Build log

amos-2.0.8:20090728-221757.log (text/plain), 22.30 KB, created by Diego Elio Pettenò (RETIRED) on 2009-07-29 10:46:48 UTC

>>> Unpacking source...
>>> Unpacking amos-2.0.8.tar.gz to /var/tmp/portage/sci-biology/amos-2.0.8/work
>>> Source unpacked in /var/tmp/portage/sci-biology/amos-2.0.8/work
>>> Compiling source in /var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8 ...
 * econf: updating amos-2.0.8/config/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating amos-2.0.8/config/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
configure: loading site script /usr/share/config.site
configure: loading site script /usr/share/crossdev/include/site/linux
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether i686-pc-linux-gnu-g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of i686-pc-linux-gnu-g++... gcc3
checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc
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 ANSI C... none needed
checking dependency style of i686-pc-linux-gnu-gcc... gcc3
checking for gawk... (cached) gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib
checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E
checking for perl... /usr/bin/perl
checking for nucmer... /usr/bin/nucmer
checking for delta-filter... /usr/bin/delta-filter
checking for show-coords... /usr/bin/show-coords
checking for pow in -lm... yes
checking for fopen in -lc... yes
checking for main in -lz... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... 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 fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (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 pid_t... yes
checking for size_t... yes
checking for mode_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking whether byte ordering is bigendian... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGE_FILES value needed for large files... no
checking whether bitfields are packed htol... no
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for Qt... yes
checking whether Qt works... no
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking for getopt_long_only... yes
checking for working strtod... yes
checking for isascii... yes
checking for strtol... yes
checking for unistd.h... (cached) yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking types of arguments for select... int,fd_set *,struct timeval *
checking for strftime... yes
checking for dup2... yes
checking for floor... yes
checking for localtime... yes
checking for lstat... yes
checking for memmove... yes
checking for memset... yes
checking for mkdir... yes
checking for pow... yes
checking for rmdir... yes
checking for sqrt... yes
checking for stat... yes
checking for strchr... yes
checking for strdup... yes
checking for strstr... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking whether to build AMOScmp... (cached) no
checking whether to build minimus... (cached) no
checking whether to build Simulator... (cached) no
checking whether to build all... (cached) yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating src/Makefile
config.status: creating src/GNU/Makefile
config.status: creating src/AMOS/Makefile
config.status: creating src/Bambus/Makefile
config.status: creating src/Bambus/Bundler/Makefile
config.status: creating src/Common/Makefile
config.status: creating src/Graph/Makefile
config.status: creating src/Slice/Makefile
config.status: creating src/CelMsg/Makefile
config.status: creating src/Message/Makefile
config.status: creating src/Bank/Makefile
config.status: creating src/Align/Makefile
config.status: creating src/Tigger/Makefile
config.status: creating src/Compare/Makefile
config.status: creating src/Casm/Makefile
config.status: creating src/CtgTrim/Makefile
config.status: creating src/Sim/Makefile
config.status: creating src/Validation/Makefile
config.status: creating src/Converters/Makefile
config.status: creating src/Utils/Makefile
config.status: creating src/PerlModules/Makefile
config.status: creating src/PythonModules/Makefile
config.status: creating src/Pipeline/Makefile
config.status: creating src/Staden/Makefile
config.status: creating src/Staden/read/Makefile
config.status: creating src/Staden/progs/Makefile
config.status: creating src/bankViewer/Makefile
config.status: creating src/Contig/Makefile
config.status: creating src/Foundation/Makefile
config.status: creating src/Persistant/Makefile
config.status: creating config.h
config.status: executing depfiles commands

-- AMOS Assembler 2.0.8 Configuration Results --
  C compiler:          i686-pc-linux-gnu-gcc -O2 -pipe
  C++ compiler:        i686-pc-linux-gnu-g++ -O2 -pipe
  GCC version:         i686-pc-linux-gnu-gcc (Gentoo 4.4.1 p1.0) 4.4.1
  Host System type:    i686-pc-linux-gnu
  Install prefix:      /usr
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email <[e-mail]> with questions and bug reports.

