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Gentoo's Bugzilla – Attachment 393686 Details for
Bug 536172
sci-biology/mira-3.9.18 - libtool: Version mismatch error. This is libtool 2.4.4, but the definition of this LT_INIT comes from libtool 2.4.2.
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emerge log
sci-biology:mira-3.9.18:20150110-070319.log (text/plain), 111.80 KB, created by
Toralf Förster
on 2015-01-11 12:48:24 UTC
(
hide
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Description:
emerge log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2015-01-11 12:48:24 UTC
Size:
111.80 KB
patch
obsolete
> * Package: sci-biology/mira-3.9.18 > * 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-3.9.18.tar.bz2 to /var/tmp/portage/sci-biology/mira-3.9.18/work >>>> Unpacking mira_3rdparty_06-07-2012.tar.bz2 to /var/tmp/portage/sci-biology/mira-3.9.18/work >>>> Source unpacked in /var/tmp/portage/sci-biology/mira-3.9.18/work >>>> Preparing source in /var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18 ... > * Applying mira-3.4.0.2-boost-1.50.patch ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18' ... > * Running libtoolize --install --copy --force --automake ... > [ ok ] > * Running aclocal -I config/m4 -I m4 ... > [ ok ] > * Running autoconf -I config/m4 ... > [ ok ] > * Running automake --add-missing --copy --force-missing ... > [ ok ] > * Running elibtoolize in: mira-3.9.18/ > * Applying portage/1.2.0 patch ... > * Applying sed/1.5.6 patch ... > * Applying target-nm/2.4.2 patch ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18 ... > * econf: updating mira-3.9.18/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating mira-3.9.18/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 >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 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: -O2 -pipe -I/usr/include >CXXFLAGS now: -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: -O2 -pipe -I/usr/include >CXXFLAGS now: -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: -O2 -pipe -I/usr/include >CXXFLAGS now: -DAJ_Linux64 -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: -O2 -pipe -I/usr/include >CXXFLAGS now: -DAJ_Linux64 -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 whether the shell understands some XSI constructs... yes >checking whether the shell understands "+="... yes >checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop >checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-dlltool... no >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok >checking for sysroot... no >checking for x86_64-pc-linux-gnu-mt... no >checking for mt... no >checking if : is a manifest tool... no >checking for dlfcn.h... yes >checking for objdir... .libs >checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking whether -lc should be explicitly linked in... no >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether stripping libraries is possible... yes >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... yes >checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E >checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (cached) GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether make sets $(MAKE)... (cached) yes >checking whether ln -s works... yes >checking for a sed that does not truncate output... (cached) /bin/sed >checking for flex... 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: -O2 -pipe -I/usr/include >CXXFLAGS now: -DAJ_Linux64 -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: -O2 -pipe -I/usr/include >CXXFLAGS now: -DAJ_Linux64 -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: -O2 -pipe -I/usr/include -Wl,-rpath,/usr/lib64 >CXXFLAGS now: -DAJ_Linux64 -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: -O2 -pipe -I/usr/include -Wl,-rpath,/usr/lib64 >CXXFLAGS now: -DAJ_Linux64 -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: -O2 -pipe -I/usr/include -Wl,-rpath,/usr/lib64 >CXXFLAGS now: -DAJ_Linux64 -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: -O2 -pipe -I/usr/include -Wl,-rpath,/usr/lib64 >CXXFLAGS now: -DAJ_Linux64 -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: -O2 -pipe -I/usr/include -Wl,-rpath,/usr/lib64 >CXXFLAGS now: -DAJ_Linux64 -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: -O2 -pipe -I/usr/include -Wl,-rpath,/usr/lib64 >CXXFLAGS now: -DAJ_Linux64 -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: -O2 -pipe -I/usr/include -Wl,-rpath,/usr/lib64 >CXXFLAGS now: -DAJ_Linux64 -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 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 -I/usr/include >CXXFLAGS now: -DAJ_Linux64 -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 -lexpat >+++++++++++++++++++++++++++++++++++++ >checking if zlib is wanted... yes > >+++++++++++++++++++++++++++++++++++++ >CFLAGS now: -O2 -pipe -I/usr/include -I/usr/include >CXXFLAGS now: -DAJ_Linux64 -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 -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/progs/Makefile >config.status: creating doc/Makefile >config.status: creating doc/docbook/Makefile >config.status: creating distribution/Makefile >config.status: executing depfiles commands >config.status: executing libtool commands > >-------------------------------------------------------------------------------- > Summary of MIRA configuration >-------------------------------------------------------------------------------- > >Building version ................................. 