Attachment 437530 Details for Bug 585942 – sci-biology:mira-4.0.2:20160614-151330.log

sci-biology:mira-4.0.2:20160614-151330.log

sci-biology:mira-4.0.2:20160614-151330.log (text/plain), 56.56 KB, created by Toralf Förster on 2016-06-14 15:32:11 UTC

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Creator: Toralf Förster

Created: 2016-06-14 15:32:11 UTC

Size: 56.56 KB

patch

obsolete

> * Package:    sci-biology/mira-4.0.2
> * Repository: gentoo
> * Maintainer: sci-biology@gentoo.org
> * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
> * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>>> Unpacking source...
>>>> Unpacking mira-4.0.2.tar.bz2 to /var/tmp/portage/sci-biology/mira-4.0.2/work
>>>> Unpacking mira_3rdparty_06-07-2012.tar.bz2 to /var/tmp/portage/sci-biology/mira-4.0.2/work
>>>> Source unpacked in /var/tmp/portage/sci-biology/mira-4.0.2/work
>>>> Preparing source in /var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2 ...
> * Applying mira-3.4.0.2-boost-1.50.patch ...
> [ ok ]
> * Applying mira-4.0.2-cout.patch ...
> [ ok ]
> * Running eautoreconf in '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2' ...
> * Running libtoolize --install --copy --force --automake ...
> [ ok ]
> * Running aclocal -I m4 ...
> [ ok ]
> * Running autoconf --force ...
> [ ok ]
> * Running automake --add-missing --copy --force-missing ...
> [ ok ]
> * Running elibtoolize in: mira-4.0.2/
> *   Applying portage/1.2.0 patch ...
> *   Applying sed/1.5.6 patch ...
> *   Applying as-needed/2.4.3 patch ...
>>>> Source prepared.
>>>> Configuring source in /var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2 ...
> * econf: updating mira-4.0.2/config.sub with /usr/share/gnuconfig/config.sub
> * econf: updating mira-4.0.2/config.guess with /usr/share/gnuconfig/config.guess
>./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --with-boost=/usr/lib64 --with-boost-libdir=/usr/lib64 --with-boost-thread=boost_thread-mt
>configure: loading site script /usr/share/config.site
>checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/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 whether make supports nested variables... yes
>checking whether UID '250' is supported by ustar format... yes
>checking whether GID '250' is supported by ustar format... yes
>checking how to create a ustar tar archive... gnutar
>checking whether to add --prefix as include path... yes
>
>+++++++++++++++++++++++++++++++++++++
>systemuname: Linux
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include
>CXXFLAGS now: -march=native -O2 -pipe  -I/usr/include
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
>+++++++++++++++++++++++++++++++++++++
>checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
>checking whether the C compiler works... yes
>checking for C compiler default output file name... a.out
>checking for suffix of executables... 
>checking whether we are cross compiling... no
>checking for suffix of object files... o
>checking whether we are using the GNU C compiler... yes
>checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
>checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
>checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
>checking for style of include used by make... GNU
>checking dependency style of x86_64-pc-linux-gnu-gcc... none
>checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
>checking whether we are using the GNU C++ compiler... yes
>checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
>checking dependency style of x86_64-pc-linux-gnu-g++... none
>
>+++++++++++++++++++++++++++++++++++++
>systemuname: Linux
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include
>CXXFLAGS now: -march=native -O2 -pipe  -I/usr/include
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
>+++++++++++++++++++++++++++++++++++++
>checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
>checking for grep that handles long lines and -e... /bin/grep
>checking for egrep... /bin/grep -E
>checking for ANSI C header files... yes
>checking for sys/types.h... yes
>checking for sys/stat.h... yes
>checking for stdlib.h... yes
>checking for string.h... yes
>checking for memory.h... yes
>checking for strings.h... yes
>checking for inttypes.h... yes
>checking for stdint.h... yes
>checking for unistd.h... yes
>checking for int64_t... yes
>
>+++++++++++++++++++++++++++++++++++++
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
>+++++++++++++++++++++++++++++++++++++
>checking whether long has 64bit... yes
>checking whether enabling 64bit compilation support... yes
>checking build system type... x86_64-pc-linux-gnu
>checking for compiler optimisation settings...  