WARNING! Qt3 toolkit malfunctioning but is required to run AMOS GUIs
   try compiling GUIs manually or reinstall Qt3 toolkit to build GUIs
   see config.log for more information on what went wrong
make -j14 -j1 
make  all-recursive
make[1]: Entering directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8'
Making all in src
make[2]: Entering directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8/src'
Making all in GNU
make[3]: Entering directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8/src/GNU'
make  all-am
make[4]: Entering directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8/src/GNU'
if i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT gnu.o -MD -MP -MF ".deps/gnu.Tpo" -c -o gnu.o gnu.c; \
	then mv -f ".deps/gnu.Tpo" ".deps/gnu.Po"; else rm -f ".deps/gnu.Tpo"; exit 1; fi
rm -f libGNU.a
ar cru libGNU.a gnu.o 
i686-pc-linux-gnu-ranlib libGNU.a
make[4]: Leaving directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8/src/GNU'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8/src/GNU'
Making all in AMOS
make[3]: Entering directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8/src/AMOS'
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-BankStream_AMOS.o -MD -MP -MF ".deps/libAMOS_a-BankStream_AMOS.Tpo" -c -o libAMOS_a-BankStream_AMOS.o `test -f 'BankStream_AMOS.cc' || echo './'`BankStream_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-BankStream_AMOS.Tpo" ".deps/libAMOS_a-BankStream_AMOS.Po"; else rm -f ".deps/libAMOS_a-BankStream_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Bank_AMOS.hh:22,
                 from BankStream_AMOS.hh:13,
                 from BankStream_AMOS.cc:10:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-Bank_AMOS.o -MD -MP -MF ".deps/libAMOS_a-Bank_AMOS.Tpo" -c -o libAMOS_a-Bank_AMOS.o `test -f 'Bank_AMOS.cc' || echo './'`Bank_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-Bank_AMOS.Tpo" ".deps/libAMOS_a-Bank_AMOS.Po"; else rm -f ".deps/libAMOS_a-Bank_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Bank_AMOS.hh:22,
                 from Bank_AMOS.cc:10:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-ContigEdge_AMOS.o -MD -MP -MF ".deps/libAMOS_a-ContigEdge_AMOS.Tpo" -c -o libAMOS_a-ContigEdge_AMOS.o `test -f 'ContigEdge_AMOS.cc' || echo './'`ContigEdge_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-ContigEdge_AMOS.Tpo" ".deps/libAMOS_a-ContigEdge_AMOS.Po"; else rm -f ".deps/libAMOS_a-ContigEdge_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Message_AMOS.hh:14,
                 from Universal_AMOS.hh:13,
                 from Link_AMOS.hh:13,
                 from Edge_AMOS.hh:13,
                 from ContigEdge_AMOS.hh:13,
                 from ContigEdge_AMOS.cc:10:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-ContigIterator_AMOS.o -MD -MP -MF ".deps/libAMOS_a-ContigIterator_AMOS.Tpo" -c -o libAMOS_a-ContigIterator_AMOS.o `test -f 'ContigIterator_AMOS.cc' || echo './'`ContigIterator_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-ContigIterator_AMOS.Tpo" ".deps/libAMOS_a-ContigIterator_AMOS.Po"; else rm -f ".deps/libAMOS_a-ContigIterator_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Message_AMOS.hh:14,
                 from Universal_AMOS.hh:13,
                 from Sequence_AMOS.hh:13,
                 from Contig_AMOS.hh:13,
                 from ContigIterator_AMOS.hh:15,
                 from ContigIterator_AMOS.cc:3:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-ContigLink_AMOS.o -MD -MP -MF ".deps/libAMOS_a-ContigLink_AMOS.Tpo" -c -o libAMOS_a-ContigLink_AMOS.o `test -f 'ContigLink_AMOS.cc' || echo './'`ContigLink_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-ContigLink_AMOS.Tpo" ".deps/libAMOS_a-ContigLink_AMOS.Po"; else rm -f ".deps/libAMOS_a-ContigLink_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Message_AMOS.hh:14,
                 from Universal_AMOS.hh:13,
                 from Link_AMOS.hh:13,
                 from ContigLink_AMOS.hh:13,
                 from ContigLink_AMOS.cc:10:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-Contig_AMOS.o -MD -MP -MF ".deps/libAMOS_a-Contig_AMOS.Tpo" -c -o libAMOS_a-Contig_AMOS.o `test -f 'Contig_AMOS.cc' || echo './'`Contig_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-Contig_AMOS.Tpo" ".deps/libAMOS_a-Contig_AMOS.Po"; else rm -f ".deps/libAMOS_a-Contig_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Message_AMOS.hh:14,
