config.log

config.log (text/plain), 65.02 KB, created by Juergen Rose on 2015-05-06 20:16:46 UTC

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by EMBOSS configure 6.6.0, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0/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 --docdir=/usr/share/doc/emboss-6.6.0 --enable-shared --disable-static --with-x --with-pngdriver=/usr --with-hpdf=/usr --with-mysql=/usr/bin/mysql_config --with-postgresql=/usr/bin/pg_config --enable-large --without-java --enable-systemlibs

## --------- ##
## Platform. ##
## --------- ##

hostname = lynx
uname -m = x86_64
uname -r = 4.0.1-gentoo
uname -s = Linux
uname -v = #1 SMP Mon May 4 16:24:12 CEST 2015

/usr/bin/uname -p = Intel(R) Core(TM) i7-3630QM CPU @ 2.40GHz
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/lib/portage/python2.7/ebuild-helpers/xattr
PATH: /usr/lib/portage/python2.7/ebuild-helpers
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /opt/bin
PATH: /usr/x86_64-pc-linux-gnu/gcc-bin/4.9.2
PATH: /usr/x86_64-pc-linux-gnu/avr/gcc-bin/4.4.4
PATH: /opt/intel/composerxe-2015_update2.2.164/bin/intel64
PATH: /opt/intel/composerxe-2015_update2.2.164/mpirt/bin/intel64
PATH: /opt/intel/composerxe-2015_update2.2.164/bin/ia32
PATH: /opt/intel/composerxe-2015_update2.2.164/mpirt/bin/ia32
PATH: /opt/nvidia-cg-toolkit/bin
PATH: /usr/lib64/subversion/bin
PATH: /opt/eagle/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2487: loading site script /usr/share/config.site
| #!/bin/sh
| # Copyright 2009-2014 Gentoo Foundation
| # Distributed under the terms of the GNU General Public License v2
| 
| TOPDIR=/usr/share/crossdev/include/site
| 
| config_site_arch() {
| 	local host="${CHOST%%-*}"
| 
| 	case ${host} in
| 	arm*b*)  host=armeb ;;
| 	arm*)    host=arm ;;
| 	mips*l*) host=mipsel ;;
| 	mips*)   host=mips ;;
| 	esac
| 
| 	echo "${host}"
| }
| 
| config_site_names() {
| 	local site_arch="$(config_site_arch)"
| 	local sites=""
| 	local x
| 
| 	case ${CHOST} in
| 	*-linux-*)          sites="linux ${site_arch}-linux" ;;
| 	*-darwin*)          sites="darwin ${site_arch}-darwin" ;;
| 	esac
| 
| 	case ${CHOST} in
| 	*-linux-uclibc)     sites="linux-uclibc ${site_arch}-linux-uclibc" ;;
| 	*-linux-gnu)        sites="linux-gnu ${site_arch}-linux-gnu" ;;
| 	*-linux-uclibceabi) sites="linux-uclibceabi ${site_arch}-linux-uclibceabi" ;;
| 	*-linux-gnueabi)    sites="linux-gnueabi ${site_arch}-linux-gnueabi" ;;
| 	esac
| 
| 	for x in ${sites} ${CHOST}; do
| 		[ -e "${TOPDIR}/${x}" ] && echo "${TOPDIR}/${x}"
| 	done
| }
| 
| # Only kick in for cross-compiles so we don't break native builds #427184
| if [ "${CBUILD:-${CHOST}}" != "${CHOST}" ] ; then
| 	sites="$(config_site_names)"
| 	if [ -n "${sites}" ] ; then
| 		for site in ${sites}; do
| 			echo "${0##*/}: loading site script ${site}"
| 			. "${site}"
| 		done
| 	fi
| 	unset site sites
| fi
configure:2597: checking for gawk
configure:2613: found /usr/bin/gawk
configure:2624: result: gawk
configure:2645: checking for x86_64-pc-linux-gnu-icc
configure:2675: result: no
configure:2645: checking for x86_64-pc-linux-gnu-gcc
configure:2661: found /usr/bin/x86_64-pc-linux-gnu-gcc
configure:2672: result: x86_64-pc-linux-gnu-gcc
configure:2747: checking for C compiler version
configure:2756: x86_64-pc-linux-gnu-gcc --version >&5
x86_64-pc-linux-gnu-gcc (Gentoo 4.9.2 p1.2, pie-0.6.2) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2767: $? = 0
configure:2756: x86_64-pc-linux-gnu-gcc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.2/x86_64-pc-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.9.2/work/gcc-4.9.2/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.2 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.2 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.2/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.2/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.9.2/python --enable-languages=c,c++,java,objc,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.9.2 p1.2, pie-0.6.2' --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --enable-lto --without-cloog --enable-libsanitizer
Thread model: posix
gcc version 4.9.2 (Gentoo 4.9.2 p1.2, pie-0.6.2) 
configure:2767: $? = 0
configure:2756: x86_64-pc-linux-gnu-gcc -V >&5
x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-V'
x86_64-pc-linux-gnu-gcc: fatal error: no input files
compilation terminated.
configure:2767: $? = 1
configure:2756: x86_64-pc-linux-gnu-gcc -qversion >&5
x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-qversion'
x86_64-pc-linux-gnu-gcc: fatal error: no input files
compilation terminated.
