deps/contig.Po make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src/mira' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0/src' make: *** [all-recursive] Error 1 emake failed * ERROR: sci-biology/mira-3.2.0 failed (compile phase): * died running emake, base_src_make * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 2954: Called base_src_compile * environment, line 534: Called base_src_make * environment, line 572: Called die * The specific snippet of code: * emake "$@" || die "died running emake, $FUNCNAME"; * * If you need support, post the output of 'emerge --info =sci-biology/mira-3.2.0', * the complete build log and the output of 'emerge -pqv =sci-biology/mira-3.2.0'. * The complete build log is located at '/var/log/portage/build/sci-biology/mira-3.2.0:20110426-024658.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mira-3.2.0/temp/environment'. * S: '/var/tmp/portage/sci-biology/mira-3.2.0/work/mira-3.2.0'