                 from Universal_AMOS.hh:13,
                 from Sequence_AMOS.hh:13,
                 from Contig_AMOS.hh:13,
                 from Contig_AMOS.cc:11:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-Edge_AMOS.o -MD -MP -MF ".deps/libAMOS_a-Edge_AMOS.Tpo" -c -o libAMOS_a-Edge_AMOS.o `test -f 'Edge_AMOS.cc' || echo './'`Edge_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-Edge_AMOS.Tpo" ".deps/libAMOS_a-Edge_AMOS.Po"; else rm -f ".deps/libAMOS_a-Edge_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Message_AMOS.hh:14,
                 from Universal_AMOS.hh:13,
                 from Link_AMOS.hh:13,
                 from Edge_AMOS.hh:13,
                 from Edge_AMOS.cc:10:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-Feature_AMOS.o -MD -MP -MF ".deps/libAMOS_a-Feature_AMOS.Tpo" -c -o libAMOS_a-Feature_AMOS.o `test -f 'Feature_AMOS.cc' || echo './'`Feature_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-Feature_AMOS.Tpo" ".deps/libAMOS_a-Feature_AMOS.Po"; else rm -f ".deps/libAMOS_a-Feature_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Message_AMOS.hh:14,
                 from Universal_AMOS.hh:13,
                 from Feature_AMOS.hh:13,
                 from Feature_AMOS.cc:10:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-Fragment_AMOS.o -MD -MP -MF ".deps/libAMOS_a-Fragment_AMOS.Tpo" -c -o libAMOS_a-Fragment_AMOS.o `test -f 'Fragment_AMOS.cc' || echo './'`Fragment_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-Fragment_AMOS.Tpo" ".deps/libAMOS_a-Fragment_AMOS.Po"; else rm -f ".deps/libAMOS_a-Fragment_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Message_AMOS.hh:14,
                 from Universal_AMOS.hh:13,
                 from Fragment_AMOS.hh:13,
                 from Fragment_AMOS.cc:10:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-Group_AMOS.o -MD -MP -MF ".deps/libAMOS_a-Group_AMOS.Tpo" -c -o libAMOS_a-Group_AMOS.o `test -f 'Group_AMOS.cc' || echo './'`Group_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-Group_AMOS.Tpo" ".deps/libAMOS_a-Group_AMOS.Po"; else rm -f ".deps/libAMOS_a-Group_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Message_AMOS.hh:14,
                 from Universal_AMOS.hh:13,
                 from Group_AMOS.hh:13,
                 from Group_AMOS.cc:10:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../..     -O2 -pipe -MT libAMOS_a-IDMap_AMOS.o -MD -MP -MF ".deps/libAMOS_a-IDMap_AMOS.Tpo" -c -o libAMOS_a-IDMap_AMOS.o `test -f 'IDMap_AMOS.cc' || echo './'`IDMap_AMOS.cc; \
	then mv -f ".deps/libAMOS_a-IDMap_AMOS.Tpo" ".deps/libAMOS_a-IDMap_AMOS.Po"; else rm -f ".deps/libAMOS_a-IDMap_AMOS.Tpo"; exit 1; fi
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ext/hash_map:59,
                 from utility_AMOS.hh:38,
                 from Message_AMOS.hh:14,
                 from IDMap_AMOS.hh:13,
                 from IDMap_AMOS.cc:10:
/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
IDMap_AMOS.cc: In member function 'void AMOS::IDMap_t::read(const std::string&)':
IDMap_AMOS.cc:504: error: 'fopen' was not declared in this scope
IDMap_AMOS.cc:509: error: 'fscanf' was not declared in this scope
IDMap_AMOS.cc:515: error: 'fscanf' was not declared in this scope
IDMap_AMOS.cc:517: error: 'getc' was not declared in this scope
IDMap_AMOS.cc:529: error: 'EOF' was not declared in this scope
IDMap_AMOS.cc:540: error: 'EOF' was not declared in this scope
IDMap_AMOS.cc:557: error: 'fclose' was not declared in this scope
make[3]: *** [libAMOS_a-IDMap_AMOS.o] Error 1
make[3]: Leaving directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8/src/AMOS'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/var/tmp/portage/sci-biology/amos-2.0.8/work/amos-2.0.8'
make: *** [all] Error 2
 [31;01m*[0m 
 [31;01m*[0m ERROR: sci-biology/amos-2.0.8 failed.
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line   49:  Called src_compile
 [31;01m*[0m             environment, line 2729:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       emake -j1 || die "emake failed"
 [31;01m*[0m  The die message:
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the topmost build error, and the call stack if relevant.
 [31;01m*[0m A complete build log is located at '/var/log/portage/sci-biology/amos-2.0.8:20090728-221757.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/amos-2.0.8/temp/environment'.
 [31;01m*[0m