configure:2767: $? = 1
configure:2787: checking whether the C compiler works
configure:2809: x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe   -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:2813: $? = 0
configure:2861: result: yes
configure:2864: checking for C compiler default output file name
configure:2866: result: a.out
configure:2872: checking for suffix of executables
configure:2879: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe   -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:2883: $? = 0
configure:2905: result: 
configure:2927: checking whether we are cross compiling
configure:2935: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe   -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:2939: $? = 0
configure:2946: ./conftest
configure:2950: $? = 0
configure:2965: result: no
configure:2970: checking for suffix of object files
configure:2992: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:2996: $? = 0
configure:3017: result: o
configure:3021: checking whether we are using the GNU C compiler
configure:3040: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:3040: $? = 0
configure:3049: result: yes
configure:3058: checking whether x86_64-pc-linux-gnu-gcc accepts -g
configure:3078: x86_64-pc-linux-gnu-gcc -c -g  conftest.c >&5
configure:3078: $? = 0
configure:3119: result: yes
configure:3136: checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89
configure:3199: x86_64-pc-linux-gnu-gcc  -c -march=native -O2 -pipe   conftest.c >&5
configure:3199: $? = 0
configure:3212: result: none needed
configure:3269: checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together
configure:3291: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o
configure:3294: $? = 0
configure:3291: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o
configure:3294: $? = 0
configure:3306: result: yes
configure:3337: checking for x86_64-pc-linux-gnu-icpc
configure:3367: result: no
configure:3337: checking for x86_64-pc-linux-gnu-g++
configure:3353: found /usr/bin/x86_64-pc-linux-gnu-g++
configure:3364: result: x86_64-pc-linux-gnu-g++
configure:3435: checking for C++ compiler version
configure:3444: x86_64-pc-linux-gnu-g++ --version >&5
x86_64-pc-linux-gnu-g++ (Gentoo 4.9.2 p1.2, pie-0.6.2) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:3455: $? = 0
configure:3444: x86_64-pc-linux-gnu-g++ -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.2/x86_64-pc-linux-gnu-g++
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.9.2/work/gcc-4.9.2/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.2 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.2 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.2/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.2/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.9.2/python --enable-languages=c,c++,java,objc,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.9.2 p1.2, pie-0.6.2' --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --enable-lto --without-cloog --enable-libsanitizer
Thread model: posix
gcc version 4.9.2 (Gentoo 4.9.2 p1.2, pie-0.6.2) 
configure:3455: $? = 0
configure:3444: x86_64-pc-linux-gnu-g++ -V >&5
x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-V'
x86_64-pc-linux-gnu-g++: fatal error: no input files
compilation terminated.
configure:3455: $? = 1
configure:3444: x86_64-pc-linux-gnu-g++ -qversion >&5
x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-qversion'
x86_64-pc-linux-gnu-g++: fatal error: no input files
compilation terminated.
configure:3455: $? = 1
configure:3459: checking whether we are using the GNU C++ compiler
configure:3478: x86_64-pc-linux-gnu-g++ -c -march=native -O2 -pipe  conftest.cpp >&5
configure:3478: $? = 0
configure:3487: result: yes
configure:3496: checking whether x86_64-pc-linux-gnu-g++ accepts -g
configure:3516: x86_64-pc-linux-gnu-g++ -c -g  conftest.cpp >&5
configure:3516: $? = 0
configure:3557: result: yes
configure:3585: checking how to run the C preprocessor
configure:3616: x86_64-pc-linux-gnu-gcc -E  conftest.c
configure:3616: $? = 0
configure:3630: x86_64-pc-linux-gnu-gcc -E  conftest.c
conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:3630: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3655: result: x86_64-pc-linux-gnu-gcc -E
configure:3675: x86_64-pc-linux-gnu-gcc -E  conftest.c
configure:3675: $? = 0
configure:3689: x86_64-pc-linux-gnu-gcc -E  conftest.c
conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:3689: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3731: checking for a BSD-compatible install
configure:3799: result: /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c
configure:3810: checking whether ln -s works
configure:3814: result: yes
configure:3821: checking whether make sets $(MAKE)
configure:3843: result: yes
configure:3852: checking for a thread-safe mkdir -p
configure:3891: result: /bin/mkdir -p
configure:3897: checking whether build environment is sane
configure:3952: result: yes
configure:4121: checking for style of include used by make
configure:4149: result: GNU
configure:4183: checking whether make supports nested variables
configure:4200: result: yes
configure:4285: checking dependency style of x86_64-pc-linux-gnu-gcc
configure:4396: result: none
configure:4413: checking dependency style of x86_64-pc-linux-gnu-g++
configure:4524: result: none
configure:4613: checking build system type
configure:4627: result: x86_64-pc-linux-gnu
configure:4647: checking host system type
configure:4660: result: x86_64-pc-linux-gnu
configure:4701: checking how to print strings
configure:4728: result: printf
configure:4749: checking for a sed that does not truncate output
configure:4813: result: /bin/sed
configure:4831: checking for grep that handles long lines and -e
configure:4889: result: /bin/grep
configure:4894: checking for egrep
configure:4956: result: /bin/grep -E
configure:4961: checking for fgrep
configure:5023: result: /bin/grep -F
configure:5058: checking for ld used by x86_64-pc-linux-gnu-gcc
configure:5125: result: /usr/x86_64-pc-linux-gnu/bin/ld
configure:5132: checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld
configure:5147: result: yes
configure:5159: checking for BSD- or MS-compatible name lister (nm)
configure:5213: result: /usr/bin/x86_64-pc-linux-gnu-nm -B
configure:5343: checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface
configure:5350: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:5353: /usr/bin/x86_64-pc-linux-gnu-nm -B "conftest.o"
configure:5356: output
0000000000000000 B some_variable
configure:5363: result: BSD nm
configure:5367: checking the maximum length of command line arguments
configure:5498: result: 1572864
configure:5546: checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format
configure:5586: result: func_convert_file_noop
configure:5593: checking how to convert x86_64-pc-linux-gnu file names to toolchain format
configure:5613: result: func_convert_file_noop
configure:5620: checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files
configure:5627: result: -r
configure:5661: checking for x86_64-pc-linux-gnu-objdump
configure:5677: found /usr/bin/x86_64-pc-linux-gnu-objdump
configure:5688: result: x86_64-pc-linux-gnu-objdump
configure:5760: checking how to recognize dependent libraries
configure:5960: result: pass_all
configure:6005: checking for x86_64-pc-linux-gnu-dlltool
configure:6035: result: no
configure:6045: checking for dlltool
configure:6075: result: no
configure:6105: checking how to associate runtime and link libraries
configure:6132: result: printf %s\n
configure:6149: checking for x86_64-pc-linux-gnu-ar
configure:6165: found /usr/bin/x86_64-pc-linux-gnu-ar
