Build log

mira-3.0.0:20100216-182326.log (text/plain), 14.38 KB, created by Diego Elio Pettenò (RETIRED) on 2010-02-17 13:59:16 UTC

 * CPV:  sci-biology/mira-3.0.0
 * REPO: gentoo
 * USE:  elibc_glibc kernel_linux test userland_GNU x86
>>> Unpacking source...
>>> Unpacking mira-3.0.0.tar.bz2 to /var/tmp/portage/sci-biology/mira-3.0.0/work
>>> Unpacking mira_3rdparty_31-01-2010.tar.bz2 to /var/tmp/portage/sci-biology/mira-3.0.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/mira-3.0.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/mira-3.0.0/work/mira-3.0.0 ...
 * Running eautoreconf in '/var/tmp/portage/sci-biology/mira-3.0.0/work/mira-3.0.0' ...
 * Running aclocal -I config/m4 ...
  [ ok ]
 * Running libtoolize --copy --force --install --automake ...
  [ ok ]
 * Running aclocal -I config/m4 ...
  [ ok ]
 * Running autoconf ...
  [ ok ]
 * Running automake --add-missing --copy ...
  [ ok ]
 * Running elibtoolize in: mira-3.0.0
 *   Applying portage-2.2.patch ...
 *   Applying sed-1.5.6.patch ...
 *   Applying as-needed-2.2.6.patch ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/mira-3.0.0/work/mira-3.0.0 ...
 * econf: updating mira-3.0.0/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating mira-3.0.0/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking build system type... i686-pc-linux-gnu
checking whether to add --prefix as include path... yes

+++++++++++++++++++++++++++++++++++++
systemuname: 
CFLAGS now: -O2 -pipe  -I/usr/include
CXXFLAGS now: -O2 -pipe  -I/usr/include
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether i686-pc-linux-gnu-gcc accepts -g... yes
checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of i686-pc-linux-gnu-gcc... gcc3
checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether i686-pc-linux-gnu-g++ accepts -g... yes
checking dependency style of i686-pc-linux-gnu-g++... gcc3

+++++++++++++++++++++++++++++++++++++
systemuname: Linux
CFLAGS now: -O2 -pipe  -I/usr/include
CXXFLAGS now: -O2 -pipe  -I/usr/include
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for int64_t... yes

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O2 -pipe  -I/usr/include
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking whether long long has 64bit... no
checking whether enabling 64bit compilation support... no
checking for compiler optimisation settings... -O2

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O2 -pipe  -I/usr/include -O2 
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include -O2 
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking host system type... i686-pc-linux-gnu
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by i686-pc-linux-gnu-gcc... /usr/i686-pc-linux-gnu/bin/ld
checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/i686-pc-linux-gnu/bin/ld option to reload object files... -r
checking for i686-pc-linux-gnu-objdump... i686-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar
checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-strip
checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib
checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether i686-pc-linux-gnu-g++ accepts -g... (cached) yes
checking dependency style of i686-pc-linux-gnu-g++... (cached) gcc3
checking how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E
checking for objdir... .libs
checking if i686-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for i686-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
checking if i686-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
checking if i686-pc-linux-gnu-gcc static flag -static works... yes
checking if i686-pc-linux-gnu-gcc supports -c -o file.o... yes
checking if i686-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
checking whether the i686-pc-linux-gnu-gcc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for ld used by i686-pc-linux-gnu-g++... /usr/i686-pc-linux-gnu/bin/ld
checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes
checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking for i686-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
checking if i686-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
checking if i686-pc-linux-gnu-g++ static flag -static works... yes
checking if i686-pc-linux-gnu-g++ supports -c -o file.o... yes
checking if i686-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... (cached) /bin/sed
checking for flex... no
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for flex... yes
checking for ANSI C header files... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for C/C++ restrict keyword... __restrict
checking whether struct tm is in sys/time.h or time.h... time.h
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking whether lstat correctly handles trailing slash... yes
checking whether stat accepts an empty string... no
checking for strftime... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for isblank... yes

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O2 -pipe  -I/usr/include -O2 
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include -O2 
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O2 -pipe  -I/usr/include -O2 
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include -O2 
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking whether the compiler implements namespaces... yes
checking whether the compiler supports ISO C++ standard library... yes
checking whether the compiler supports Standard Template Library... yes