>
>+++++++++++++++++++++++++++++++++++++
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include  
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include  
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
>+++++++++++++++++++++++++++++++++++++
>checking host system type... x86_64-pc-linux-gnu
>checking how to print strings... printf
>checking for a sed that does not truncate output... /bin/sed
>checking for fgrep... /bin/grep -F
>checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
>checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
>checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B
>checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm
>checking whether ln -s works... yes
>checking the maximum length of command line arguments... 1572864
>checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
>checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
>checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
>checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
>checking how to recognize dependent libraries... pass_all
>checking for x86_64-pc-linux-gnu-dlltool... no
>checking for dlltool... no
>checking how to associate runtime and link libraries... printf %s\n
>checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
>checking for archiver @FILE support... @
>checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
>checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
>checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok
>checking for sysroot... no
>checking for a working dd... /bin/dd
>checking how to truncate binary pipes... /bin/dd bs=4096 count=1
>checking for x86_64-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 x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
>checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
>checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
>checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes
>checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
>checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
>checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking whether -lc should be explicitly linked in... no
>checking dynamic linker characteristics... GNU/Linux ld.so
>checking how to hardcode library paths into programs... immediate
>checking whether stripping libraries is possible... yes
>checking if libtool supports shared libraries... yes
>checking whether to build shared libraries... yes
>checking whether to build static libraries... yes
>checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
>checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
>checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
>checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
>checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
>checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
>checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
>checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
>checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking dynamic linker characteristics... (cached) GNU/Linux ld.so
>checking how to hardcode library paths into programs... immediate
>checking whether make sets $(MAKE)... (cached) yes
>checking whether ln -s works... yes
>checking for a sed that does not truncate output... (cached) /bin/sed
>checking for flex... yes
>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 xxd... yes
>checking for ANSI C header files... (cached) yes
>checking for stdbool.h that conforms to C99... yes
>checking for _Bool... yes
>checking for an ANSI C-conforming const... yes
>checking for inline... inline
>checking for C/C++ restrict keyword... __restrict
>checking whether struct tm is in sys/time.h or time.h... time.h
>checking for stdlib.h... (cached) yes
>checking for GNU libc compatible malloc... yes
>checking for stdlib.h... (cached) yes
>checking for GNU libc compatible realloc... yes
>checking whether lstat correctly handles trailing slash... yes
>checking whether stat accepts an empty string... no
>checking for strftime... yes
>checking for floor... no
>checking for memset... yes
>checking for pow... no
>checking for sqrt... no
>checking for special C compiler options needed for large files... no
>checking for _FILE_OFFSET_BITS value needed for large files... no
>checking for _LARGEFILE_SOURCE value needed for large files... no
>checking for isblank... yes
>
>+++++++++++++++++++++++++++++++++++++
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include  
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include  
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
>+++++++++++++++++++++++++++++++++++++
>checking whether the compiler implements namespaces... yes
>checking whether the compiler supports ISO C++ standard library... yes
>checking whether the compiler supports Standard Template Library... yes
>checking for boostlib >= 1.46.0... yes
>
>+++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS:    -I/usr/lib64/include
> BOOST LDFLAGS:     -L/usr/lib64
> ac_boost_path:     /usr/lib64
> ac_boost_lib_path: /usr/lib64
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include  
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include  
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
>+++++++++++++++++++++++++++++++++++++
>
>+++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS:    -I/usr/lib64/include
> BOOST LDFLAGS:     -L/usr/lib64
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include   -Wl,-rpath,/usr/lib64
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include  
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
>+++++++++++++++++++++++++++++++++++++
>checking whether the Boost::Thread library is available... yes
>checking for exit in -lboost_thread-mt... yes
>
>+++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS:    -pthread -I/usr/lib64/include
> BOOST LDFLAGS:     -L/usr/lib64
> ac_boost_path:     /usr/lib64