configure:6176: result: x86_64-pc-linux-gnu-ar
configure:6257: checking for archiver @FILE support
configure:6274: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:6274: $? = 0
configure:6277: x86_64-pc-linux-gnu-ar cru libconftest.a @conftest.lst >&5
configure:6280: $? = 0
configure:6285: x86_64-pc-linux-gnu-ar cru libconftest.a @conftest.lst >&5
x86_64-pc-linux-gnu-ar: conftest.o: No such file or directory
configure:6288: $? = 1
configure:6300: result: @
configure:6318: checking for x86_64-pc-linux-gnu-strip
configure:6334: found /usr/bin/x86_64-pc-linux-gnu-strip
configure:6345: result: x86_64-pc-linux-gnu-strip
configure:6417: checking for x86_64-pc-linux-gnu-ranlib
configure:6433: found /usr/bin/x86_64-pc-linux-gnu-ranlib
configure:6444: result: x86_64-pc-linux-gnu-ranlib
configure:6586: checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object
configure:6739: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:6742: $? = 0
configure:6746: /usr/bin/x86_64-pc-linux-gnu-nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' | sed '/ __gnu_lto/d' \> conftest.nm
configure:6749: $? = 0
configure:6815: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe   -Wl,-O1 -Wl,--as-needed conftest.c conftstm.o >&5
configure:6818: $? = 0
configure:6856: result: ok
configure:6903: checking for sysroot
configure:6933: result: no
configure:6940: checking for a working dd
configure:6978: result: /bin/dd
configure:6982: checking how to truncate binary pipes
configure:6997: result: /bin/dd bs=4096 count=1
configure:7133: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:7136: $? = 0
configure:7286: checking for x86_64-pc-linux-gnu-mt
configure:7316: result: no
configure:7326: checking for mt
configure:7342: found /usr/sbin/mt
configure:7353: result: mt
configure:7376: checking if mt is a manifest tool
configure:7382: mt '-?'
usage: mt [-v] [--version] [-h] [ -f device ] command [ count ]
configure:7390: result: no
configure:8063: checking for ANSI C header files
configure:8083: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8083: $? = 0
configure:8156: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe   -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:8156: $? = 0
configure:8156: ./conftest
configure:8156: $? = 0
configure:8167: result: yes
configure:8180: checking for sys/types.h
configure:8180: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8180: $? = 0
configure:8180: result: yes
configure:8180: checking for sys/stat.h
configure:8180: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8180: $? = 0
configure:8180: result: yes
configure:8180: checking for stdlib.h
configure:8180: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8180: $? = 0
configure:8180: result: yes
configure:8180: checking for string.h
configure:8180: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8180: $? = 0
configure:8180: result: yes
configure:8180: checking for memory.h
configure:8180: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8180: $? = 0
configure:8180: result: yes
configure:8180: checking for strings.h
configure:8180: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8180: $? = 0
configure:8180: result: yes
configure:8180: checking for inttypes.h
configure:8180: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8180: $? = 0
configure:8180: result: yes
configure:8180: checking for stdint.h
configure:8180: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8180: $? = 0
configure:8180: result: yes
configure:8180: checking for unistd.h
configure:8180: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8180: $? = 0
configure:8180: result: yes
configure:8194: checking for dlfcn.h
configure:8194: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:8194: $? = 0
configure:8194: result: yes
configure:8461: checking for objdir
configure:8476: result: .libs
configure:8740: checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions
configure:8758: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C
configure:8762: $? = 0
configure:8775: result: no
configure:9133: checking for x86_64-pc-linux-gnu-gcc option to produce PIC
configure:9140: result: -fPIC -DPIC
configure:9148: checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works
configure:9166: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   -fPIC -DPIC -DPIC conftest.c >&5
configure:9170: $? = 0
configure:9183: result: yes
configure:9212: checking if x86_64-pc-linux-gnu-gcc static flag -static works
configure:9240: result: yes
configure:9255: checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o
configure:9276: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   -o out/conftest2.o conftest.c >&5
configure:9280: $? = 0
configure:9302: result: yes
configure:9310: checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o
configure:9357: result: yes
configure:9390: 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
configure:10649: result: yes
configure:10686: checking whether -lc should be explicitly linked in
configure:10694: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe   conftest.c >&5
configure:10697: $? = 0
configure:10712: x86_64-pc-linux-gnu-gcc -shared  -fPIC -DPIC conftest.o  -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /bin/grep  -lc  \>/dev/null 2\>\&1
configure:10715: $? = 0
configure:10729: result: no
configure:10889: checking dynamic linker characteristics
configure:11483: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe   -Wl,-O1 -Wl,--as-needed -Wl,-rpath -Wl,/foo conftest.c  >&5
configure:11483: $? = 0
configure:11720: result: GNU/Linux ld.so
configure:11842: checking how to hardcode library paths into programs
configure:11867: result: immediate
configure:12415: checking whether stripping libraries is possible
configure:12420: result: yes
configure:12455: checking if libtool supports shared libraries
configure:12457: result: yes
configure:12460: checking whether to build shared libraries
configure:12485: result: yes
configure:12488: checking whether to build static libraries
configure:12492: result: no
configure:12515: checking how to run the C++ preprocessor
configure:12542: x86_64-pc-linux-gnu-g++ -E  conftest.cpp
configure:12542: $? = 0
configure:12556: x86_64-pc-linux-gnu-g++ -E  conftest.cpp
conftest.cpp:23:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:12556: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:12581: result: x86_64-pc-linux-gnu-g++ -E
configure:12601: x86_64-pc-linux-gnu-g++ -E  conftest.cpp
configure:12601: $? = 0
configure:12615: x86_64-pc-linux-gnu-g++ -E  conftest.cpp
conftest.cpp:23:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:12615: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:12777: checking for ld used by x86_64-pc-linux-gnu-g++
configure:12844: result: /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
configure:12851: checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld
configure:12866: result: yes
configure:12921: 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
configure:13994: result: yes
configure:14030: x86_64-pc-linux-gnu-g++ -c -march=native -O2 -pipe  conftest.cpp >&5
configure:14033: $? = 0
configure:14514: checking for x86_64-pc-linux-gnu-g++ option to produce PIC
configure:14521: result: -fPIC -DPIC
configure:14529: checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works
configure:14547: x86_64-pc-linux-gnu-g++ -c -march=native -O2 -pipe  -fPIC -DPIC -DPIC conftest.cpp >&5
configure:14551: $? = 0
configure:14564: result: yes
configure:14587: checking if x86_64-pc-linux-gnu-g++ static flag -static works
configure:14615: result: yes
configure:14627: checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o