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O2 -pipe  -I/usr/include -O2 
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include -O2 
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking for Expat XML Parser headers in /usr/include... found
checking for Expat XML Parser libraries... not found
checking for Expat XML Parser... no

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O2 -pipe  -I/usr/include -O2 
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include -O2 
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking for boostlib >= 1.35.0... yes

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib
CFLAGS now: -O2 -pipe  -I/usr/include -O2 
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include -O2 
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib
CFLAGS now: -O2 -pipe  -I/usr/include -O2 
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include -O2 
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread-1_35... yes

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -pthread -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib
 ac_boost_path:     
 ac_boost_lib_path: 
 BOOST_THREAD_LIB:  -lboost_thread-1_35
CFLAGS now: -O2 -pipe  -I/usr/include -O2 
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include -O2 
LDFLAGS now: -Wl,-O1 -L/usr/lib
+++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -pthread -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib
 ac_boost_path:     
 ac_boost_lib_path: 
 BOOST_THREAD_LIB:  -lboost_thread-1_35

CFLAGS now: -O2 -pipe  -I/usr/include -O2 
CXXFLAGS now: -DAJ_Linux64 -O2 -pipe  -I/usr/include -O2  -pthread -I/usr/include
LDFLAGS now: -Wl,-O1 -L/usr/lib -L/usr/lib -lboost_thread-1_35
+++++++++++++++++++++++++++++++++++++
checking for flex version compatible with MIRA... yes
checking for purify... no
checking whether mira should compile in public quiet mode... yes
checking whether mira should compile a development version... no
checking whether mira should compile with bound tracking... yes
checking whether mira should compile with bug tracking... yes
checking whether mira should compile with extended bug tracking... no
checking whether mira should compile with function trace... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/stdinc/Makefile
config.status: creating src/lec/Makefile
config.status: creating src/errorhandling/Makefile
config.status: creating src/util/Makefile
config.status: creating src/io/Makefile
config.status: creating src/mira/Makefile
config.status: creating src/EdIt/Makefile
config.status: creating src/caf/Makefile
config.status: creating src/examine/Makefile
config.status: creating src/knn_abi373/Makefile
config.status: creating src/knn_alf/Makefile
config.status: creating src/support/Makefile
config.status: creating src/scripts/Makefile
config.status: creating src/test/Makefile
config.status: creating src/test/io/Makefile
config.status: creating src/test/io/scf/Makefile
config.status: creating src/test/io/fasta/Makefile
config.status: creating src/test/io/generalio/Makefile
config.status: creating src/test/mira/Makefile
config.status: creating src/test/mira/align/Makefile
config.status: creating src/test/mira/read/Makefile
config.status: creating src/test/mira/readpool/Makefile
config.status: creating src/examples_programming/Makefile
config.status: creating src/progs/Makefile
config.status: creating doc/Makefile
config.status: creating distribution/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands

--------------------------------------------------------------------------------
                       Summary of MIRA configuration
--------------------------------------------------------------------------------


Could not find expat. Please install the Expat library.
Have a look at your distribution which should already have
 an already prepackaged version for you to install.
If not, have a look at http://sourceforge.net/projects/expat/

If you have expat installed at a non-standard location, please tell
 this to the configure script with the '--with-expat*' options.

Packages/programs needed for the compilation were not found.
Please install these first and then try again.

If you installed them, perhaps you forgot to give the configure script
options to tell where they are?


!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sci-biology/mira-3.0.0/work/mira-3.0.0/config.log
 * ERROR: sci-biology/mira-3.0.0 failed:
 *   econf failed
 * 
 * Call stack:
 *     ebuild.sh, line   54:  Called src_configure
 *   environment, line 3102:  Called base_src_configure
 *   environment, line  542:  Called econf
 *     ebuild.sh, line  544:  Called die
 * The specific snippet of code:
 *   			die "econf failed"
 * 
 * If you need support, post the output of 'emerge --info =sci-biology/mira-3.0.0',
 * the complete build log and the output of 'emerge -pqv =sci-biology/mira-3.0.0'.
Merge of sci-biology/mira-3.0.0 at 2010-02-16T18:23:26+00:00
failed
 * The complete build log is located at '/var/log/portage/build/sci-biology/mira-3.0.0:20100216-182326.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mira-3.0.0/temp/environment'.
 * S: '/var/tmp/portage/sci-biology/mira-3.0.0/work/mira-3.0.0'