> ac_boost_lib_path: /usr/lib64
> BOOST_THREAD_LIB:  -lboost_thread-mt
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include   -Wl,-rpath,/usr/lib64
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include  
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
>+++++++++++++++++++++++++++++++++++++
>+++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS:    -pthread -I/usr/lib64/include
> BOOST LDFLAGS:     -L/usr/lib64
> ac_boost_path:     /usr/lib64
> ac_boost_lib_path: /usr/lib64
> BOOST_THREAD_LIB:  -lboost_thread-mt
>
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include   -Wl,-rpath,/usr/lib64
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64
>LIBS now:  -lboost_thread-mt
>+++++++++++++++++++++++++++++++++++++
>checking whether the Boost::Regex library is available... yes
>checking for exit in -lboost_regex-mt... yes
>+++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS:    -pthread -I/usr/lib64/include
> BOOST LDFLAGS:     -L/usr/lib64
> ac_boost_path:     /usr/lib64
> ac_boost_lib_path: /usr/lib64
> BOOST_REGEX_LIB:   -lboost_regex-mt -lboost_system
>
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include   -Wl,-rpath,/usr/lib64
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include
>LIBS now:  -lboost_thread-mt -lboost_regex-mt -lboost_system
>+++++++++++++++++++++++++++++++++++++
>checking whether the Boost::System library is available... yes
>checking for exit in -lboost_system-mt... yes
>+++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS:    -pthread -I/usr/lib64/include
> BOOST LDFLAGS:     -L/usr/lib64
> ac_boost_path:     /usr/lib64
> ac_boost_lib_path: /usr/lib64
> BOOST_SYSTEM_LIB:   -lboost_system-mt
>
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include   -Wl,-rpath,/usr/lib64
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include
>LIBS now:  -lboost_thread-mt -lboost_regex-mt -lboost_system -lboost_system-mt
>+++++++++++++++++++++++++++++++++++++
>checking whether the Boost::Filesystem library is available... yes
>checking for exit in -lboost_filesystem-mt... yes
>+++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS:    -pthread -I/usr/lib64/include
> BOOST LDFLAGS:     -L/usr/lib64
> ac_boost_path:     /usr/lib64
> ac_boost_lib_path: /usr/lib64
> BOOST_FILESYSTEM_LIB:   -lboost_filesystem-mt
>
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include   -Wl,-rpath,/usr/lib64
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include
>LIBS now:  -lboost_thread-mt -lboost_regex-mt -lboost_system -lboost_system-mt -lboost_filesystem-mt
>+++++++++++++++++++++++++++++++++++++
>checking whether the Boost::IOStreams library is available... yes
>checking for exit in -lboost_iostreams-mt... yes
>+++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS:    -pthread -I/usr/lib64/include
> BOOST LDFLAGS:     -L/usr/lib64
> ac_boost_path:     /usr/lib64
> ac_boost_lib_path: /usr/lib64
> BOOST_IOSTREAMS_LIB:   -lboost_iostreams-mt
>
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include   -Wl,-rpath,/usr/lib64
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include
>LIBS now:  -lboost_thread-mt -lboost_regex-mt -lboost_system -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt
>+++++++++++++++++++++++++++++++++++++
>checking for clock_gettime in -lrt... yes
>+++++++++++++++++++++++++++++++++++++
>Need to specifically use rt library
>LIBS now:  -lboost_thread-mt -lboost_regex-mt -lboost_system -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lrt
>+++++++++++++++++++++++++++++++++++++
>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: -march=native -O2 -pipe  -I/usr/include   -I/usr/include
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64 -L/usr/lib
>LIBS now:  -lboost_thread-mt -lboost_regex-mt -lboost_system -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lrt -lexpat
>+++++++++++++++++++++++++++++++++++++
>checking if zlib is wanted... yes
>
>+++++++++++++++++++++++++++++++++++++
>CFLAGS now: -march=native -O2 -pipe  -I/usr/include   -I/usr/include
>CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include
>LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64 -L/usr/lib
>LIBS now:  -lboost_thread-mt -lboost_regex-mt -lboost_system -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lrt -lexpat -lm -lz -lbz2
>+++++++++++++++++++++++++++++++++++++
>checking for flex version compatible with MIRA... yes
>checking for purify... no
>checking whether linking with tcmalloc works... yes
>checking whether mira should compile in public quiet mode... yes
>checking whether mira should compile 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
>checking that generated files are newer than configure... done
>configure: creating ./config.status
>config.status: creating Makefile
>config.status: creating src/Makefile
>config.status: creating src/stdinc/Makefile
>config.status: creating src/debuggersupport/Makefile
>config.status: creating src/memorc/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/caf/Makefile
>config.status: creating src/support/Makefile
>config.status: creating src/scripts/Makefile
>config.status: creating src/modules/Makefile
>config.status: creating src/progs/Makefile
>config.status: creating doc/Makefile
>config.status: creating doc/docbook/Makefile
>config.status: creating distribution/Makefile
>config.status: executing depfiles commands
>config.status: executing libtool commands
>
>--------------------------------------------------------------------------------
>                       Summary of MIRA configuration
>--------------------------------------------------------------------------------
>
>Building version ................................. 4.0.2_linux-gnu_x86_64_dynamic
>
>We are building on ............................... Linux
>CPU supports 64 bit? ............................. yes
>Compiler ......................................... x86_64-pc-linux-gnu-gcc
>Compiler optimisation flags used ................. 