configure:14648: x86_64-pc-linux-gnu-g++ -c -march=native -O2 -pipe  -o out/conftest2.o conftest.cpp >&5
configure:14652: $? = 0
configure:14674: result: yes
configure:14679: checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o
configure:14726: result: yes
configure:14756: 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
configure:14796: result: yes
configure:14937: checking dynamic linker characteristics
configure:15695: result: GNU/Linux ld.so
configure:15760: checking how to hardcode library paths into programs
configure:15785: result: immediate
configure:16586: checking for X
configure:16725: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c -lX11  >&5
configure:16725: $? = 0
configure:16775: result: libraries , headers 
configure:16874: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c   -lX11 >&5
configure:16874: $? = 0
configure:16972: checking for gethostbyname
configure:16972: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:16972: $? = 0
configure:16972: result: yes
configure:17069: checking for connect
configure:17069: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:17069: $? = 0
configure:17069: result: yes
configure:17118: checking for remove
configure:17118: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:17118: $? = 0
configure:17118: result: yes
configure:17167: checking for shmat
configure:17167: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:17167: $? = 0
configure:17167: result: yes
configure:17225: checking for IceConnectionNumber in -lICE
configure:17250: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c -lICE   >&5
configure:17250: $? = 0
configure:17259: result: yes
configure:17272: checking for dirent.h that defines DIR
configure:17291: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
configure:17291: $? = 0
configure:17299: result: yes
configure:17312: checking for library containing opendir
configure:17343: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:17343: $? = 0
configure:17360: result: none required
configure:17427: checking for ANSI C header files
configure:17531: result: yes
configure:17543: checking for unistd.h
configure:17543: result: yes
configure:17543: checking TargetConfig.h usability
configure:17543: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
conftest.c:59:26: fatal error: TargetConfig.h: No such file or directory
 #include <TargetConfig.h>
                          ^
compilation terminated.
configure:17543: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h.  */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| #  include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| #  include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| #include <TargetConfig.h>
configure:17543: result: no
configure:17543: checking TargetConfig.h presence
configure:17543: x86_64-pc-linux-gnu-gcc -E  conftest.c
conftest.c:26:26: fatal error: TargetConfig.h: No such file or directory
 #include <TargetConfig.h>
                          ^
compilation terminated.
configure:17543: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h.  */
| #include <TargetConfig.h>
configure:17543: result: no
configure:17543: checking for TargetConfig.h
configure:17543: result: no
configure:17556: checking whether byte ordering is bigendian
configure:17571: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
conftest.c:27:9: error: unknown type name 'not'
         not a universal capable compiler
         ^
conftest.c:27:15: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'universal'
         not a universal capable compiler
               ^
conftest.c:27:15: error: unknown type name 'universal'
configure:17571: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h.  */
| #ifndef __APPLE_CC__
| 	       not a universal capable compiler
| 	     #endif
| 	     typedef int dummy;
| 
configure:17616: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
configure:17616: $? = 0
configure:17634: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
conftest.c: In function 'main':
conftest.c:33:4: error: unknown type name 'not'
    not big endian
    ^
conftest.c:33:12: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'endian'
    not big endian
            ^
configure:17634: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h.  */
| #include <sys/types.h>
| 		#include <sys/param.h>
| 
| int
| main ()
| {
| #if BYTE_ORDER != BIG_ENDIAN
| 		 not big endian
| 		#endif
| 
|   ;
|   return 0;
| }
configure:17762: result: no
configure:17780: checking for an ANSI C-conforming const
configure:17846: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
configure:17846: $? = 0
configure:17853: result: yes
configure:17861: checking for inline
configure:17877: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
configure:17877: $? = 0
configure:17885: result: inline
configure:17903: checking for pid_t
configure:17903: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
configure:17903: $? = 0
configure:17903: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
conftest.c: In function 'main':
conftest.c:62:20: error: expected expression before ')' token
 if (sizeof ((pid_t)))
                    ^
configure:17903: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h.  */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| #  include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| #  include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((pid_t)))
| 	    return 0;
|   ;
|   return 0;
| }
configure:17903: result: yes
configure:17914: checking for size_t
configure:17914: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
configure:17914: $? = 0
configure:17914: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
conftest.c: In function 'main':
conftest.c:62:21: error: expected expression before ')' token
 if (sizeof ((size_t)))
                     ^
configure:17914: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h.  */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| #  include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| #  include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((size_t)))
| 	    return 0;
|   ;
|   return 0;
| }
configure:17914: result: yes
configure:17925: checking whether struct tm is in sys/time.h or time.h
configure:17945: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
configure:17945: $? = 0
configure:17952: result: time.h
configure:17963: checking whether getpgrp requires zero arguments
configure:17980: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
conftest.c: In function 'main':
conftest.c:62:1: error: too many arguments to function 'getpgrp'
 getpgrp (0);
 ^
In file included from conftest.c:57:0:
/usr/include/unistd.h:634:16: note: declared here
 extern __pid_t getpgrp (void) __THROW;
                ^
configure:17980: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h.  */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| #  include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| #  include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| getpgrp (0);
|   ;
|   return 0;
| }
configure:17988: result: yes
configure:17998: checking for strftime
configure:17998: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
conftest.c:50:6: warning: conflicting types for built-in function 'strftime'
 char strftime ();
      ^
configure:17998: $? = 0
configure:17998: result: yes
configure:18053: checking vfork.h usability
configure:18053: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2  conftest.c >&5
conftest.c:61:19: fatal error: vfork.h: No such file or directory
 #include <vfork.h>
                   ^
compilation terminated.