3.9.18_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 : -O2 -pipe -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type >Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -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 -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-3.9.18/work/mira-3.9.18 ... >make -j1 >make all-recursive >make[1]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18' >Making all in src >make[2]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src' >make all-recursive >make[3]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src' >Making all in debuggersupport >make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/debuggersupport' >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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-3.9.18/work/mira-3.9.18/src/debuggersupport' >Making all in io >make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/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-3.9.18/work/mira-3.9.18/src/io' >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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-3.9.18/work/mira-3.9.18/src/io' >make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/io' >Making all in stdinc >make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/stdinc' >make[4]: Nothing to be done for 'all'. >make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/stdinc' >Making all in errorhandling >make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/errorhandling' >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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-3.9.18/work/mira-3.9.18/src/errorhandling' >Making all in util >make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/util' >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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:624:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) {cout << bla; cout.flush(); } > ^ >fileanddisk.C:53:0: note: this is the location of the previous definition > #define CEBUG(bla) > ^ >fileanddisk.C:694:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >fileanddisk.C:624:0: 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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 >make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/util' >Making all in mira >make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/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-3.9.18/work/mira-3.9.18/src/mira' >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 preventinitfiasco.o preventinitfiasco.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 sam_collect.o sam_collect.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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:910:33: 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:941:33: 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:1023:33: 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:1117:33: 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:1189:33: 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:1601:33: 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:6306:26: warning: deprecated conversion from 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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 parameters.o parameters.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 pcrcontainer.o pcrcontainer.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 adsfacts.o adsfacts.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 align.o align.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_output.o assembly_output.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_info.o assembly_info.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_consensus.o contig_consensus.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_covanalysis.o contig_covanalysis.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_edit.o contig_edit.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_featureinfo.o contig_featureinfo.C >contig_featureinfo.C:502:0: warning: "CEBUGF2" redefined [enabled by default] > #define CEBUGF2 > ^ >contig_featureinfo.C:463:0: note: this is the location of the previous definition > #define CEBUGF2(bla) > ^ >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_pairconsistency.o contig_pairconsistency.C >contig_pairconsistency.C:282:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >contig_pairconsistency.C:33:0: note: this is the location of the previous definition > #define CEBUG(bla) {cout << bla; cout.flush();} > ^ >contig_pairconsistency.C:284:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) {cout << bla; cout.flush();} > ^ >contig_pairconsistency.C:282:0: note: this is the location of the previous definition > #define CEBUG(bla) > ^ >contig_pairconsistency.C:330:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >contig_pairconsistency.C:284:0: 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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_output.o contig_output.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 dynamic.o dynamic.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 gbf_parse.o gbf_parse.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src 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-DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 multitag.o multitag.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 readgrouplib.o readgrouplib.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 readpool.o readpool.