Attachment 271209 Details for Bug 364917 – Build log

Build log

mira-3.2.0:20110426-024658.log (text/plain), 66.81 KB, created by Diego Elio Pettenò (RETIRED) on 2011-04-26 12:11:28 UTC

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Creator: Diego Elio Pettenò (RETIRED)

Created: 2011-04-26 12:11:28 UTC

Size: 66.81 KB

patch

obsolete

> * 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 âRead::REA_bposhashstat_defaultâ [-fpermissive]
>../mira/read.H:158:10: note: âconst struct Read::bposhashstat_tâ 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'

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Attachments on bug 364917: 271209