configure:18053: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| #define GETPGRP_VOID 1
| #define HAVE_STRFTIME 1
| /* end confdefs.h.  */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| #  include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| #  include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| #include <vfork.h>
configure:18053: result: no
configure:18053: checking vfork.h presence
configure:18053: x86_64-pc-linux-gnu-gcc -E  conftest.c
conftest.c:28:19: fatal error: vfork.h: No such file or directory
 #include <vfork.h>
                   ^
compilation terminated.
configure:18053: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| #define GETPGRP_VOID 1
| #define HAVE_STRFTIME 1
| /* end confdefs.h.  */
| #include <vfork.h>
configure:18053: result: no
configure:18053: checking for vfork.h
configure:18053: result: no
configure:18066: checking for fork
configure:18066: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
conftest.c:51:6: warning: conflicting types for built-in function 'fork'
 char fork ();
      ^
configure:18066: $? = 0
configure:18066: result: yes
configure:18066: checking for vfork
configure:18066: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:18066: $? = 0
configure:18066: result: yes
configure:18076: checking for working fork
configure:18098: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:18098: $? = 0
configure:18098: ./conftest
configure:18098: $? = 0
configure:18108: result: yes
configure:18129: checking for working vfork
configure:18239: result: yes
configure:18266: checking for vprintf
configure:18266: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
conftest.c:55:6: warning: conflicting types for built-in function 'vprintf'
 char vprintf ();
      ^
configure:18266: $? = 0
configure:18266: result: yes
configure:18272: checking for _doprnt
configure:18272: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
/var/tmp/portage/sci-biology/emboss-6.6.0/temp/ccNqczjV.o: In function `main':
conftest.c:(.text.startup+0x7): undefined reference to `_doprnt'
collect2: error: ld returned 1 exit status
configure:18272: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "EMBOSS"
| #define PACKAGE_TARNAME "EMBOSS"
| #define PACKAGE_VERSION "6.6.0"
| #define PACKAGE_STRING "EMBOSS 6.6.0"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL "http://emboss.open-bio.org/"
| #define PACKAGE "EMBOSS"
| #define VERSION "6.6.0"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_DIRENT_H 1
| #define STDC_HEADERS 1
| #define HAVE_UNISTD_H 1
| #define GETPGRP_VOID 1
| #define HAVE_STRFTIME 1
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_VPRINTF 1
| /* end confdefs.h.  */
| /* Define _doprnt to an innocuous variant, in case <limits.h> declares _doprnt.
|    For example, HP-UX 11i <limits.h> declares gettimeofday.  */
| #define _doprnt innocuous__doprnt
| 
| /* System header to define __stub macros and hopefully few prototypes,
|     which can conflict with char _doprnt (); below.
|     Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
|     <limits.h> exists even on freestanding compilers.  */
| 
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
| 
| #undef _doprnt
| 
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| char _doprnt ();
| /* The GNU C library defines this for functions which it implements
|     to always fail with ENOSYS.  Some functions are actually named
|     something starting with __ and the normal name is an alias.  */
| #if defined __stub__doprnt || defined __stub____doprnt
| choke me
| #endif
| 
| int
| main ()
| {
| return _doprnt ();
|   ;
|   return 0;
| }
configure:18272: result: no
configure:18286: checking for memmove
configure:18286: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
conftest.c:56:6: warning: conflicting types for built-in function 'memmove'
 char memmove ();
      ^
configure:18286: $? = 0
configure:18286: result: yes
configure:18311: checking X11/Xlib.h usability
configure:18311: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe  -O2   conftest.c >&5
configure:18311: $? = 0
configure:18311: result: yes
configure:18311: checking X11/Xlib.h presence
configure:18311: x86_64-pc-linux-gnu-gcc -E  conftest.c
configure:18311: $? = 0
configure:18311: result: yes
configure:18311: checking for X11/Xlib.h
configure:18311: result: yes
configure:18349: checking for socket in -lc
configure:18374: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2   -Wl,-O1 -Wl,--as-needed conftest.c -lc   >&5
configure:18374: $? = 0
configure:18383: result: yes
configure:18391: checking for main in -lm
configure:18410: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2   -Wl,-O1 -Wl,--as-needed conftest.c -lm   >&5
configure:18410: $? = 0
configure:18419: result: yes
