sci-biology:mira-4.0.2:20150818-160123.log

sci-biology:mira-4.0.2:20150818-160123.log (text/plain), 12.44 KB, created by Toralf Förster on 2015-08-18 17:39:03 UTC

 * Package:    sci-biology/mira-4.0.2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking mira-4.0.2.tar.bz2 to /var/tmp/portage/sci-biology/mira-4.0.2/work
>>> Unpacking mira_3rdparty_06-07-2012.tar.bz2 to /var/tmp/portage/sci-biology/mira-4.0.2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/mira-4.0.2/work
>>> Preparing source in /var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2 ...
 * Applying mira-3.4.0.2-boost-1.50.patch ...
 [ ok ]
 * Applying mira-4.0.2-cout.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2' ...
 * Running libtoolize --install --copy --force --automake ...
 [ ok ]
 * Running aclocal -I m4 ...
 [ ok ]
 * Running autoconf --force ...
 [ ok ]
 * Running automake --add-missing --copy --force-missing ...
 [ ok ]
 * Running elibtoolize in: mira-4.0.2/
 *   Applying portage/1.2.0 patch ...
 *   Applying sed/1.5.6 patch ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2 ...
 * econf: updating mira-4.0.2/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating mira-4.0.2/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --with-boost=/usr/lib64 --with-boost-libdir=/usr/lib64 --with-boost-thread=boost_thread-mt
checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '250' is supported by ustar format... yes
checking whether GID '250' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether to add --prefix as include path... yes

+++++++++++++++++++++++++++++++++++++
systemuname: Linux
CFLAGS now: -march=native -O2 -pipe  -I/usr/include
CXXFLAGS now: -march=native -O2 -pipe  -I/usr/include
LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking dependency style of x86_64-pc-linux-gnu-g++... none

+++++++++++++++++++++++++++++++++++++
systemuname: Linux
CFLAGS now: -march=native -O2 -pipe  -I/usr/include
CXXFLAGS now: -march=native -O2 -pipe  -I/usr/include
LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for int64_t... yes

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -march=native -O2 -pipe  -I/usr/include
CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include
LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking whether long has 64bit... yes
checking whether enabling 64bit compilation support... yes
checking build system type... x86_64-pc-linux-gnu
checking for compiler optimisation settings...  

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -march=native -O2 -pipe  -I/usr/include  
CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include  
LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B
checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-pc-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
checking for archiver @FILE support... @
checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for x86_64-pc-linux-gnu-mt... no
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... (cached) /bin/sed
checking for flex... yes
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for flex... yes
checking for xxd... yes
checking for ANSI C header files... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for C/C++ restrict keyword... __restrict
checking whether struct tm is in sys/time.h or time.h... time.h
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking whether lstat correctly handles trailing slash... yes
checking whether stat accepts an empty string... no
checking for strftime... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for isblank... yes

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -march=native -O2 -pipe  -I/usr/include  
CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include  
LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking whether the compiler implements namespaces... yes
checking whether the compiler supports ISO C++ standard library... yes
checking whether the compiler supports Standard Template Library... yes
checking for boostlib >= 1.46.0... yes

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -I/usr/lib64/include
 BOOST LDFLAGS:     -L/usr/lib64
 ac_boost_path:     /usr/lib64
 ac_boost_lib_path: /usr/lib64
CFLAGS now: -march=native -O2 -pipe  -I/usr/include  
CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include  
LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
+++++++++++++++++++++++++++++++++++++

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -I/usr/lib64/include
 BOOST LDFLAGS:     -L/usr/lib64
CFLAGS now: -march=native -O2 -pipe  -I/usr/include   -Wl,-rpath,/usr/lib64
CXXFLAGS now: -DAJ_Linux64 -march=native -O2 -pipe  -I/usr/include  
LDFLAGS now: -Wl,-O1 -Wl,--as-needed -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread-mt... no
checking for exit in -lboost_thread-boost_thread-mt... no
configure: error: Could not link against boost_thread-boost_thread-mt !

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2/config.log
 * ERROR: sci-biology/mira-4.0.2::gentoo failed (configure phase):
 *   econf failed
 * 
 * Call stack:
 *               ebuild.sh, line   93:  Called src_configure
 *             environment, line 2662:  Called econf '--with-boost=/usr/lib64' '--with-boost-libdir=/usr/lib64' '--with-boost-thread=boost_thread-mt'
 *        phase-helpers.sh, line  662:  Called __helpers_die 'econf failed'
 *   isolated-functions.sh, line  117:  Called die
 * The specific snippet of code:
 *   		die "$@"
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/mira-4.0.2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/mira-4.0.2::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:mira-4.0.2:20150818-160123.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/mira-4.0.2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mira-4.0.2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2'
 * S: '/var/tmp/portage/sci-biology/mira-4.0.2/work/mira-4.0.2'