>Do we compile in 64 bit? ......................... yes
>Building completely static? ...................... no
>BOOST expected to compile and link? .............. yes
>Linking with TCmalloc library? ................... yes
>
>Can MIRA be built on this system? ................ yes
>
>Using CFLAGS   : -march=native -O2 -pipe  -I/usr/include   -I/usr/include -Werror=uninitialized -Werror=return-type 
>Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value
>Using LDFLAGS  : -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64 -L/usr/lib
>Using LIBS     :  -lboost_thread-mt -lboost_regex-mt -lboost_system -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lrt -lexpat -lm -lz -lbz2 -ltcmalloc_minimal
>
>Looks good, we do not expect compilation problems.
>--------------------------------------------------------------------------------
>
>Type 'make' to make the binaries
>and then 'make install' to install them.
>>>> Source configured.
>>>> Compiling source in /var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2 ...
>make -j1 
>make  all-recursive
>make[1]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2'
>Making all in src
>make[2]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src'
>make  all-recursive
>make[3]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src'
>Making all in debuggersupport
>make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/debuggersupport'
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o dbgsupport.o dbgsupport.C
>rm -f libmiradebuggersupport.a
>x86_64-pc-linux-gnu-ar cru libmiradebuggersupport.a dbgsupport.o 
>x86_64-pc-linux-gnu-ranlib libmiradebuggersupport.a
>make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/debuggersupport'
>Making all in io
>make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/io'
>Making .H out of .xxd mira_ft_set.xxd.H
>Making .H out of .xxd gap4_ft_so_map.xxd.H
>Reducing so.obo for smaller so.obo.xxd
>Making .H out of .xxd so.obo.xxd.H
>Making .H out of .xxd so2xgap4map.xxd.H
>Making .H out of .xxd oldso2so.xxd.H
>make  all-am
>make[5]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/io'
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o annotationmappings.o annotationmappings.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o exp.o exp.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o generalio.o generalio.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o fasta.o fasta.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o fastq-mira.o fastq-mira.C
>In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
>                 from /usr/include/boost/iostreams/detail/resolve.hpp:26,
>                 from /usr/include/boost/iostreams/detail/push.hpp:24,
>                 from /usr/include/boost/iostreams/filtering_stream.hpp:19,
>                 from ../../src/io/fastq-mira.H:31,
>                 from fastq-mira.C:26:
>/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
> # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
>                                                                               ^
>In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
>                 from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
>                 from /usr/include/boost/iostreams/detail/resolve.hpp:26,
>                 from /usr/include/boost/iostreams/detail/push.hpp:24,
>                 from /usr/include/boost/iostreams/filtering_stream.hpp:19,
>                 from ../../src/io/fastq-mira.H:31,
>                 from fastq-mira.C:26:
>/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
> gma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
>                                                                               ^
>In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
>                 from /usr/include/boost/iostreams/detail/resolve.hpp:26,
>                 from /usr/include/boost/iostreams/detail/push.hpp:24,
>                 from /usr/include/boost/iostreams/filtering_stream.hpp:19,
>                 from ../../src/io/fastq-mira.H:31,
>                 from fastq-mira.C:26:
>/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
> gma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
>                                                                               ^
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o phd.o phd.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o scf.o scf.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o ncbiinfoxml.o ncbiinfoxml.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o exp_flexer.o exp_flexer.cc
>rm -f libmirafio.a
>x86_64-pc-linux-gnu-ar cru libmirafio.a annotationmappings.o exp.o generalio.o fasta.o fastq-mira.o phd.o scf.o ncbiinfoxml.o exp_flexer.o  
>x86_64-pc-linux-gnu-ranlib libmirafio.a
>make[5]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/io'
>make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/io'
>Making all in stdinc
>make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/stdinc'
>make[4]: Nothing to be done for 'all'.