configure:18503: checking if docroot is given
configure:18515: result: no
configure:18524: checking if gcc profiling is selected
configure:18537: result: no
configure:18546: checking if gcov coverage is selected
configure:18558: result: no
configure:18567: checking for EMBOSS pre-indexed databases
configure:18571: checking for /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0/emboss/index/edam.xac
configure:18585: result: yes
configure:18602: checking for Java JNI
configure:18609: result: no
configure:18638: checking for Java JNI OS
configure:18664: result: no
configure:18672: checking for authorisation type
configure:18855: result: no
configure:18868: checking for threading type
configure:18946: result: no
configure:19175: checking whether to look for pdf support
configure:19181: result: yes
configure:19219: checking for HPDF_New in -lhpdf
configure:19244: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2   -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.c -lhpdf -L/usr/lib -lm  >&5
configure:19244: $? = 0
configure:19253: result: yes
configure:19324: checking for x86_64-pc-linux-gnu-pkg-config
configure:19342: found /usr/bin/x86_64-pc-linux-gnu-pkg-config
configure:19354: result: /usr/bin/x86_64-pc-linux-gnu-pkg-config
configure:19422: checking pkg-config is at least version 0.9.0
configure:19425: result: yes
configure:19434: checking whether to look for axis2c support
configure:19609: result: no
configure:19623: checking if png driver is wanted
configure:19629: result: yes
configure:19723: checking for inflateEnd in -lz
configure:19748: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2   -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.c -lz -L/usr/lib -lz -lm  -lhpdf >&5
configure:19748: $? = 0
configure:19757: result: yes
configure:19771: checking for png_destroy_read_struct in -lpng
configure:19796: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2   -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.c -lpng -L/usr/lib -lz -lm  -lhpdf >&5
configure:19796: $? = 0
configure:19805: result: yes
configure:19822: checking for gdImageCreateFromPng in -lgd
configure:19847: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2   -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.c -lgd -L/usr/lib -lgd -lpng -lz -lm -lm  -lhpdf >&5
configure:19847: $? = 0
configure:19856: result: yes
configure:19964: checking for mysql_config
configure:19995: result: /usr/bin/mysql_config
configure:20007: checking for MySQL libraries
configure:20035: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -I/usr/include/mysql -I/usr/include/mysql/..  -L/usr/lib64 -lmysqlclient -lpthread -lz -lm -lssl -lcrypto -ldl -Wl,-O1 -Wl,--as-needed conftest.c -lm  -lhpdf -lgd -lpng -lz -lm >&5
configure:20035: $? = 0
configure:20052: result: yes
configure:20158: checking for pg_config
configure:20189: result: /usr/bin/pg_config
configure:20201: checking for PostgreSQL libraries
configure:20229: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe  -O2  -I/usr/include/postgresql-9.0  -L/usr/lib64/postgresql-9.0/lib64 -lpq -Wl,-O1 -Wl,--as-needed conftest.c -lm  -lhpdf -lgd -lpng -lz -lm >&5
configure:20229: $? = 0
configure:20246: result: yes
configure:20365: checking for large file support
configure:20421: result: yes
configure:20451: checking for PCRE
configure:20458: $PKG_CONFIG --exists --print-errors "libpcre"
configure:20461: $? = 0
configure:20474: $PKG_CONFIG --exists --print-errors "libpcre"
configure:20477: $? = 0
configure:20536: result: yes
configure:20542: checking for EXPAT
configure:20549: $PKG_CONFIG --exists --print-errors "expat"
configure:20552: $? = 0
configure:20565: $PKG_CONFIG --exists --print-errors "expat"
configure:20568: $? = 0
configure:20627: result: yes
configure:20633: checking for ZLIB
configure:20640: $PKG_CONFIG --exists --print-errors "zlib"
configure:20643: $? = 0
configure:20656: $PKG_CONFIG --exists --print-errors "zlib"
configure:20659: $? = 0
configure:20718: result: yes
configure:20724: checking for PLPLOT
configure:20731: $PKG_CONFIG --exists --print-errors "plplotd"
Package plplotd was not found in the pkg-config search path.
Perhaps you should add the directory containing `plplotd.pc'
to the PKG_CONFIG_PATH environment variable
No package 'plplotd' found
configure:20734: $? = 1
configure:20747: $PKG_CONFIG --exists --print-errors "plplotd"
Package plplotd was not found in the pkg-config search path.
Perhaps you should add the directory containing `plplotd.pc'
to the PKG_CONFIG_PATH environment variable
No package 'plplotd' found
configure:20750: $? = 1
configure:20763: result: no
No package 'plplotd' found
configure:20779: error: Package requirements (plplotd) were not met:

No package 'plplotd' found

Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.