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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:1930:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) {cout << bla; cout.flush(); } > ^ >assembly.C:86:0: note: this is the location of the previous definition > #define CEBUG(bla) > ^ >assembly.C:2944:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >assembly.C:1930:0: note: this is the location of the previous definition > #define CEBUG(bla) {cout << bla; cout.flush(); } > ^ >assembly.C:2988:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) {cout << bla; cout.flush(); } > ^ >assembly.C:2944:0: note: this is the location of the previous definition > #define CEBUG(bla) > ^ >assembly.C:3117:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >assembly.C:2988:0: note: this is the location of the previous definition > #define CEBUG(bla) {cout << bla; cout.flush(); } > ^ >assembly.C:3128:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) {cout << bla; cout.flush(); } > ^ >assembly.C:3117:0: note: this is the location of the previous definition > #define CEBUG(bla) > ^ >assembly.C:3229:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >assembly.C:3128:0: 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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 bloomfilter.o bloomfilter.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 ppathfinder.o ppathfinder.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 skim.o skim.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 hashstats.o hashstats.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_io.o assembly_io.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_reduceskimhits.o assembly_reduceskimhits.C >assembly_reduceskimhits.C:1098:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) {cout << bla; cout.flush();} > ^ >assembly_reduceskimhits.C:864:0: note: this is the location of the previous definition > #define CEBUG(bla) > ^ >assembly_reduceskimhits.C:1138:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >assembly_reduceskimhits.C:1098:0: note: this is the location of the previous definition > #define CEBUG(bla) {cout << bla; cout.flush();} > ^ >assembly_reduceskimhits.C:2732:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) {cout << bla; cout.flush();} > ^ >assembly_reduceskimhits.C:1138:0: note: this is the location of the previous definition > #define CEBUG(bla) > ^ >assembly_reduceskimhits.C:2772:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >assembly_reduceskimhits.C:2732:0: note: this is the location of the previous definition > #define CEBUG(bla) {cout << bla; cout.flush();} > ^ >assembly_reduceskimhits.C:2777:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) {cout << bla; cout.flush();} > ^ >assembly_reduceskimhits.C:2772:0: note: this is the location of the previous definition > #define CEBUG(bla) > ^ >assembly_reduceskimhits.C:2856:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >assembly_reduceskimhits.C:2777:0: 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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_swalign.o assembly_swalign.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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_misc.o assembly_misc.C >assembly_misc.C:1434:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) {cout << bla; cout.flush();} > ^ >assembly_misc.C:45:0: note: this is the location of the previous definition > #define CEBUG(bla) > ^ >assembly_misc.C:1468:0: warning: "CEBUG" redefined [enabled by default] > #define CEBUG(bla) > ^ >assembly_misc.C:1434:0: 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=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 dataprocessing.o dataprocessing.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 manifest.o manifest.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 scaffolder.o scaffolder.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 seqtohash.o seqtohash.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 skim_farc.o skim_farc.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 skim_lowbph.o skim_lowbph.C >rm -f libmira.a >x86_64-pc-linux-gnu-ar cru libmira.a preventinitfiasco.o sam_collect.o read.o parameters.o pcrcontainer.o ads.o adsfacts.o align.o assembly_output.o assembly_info.o contig_analysis.o contig_consensus.o contig_covanalysis.o contig_edit.o contig_featureinfo.o contig_pairconsistency.o contig_output.o dynamic.o gbf_parse.o gff_parse.o gff_save.o parameters_flexer.o maf_parse.o multitag.o readgrouplib.o contig.o readpool.o assembly.o bloomfilter.o ppathfinder.o skim.o hashstats.o assembly_io.o assembly_reduceskimhits.o assembly_swalign.o assembly_misc.o dataprocessing.o manifest.o scaffolder.o seqtohash.o skim_farc.o skim_lowbph.o >x86_64-pc-linux-gnu-ranlib libmira.a >make[5]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/mira' >make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/mira' >Making all in caf >make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/caf' >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 caf.o caf.C >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 caf_flexer.o caf_flexer.cc >rm -f libmiracaf.a >x86_64-pc-linux-gnu-ar cru libmiracaf.a caf.o caf_flexer.o >x86_64-pc-linux-gnu-ranlib libmiracaf.a >make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/caf' >Making all in memorc >make[4]: Entering directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/memorc' >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 memorc.o memorc.C >memorc.C: In static member function âstatic void MemORC::statistics()â: >memorc.C:156:61: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âuint64 {aka long unsigned int}â [-Wformat=] > printf("Current alloc counter : %llu\n", MOC_alloccounter); > ^ >memorc.C:157:64: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âuint64 {aka long unsigned int}â [-Wformat=] > printf("Total checks performed : %llu\n", MOC_checksperformed); > ^ >memorc.C:158:65: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âstd::map<void*, MemORC::memblockinfo_t>::size_type {aka long unsigned int}â [-Wformat=] > printf("Num. memory blocks : %llu\n", MOC_memblocks.size()); > ^ >memorc.C:159:65: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âstd::map<void*, MemORC::memblockinfo_t>::size_type {aka long unsigned int}â [-Wformat=] > printf("Num. active hot blocks : %llu\n", MOC_hotblocks.size()); > ^ >memorc.C:160:72: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âstd::vector<long unsigned int>::size_type {aka long unsigned int}â [-Wformat=] > printf("Num. pending hot blocks: %llu\n", MOC_hotaidsrequested.size()); > ^ >memorc.C:161:60: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("Total mem reqested : %llu\n", MOC_reqmemalloc); > ^ >memorc.C:162:90: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âsize_t {aka long unsigned int}â [-Wformat=] > tal mem allocated : %llu (including pads and fences)\n", MOC_totalmemalloc); > ^ >memorc.C: In static member function âstatic void* MemORC::newMemBlock(size_t)â: >memorc.C:228:116: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âsize_t {aka long unsigned int}â [-Wformat=] > allocate %llu byte.\nSorry, memory allocation failed. Bailing out.\n", totaln); > ^ >memorc.C: In static member function âstatic void MemORC::deleteMemBlock(void*)â: >memorc.C:314:112: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âuint64 {aka long unsigned int}â [-Wformat=] > d):\t",reinterpret_cast<uint64>(mbI->first)-reinterpret_cast<uint64>(usraddr)); > ^ >memorc.C:321:113: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âuint64 {aka long unsigned int}â [-Wformat=] > d):\t",reinterpret_cast<uint64>(usraddr)-reinterpret_cast<uint64>(mbI->first)); > ^ >memorc.C: In static member function âstatic bool MemORC::checkMemBlock(std::map<void*, MemORC::memblockinfo_t>::iterator)â: >memorc.C:433:134: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âlong unsigned intâ [-Wformat=] > \tExpected: %x\tGot: %x\n", i*sizeof(int32),MOC_clowfencemagic[0], *fencecptr); > ^ >memorc.C:436:136: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âlong unsigned intâ [-Wformat=] > Expected: %x\tGot: %x\n", i*sizeof(int32)+1,MOC_clowfencemagic[1], *fencecptr); > ^ >memorc.C:439:136: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âlong unsigned intâ [-Wformat=] > Expected: %x\tGot: %x\n", i*sizeof(int32)+2,MOC_clowfencemagic[2], *fencecptr); > ^ >memorc.C:442:136: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âlong unsigned intâ [-Wformat=] > Expected: %x\tGot: %x\n", i*sizeof(int32)+3,MOC_clowfencemagic[3], *fencecptr); > ^ >memorc.C:503:44: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("Size: %llu\n", mbI->second.size); > ^ >memorc.C:504:50: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âuint64 {aka long unsigned int}â [-Wformat=] > printf("AllocID: %llu\n", mbI->second.allocid); > ^ >memorc.C: In static member function âstatic void MemORC::printMemBlockInfo(std::map<void*, MemORC::memblockinfo_t>::iterator)â: >memorc.C:561:50: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 3 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%p\t%llu\t",mbI->first,mbI->second.size); > ^ >memorc.C:567:40: warning: format â%lluâ expects argument of type âlong long unsigned intâ, but argument 2 has type âuint64 {aka long unsigned int}â [-Wformat=] > printf("\t%llu\n",mbI->second.allocid); > ^ >rm -f libmemorc.a >x86_64-pc-linux-gnu-ar cru libmemorc.a memorc.o >x86_64-pc-linux-gnu-ranlib libmemorc.a >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.9.18\" -DPACKAGE_STRING=\"mira\ 3.9.18\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.9.18\" -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=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -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 main.o main.C >/bin/sh ../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPUBLICQUIET -DAJ_Linux64 -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 -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib64 -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64 -L/usr/lib -o main main.o -lmiraerrorhandling -lboost_thread-mt -lboost_regex-mt -lboost_system -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lexpat -lm -lz -lbz2 -ltcmalloc_minimal >libtool: Version mismatch error. This is libtool 2.4.4, but the >libtool: definition of this LT_INIT comes from libtool 2.4.2. >libtool: You should recreate aclocal.m4 with macros from libtool 2.4.4 >libtool: and run autoconf again. >Makefile:403: recipe for target 'main' failed >make[4]: *** [main] Error 63 >make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/memorc' >Makefile:404: recipe for target 'all-recursive' failed >make[3]: *** [all-recursive] Error 1 >make[3]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src' >Makefile:358: recipe for target 'all' failed >make[2]: *** [all] Error 2 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src' >Makefile:417: recipe for target 'all-recursive' failed >make[1]: *** [all-recursive] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18' >Makefile:364: recipe for target 'all' failed >make: *** [all] Error 2 > * ERROR: sci-biology/mira-3.9.18::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/mira-3.9.18::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/mira-3.9.18::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:mira-3.9.18:20150110-070319.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/mira-3.9.18/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mira-3.9.18/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18' > * S: '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18'
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