>make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/stdinc'
>Making all in errorhandling
>make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/errorhandling'
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o errorhandling.o errorhandling.C
>rm -f libmiraerrorhandling.a
>x86_64-pc-linux-gnu-ar cru libmiraerrorhandling.a errorhandling.o 
>x86_64-pc-linux-gnu-ranlib libmiraerrorhandling.a
>make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/errorhandling'
>Making all in util
>make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/util'
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o machineinfo.o machineinfo.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o fileanddisk.o fileanddisk.C
>fileanddisk.C:691:0: warning: "CEBUG" redefined
> #define CEBUG(bla)   {cout << bla; cout.flush(); }
> ^
>fileanddisk.C:47:0: note: this is the location of the previous definition
> #define CEBUG(bla)
> ^
>fileanddisk.C:796:0: warning: "CEBUG" redefined
> #define CEBUG(bla)
> ^
>fileanddisk.C:691:0: note: this is the location of the previous definition
> #define CEBUG(bla)   {cout << bla; cout.flush(); }
> ^
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o misc.o misc.C
>rm -f libmirautil.a
>x86_64-pc-linux-gnu-ar cru libmirautil.a machineinfo.o fileanddisk.o misc.o 
>x86_64-pc-linux-gnu-ranlib libmirautil.a
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o dptools.o dptools.C
>rm -f libmiradptools.a
>x86_64-pc-linux-gnu-ar cru libmiradptools.a dptools.o 
>x86_64-pc-linux-gnu-ranlib libmiradptools.a
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o fmttext.o fmttext.C
>rm -f libmirafmttext.a
>x86_64-pc-linux-gnu-ar cru libmirafmttext.a fmttext.o 
>x86_64-pc-linux-gnu-ranlib libmirafmttext.a
>make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/util'
>Making all in mira
>make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/mira'
>Making .H out of .xxd adaptorsforclip.454.xxd.H
>Making .H out of .xxd adaptorsforclip.solexa.xxd.H
>Making .H out of .xxd adaptorsforclip.iontor.xxd.H
>Making .H out of .xxd adaptorsregex.solexa.xxd.H
>Making .H out of .xxd adaptorsregex.iontor.xxd.H
>Making .H out of .xxd seqforfilter_phix174.solexa.xxd.H
>make  all-am
>make[5]: Entering directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/mira'
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o estassembly.o estassembly.C
>rm -f libmiraestass.a
>x86_64-pc-linux-gnu-ar cru libmiraestass.a estassembly.o 
>x86_64-pc-linux-gnu-ranlib libmiraestass.a
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o assembly.o assembly.C
>assembly.C:2066:0: warning: "CEBUG" redefined
> #define CEBUG(bla)   {cout << bla; cout.flush(); }
> ^
>assembly.C:61:0: note: this is the location of the previous definition
> #define CEBUG(bla)
> ^
>assembly.C:3128:0: warning: "CEBUG" redefined
> #define CEBUG(bla)
> ^
>assembly.C:2066:0: note: this is the location of the previous definition
> #define CEBUG(bla)   {cout << bla; cout.flush(); }
> ^
>assembly.C:3172:0: warning: "CEBUG" redefined
> #define CEBUG(bla)   {cout << bla; cout.flush(); }
> ^
>assembly.C:3128:0: note: this is the location of the previous definition
> #define CEBUG(bla)
> ^
>assembly.C:3326:0: warning: "CEBUG" redefined
> #define CEBUG(bla)
> ^
>assembly.C:3172:0: note: this is the location of the previous definition
> #define CEBUG(bla)   {cout << bla; cout.flush(); }
> ^
>assembly.C:3337:0: warning: "CEBUG" redefined
> #define CEBUG(bla)   {cout << bla; cout.flush(); }
> ^
>assembly.C:3326:0: note: this is the location of the previous definition
> #define CEBUG(bla)
> ^
>assembly.C:3439:0: warning: "CEBUG" redefined
> #define CEBUG(bla)
> ^
>assembly.C:3337:0: note: this is the location of the previous definition
> #define CEBUG(bla)   {cout << bla; cout.flush(); }
> ^