Alternatively, you may set the environment variables PLPLOT_CFLAGS
and PLPLOT_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=x86_64-pc-linux-gnu
ac_cv_c_bigendian=no
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_c_inline=inline
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_ANT_set=
ac_cv_env_ANT_value=
ac_cv_env_AXIS2C_CFLAGS_set=
ac_cv_env_AXIS2C_CFLAGS_value=
ac_cv_env_AXIS2C_LIBS_set=
ac_cv_env_AXIS2C_LIBS_value=
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-march=native -O2 -pipe'
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=set
ac_cv_env_CXXFLAGS_value='-march=native -O2 -pipe'
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_EXPAT_CFLAGS_set=
ac_cv_env_EXPAT_CFLAGS_value=
ac_cv_env_EXPAT_LIBS_set=
ac_cv_env_EXPAT_LIBS_value=
ac_cv_env_JAR_set=
ac_cv_env_JAR_value=
ac_cv_env_JAVAC_set=set
ac_cv_env_JAVAC_value=/etc/java-config-2/current-system-vm/bin/javac
ac_cv_env_JAVA_set=
ac_cv_env_JAVA_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-Wl,-O1 -Wl,--as-needed'
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_LT_SYS_LIBRARY_PATH_set=
ac_cv_env_LT_SYS_LIBRARY_PATH_value=
ac_cv_env_PCRE_CFLAGS_set=
ac_cv_env_PCRE_CFLAGS_value=
ac_cv_env_PCRE_LIBS_set=
ac_cv_env_PCRE_LIBS_value=
ac_cv_env_PKG_CONFIG_LIBDIR_set=
ac_cv_env_PKG_CONFIG_LIBDIR_value=
ac_cv_env_PKG_CONFIG_PATH_set=set
ac_cv_env_PKG_CONFIG_PATH_value=/usr/lib64/pkgconfig
ac_cv_env_PKG_CONFIG_set=
ac_cv_env_PKG_CONFIG_value=
ac_cv_env_PLPLOT_CFLAGS_set=
ac_cv_env_PLPLOT_CFLAGS_value=
ac_cv_env_PLPLOT_LIBS_set=
ac_cv_env_PLPLOT_LIBS_value=
ac_cv_env_XMKMF_set=
ac_cv_env_XMKMF_value=
ac_cv_env_ZLIB_CFLAGS_set=
ac_cv_env_ZLIB_CFLAGS_value=
ac_cv_env_ZLIB_LIBS_set=
ac_cv_env_ZLIB_LIBS_value=
ac_cv_env_build_alias_set=set
ac_cv_env_build_alias_value=x86_64-pc-linux-gnu
ac_cv_env_host_alias_set=set
ac_cv_env_host_alias_value=x86_64-pc-linux-gnu
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_file__var_tmp_portage_sci_biology_emboss_6_6_0_work_EMBOSS_6_6_0_emboss_index_edam_xac=yes
ac_cv_func__doprnt=no
ac_cv_func_connect=yes
ac_cv_func_fork=yes
ac_cv_func_fork_works=yes
ac_cv_func_gethostbyname=yes
ac_cv_func_getpgrp_void=yes
ac_cv_func_memmove=yes
ac_cv_func_remove=yes
ac_cv_func_shmat=yes
ac_cv_func_strftime=yes
ac_cv_func_vfork=yes
ac_cv_func_vfork_works=yes
ac_cv_func_vprintf=yes
ac_cv_have_x='have_x=yes	ac_x_includes='\'''\''	ac_x_libraries='\'''\'''
ac_cv_header_TargetConfig_h=no
ac_cv_header_X11_Xlib_h=yes
ac_cv_header_dirent_dirent_h=yes
ac_cv_header_dlfcn_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_header_vfork_h=no
ac_cv_host=x86_64-pc-linux-gnu
ac_cv_lib_ICE_IceConnectionNumber=yes
ac_cv_lib_c_socket=yes
ac_cv_lib_gd_gdImageCreateFromPng=yes
ac_cv_lib_hpdf_HPDF_New=yes
ac_cv_lib_m_main=yes
ac_cv_lib_png_png_destroy_read_struct=yes
ac_cv_lib_z_inflateEnd=yes
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_FGREP='/bin/grep -F'
ac_cv_path_GREP=/bin/grep
ac_cv_path_MYSQL_CONFIG=/usr/bin/mysql_config
ac_cv_path_PKG_CONFIG=/usr/bin/x86_64-pc-linux-gnu-pkg-config
ac_cv_path_POSTGRESQL_CONFIG=/usr/bin/pg_config
ac_cv_path_SED=/bin/sed
ac_cv_path_install='/usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c'
ac_cv_path_lt_DD=/bin/dd
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AR=x86_64-pc-linux-gnu-ar
ac_cv_prog_AWK=gawk
ac_cv_prog_CC=x86_64-pc-linux-gnu-gcc
ac_cv_prog_CPP='x86_64-pc-linux-gnu-gcc -E'
ac_cv_prog_CXX=x86_64-pc-linux-gnu-g++
ac_cv_prog_CXXCPP='x86_64-pc-linux-gnu-g++ -E'
ac_cv_prog_OBJDUMP=x86_64-pc-linux-gnu-objdump
ac_cv_prog_RANLIB=x86_64-pc-linux-gnu-ranlib
ac_cv_prog_STRIP=x86_64-pc-linux-gnu-strip
ac_cv_prog_ac_ct_MANIFEST_TOOL=mt
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_search_opendir='none required'
ac_cv_struct_tm=time.h
ac_cv_type_pid_t=yes
ac_cv_type_size_t=yes
am_cv_CC_dependencies_compiler_type=none
am_cv_CXX_dependencies_compiler_type=none
am_cv_make_support_nested_variables=yes
am_cv_prog_cc_c_o=yes
lt_cv_ar_at_file=@
lt_cv_archive_cmds_need_lc=no
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_nm_interface='BSD nm'
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/x86_64-pc-linux-gnu/bin/ld
lt_cv_path_LDCXX='/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64'
lt_cv_path_NM='/usr/bin/x86_64-pc-linux-gnu-nm -B'
lt_cv_path_mainfest_tool=no
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_c_o_CXX=yes
lt_cv_prog_compiler_pic='-fPIC -DPIC'
lt_cv_prog_compiler_pic_CXX='-fPIC -DPIC'