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o contig.o contig.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o read.o read.C
>read.C: In member function âvoid Read::dumpAsReadname(std::ostream&)â:
>read.C:914:33: warning: format â%xâ expects argument of type âunsigned intâ, but argument 3 has type âRead*â [-Wformat=]
>       sprintf(buffer, "%x", this) ;
>                                 ^
>read.C: In member function âvoid Read::dumpAsFASTA(std::ostream&, bool, bool, bool)â:
>read.C:945:33: warning: format â%xâ expects argument of type âunsigned intâ, but argument 3 has type âRead*â [-Wformat=]
>       sprintf(buffer, "%x", this) ;
>                                 ^
>read.C: In member function âvoid Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)â:
>read.C:1027:33: warning: format â%xâ expects argument of type âunsigned intâ, but argument 3 has type âRead*â [-Wformat=]
>       sprintf(buffer, "%x", this) ;
>                                 ^
>read.C: In member function âvoid Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)â:
>read.C:1121:33: warning: format â%xâ expects argument of type âunsigned intâ, but argument 3 has type âRead*â [-Wformat=]
>       sprintf(buffer, "%x", this) ;
>                                 ^
>read.C: In member function âvoid Read::dumpAsCAF(std::ostream&)â:
>read.C:1193:33: warning: format â%xâ expects argument of type âunsigned intâ, but argument 3 has type âRead*â [-Wformat=]
>       sprintf(buffer, "%x", this) ;
>                                 ^
>read.C: In member function âvoid Read::dumpAsMAF(std::ostream&)â:
>read.C:1611:33: warning: format â%xâ expects argument of type âunsigned intâ, but argument 3 has type âRead*â [-Wformat=]
>       sprintf(buffer, "%x", this) ;
>                                 ^
>read.C: In member function âvoid Read::performHardTrim()â:
>read.C:6344:26: warning: ISO C++ forbids converting a string constant to âchar*â [-Wwrite-strings]
>     static char * nseq = "N";
>                          ^
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o contig_analysis.o contig_analysis.C
>x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o ads.o ads.C
>ads.C: In static member function âstatic bool AlignedDualSeq::staticInitialiser()â:
>ads.C:76:58: error: âpowâ was not declared in this scope
>     ADS_powofstarcounter[i]=pow(.9,static_cast<double>(i));
>                                                          ^
>make[5]: *** [Makefile:620: ads.o] Error 1
>make[5]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/mira'
>make[4]: *** [Makefile:517: all] Error 2
>make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src/mira'
>make[3]: *** [Makefile:404: all-recursive] Error 1
>make[3]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src'
>make[2]: *** [Makefile:358: all] Error 2
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/src'
>make[1]: *** [Makefile:416: all-recursive] Error 1
>make[1]: Leaving directory '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2'
>make: *** [Makefile:363: all] Error 2
> * ERROR: sci-biology/mira-4.0.2::gentoo failed (compile phase):
> *   emake failed
> * 
> * If you need support, post the output of `emerge --info '=sci-biology/mira-4.0.2::gentoo'`,
> * the complete build log and the output of `emerge -pqv '=sci-biology/mira-4.0.2::gentoo'`.
> * The complete build log is located at '/var/log/portage/sci-biology:mira-4.0.2:20160614-151330.log'.
> * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/mira-4.0.2/temp/build.log'.
> * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mira-4.0.2/temp/environment'.
> * Working directory: '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2'
> * S: '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2'

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Attachments on bug 585942: 437526 | 437528 | 437530