lt_cv_prog_compiler_pic_works=yes
lt_cv_prog_compiler_pic_works_CXX=yes
lt_cv_prog_compiler_rtti_exceptions=no
lt_cv_prog_compiler_static_works=yes
lt_cv_prog_compiler_static_works_CXX=yes
lt_cv_prog_gnu_ld=yes
lt_cv_prog_gnu_ldcxx=yes
lt_cv_sharedlib_from_linklib_cmd='printf %s\n'
lt_cv_shlibpath_overrides_runpath=yes
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[	 ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[	 ][	 ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'' | sed '\''/ __gnu_lto/d'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \(.*\) .*$/  {"\1", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/  {"\1", (void *) \&\1},/p'\'''
lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \(.*\) .*$/  {"\1", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(lib.*\)$/  {"\1", (void *) \&\1},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/  {"lib\1", (void *) \&\1},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_global_symbol_to_import=
lt_cv_sys_max_cmd_len=1572864
lt_cv_to_host_file_cmd=func_convert_file_noop
lt_cv_to_tool_file_cmd=func_convert_file_noop
lt_cv_truncate_bin='/bin/dd bs=4096 count=1'
pkg_cv_EXPAT_CFLAGS=
pkg_cv_EXPAT_LIBS='-lexpat '
pkg_cv_PCRE_CFLAGS=
pkg_cv_PCRE_LIBS='-lpcre '
pkg_cv_ZLIB_CFLAGS=
pkg_cv_ZLIB_LIBS='-lz '

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0/missing aclocal-1.15'
AJAX_FIXED_ROOT='\"/var/tmp/portage/sci-biology/emboss-6.6.0/work/emboss-6.6.0_build/emboss\"'
AJAX_SYSTEM='\"Linux\"'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE='#'
AMPDF_FALSE='#'
AMPDF_TRUE=''
AMPNG_FALSE='#'
AMPNG_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
ANT=''
AR='x86_64-pc-linux-gnu-ar'
AUTOCONF='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0/missing autoconf'
AUTOHEADER='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0/missing autoheader'
AUTOMAKE='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0/missing automake-1.15'
AWK='gawk'
AXIS2C_CFLAGS=''
AXIS2C_CPPFLAGS=''
AXIS2C_LDFLAGS=''
AXIS2C_LIBS=''
CC='x86_64-pc-linux-gnu-gcc'
CCDEPMODE='depmode=none'
CFLAGS='-march=native -O2 -pipe  -O2 '
CPP='x86_64-pc-linux-gnu-gcc -E'
CPPFLAGS=' -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64'
CXX='x86_64-pc-linux-gnu-g++'
CXXCPP='x86_64-pc-linux-gnu-g++ -E'
CXXDEPMODE='depmode=none'
CXXFLAGS='-march=native -O2 -pipe'
CYGPATH_W='echo'
DEFS=''
DEPDIR='.deps'
DEVWARN_CFLAGS=''
DLLTOOL='false'
DSYMUTIL=''
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EMBOSS_TOP='/var/tmp/portage/sci-biology/emboss-6.6.0/work/emboss-6.6.0_build'
ESYSTEMLIBS_FALSE='#'
ESYSTEMLIBS_TRUE=''
EXEEXT=''
EXPAT_CFLAGS=''
EXPAT_LIBS='-lexpat '
FGREP='/bin/grep -F'
GREP='/bin/grep'
HAVE_MEMMOVE=''
HAVE_STRERROR=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
ISAIXIA64_FALSE=''
ISAIXIA64_TRUE=''
ISCYGWIN_FALSE=''
ISCYGWIN_TRUE=''
ISSHARED_FALSE=''
ISSHARED_TRUE=''
JAR=''
JAVA=''
JAVAC='/etc/java-config-2/current-system-vm/bin/javac'
JAVA_BUILD_FALSE=''
JAVA_BUILD_TRUE='#'
JAVA_CFLAGS=''
JAVA_CPPFLAGS=' -DNO_AUTH'
JAVA_LDFLAGS=''
LD='/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64'
LDFLAGS='-Wl,-O1 -Wl,--as-needed'
LIBOBJS=''
LIBS='-lm  -lhpdf -lgd -lpng -lz -lm'
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LIPO=''
LN_S='ln -s'
LTLIBOBJS=''
LT_SYS_LIBRARY_PATH=''
MAKEINFO='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0/missing makeinfo'
MANIFEST_TOOL=':'
MKDIR_P='/bin/mkdir -p'
MYSQL_CFLAGS='-I/usr/include/mysql -I/usr/include/mysql/..'
MYSQL_CONFIG='/usr/bin/mysql_config'
MYSQL_CPPFLAGS='-I/usr/include/mysql -I/usr/include/mysql/..'
MYSQL_LDFLAGS='-L/usr/lib64 -lmysqlclient -lpthread -lz -lm -lssl -lcrypto -ldl'
MYSQL_VERSION='10.0.17'
NEEDAJAX_FALSE=''
NEEDAJAX_TRUE=''
NM='/usr/bin/x86_64-pc-linux-gnu-nm -B'
NMEDIT=''
OBJDUMP='x86_64-pc-linux-gnu-objdump'
OBJEXT='o'
OTOOL64=''
OTOOL=''
PACKAGE='EMBOSS'
PACKAGE_BUGREPORT='[e-mail]'
PACKAGE_NAME='EMBOSS'
PACKAGE_STRING='EMBOSS 6.6.0'
PACKAGE_TARNAME='EMBOSS'
PACKAGE_URL='http://emboss.open-bio.org/'
PACKAGE_VERSION='6.6.0'
PATH_SEPARATOR=':'
PCRE_CFLAGS=''
PCRE_DATE=''
PCRE_LIBS='-lpcre '
PCRE_LIB_VERSION=''
PCRE_MAJOR=''
PCRE_MINOR=''
PCRE_POSIXLIB_VERSION=''
PCRE_VERSION=''
PKG_CONFIG='/usr/bin/x86_64-pc-linux-gnu-pkg-config'
PKG_CONFIG_LIBDIR=''
PKG_CONFIG_PATH='/usr/lib64/pkgconfig'
PLPLOT_CFLAGS=''
PLPLOT_LIBS=''
POSIX_MALLOC_THRESHOLD=''
POSTGRESQL_CFLAGS='-I/usr/include/postgresql-9.0'
POSTGRESQL_CONFIG='/usr/bin/pg_config'
POSTGRESQL_CPPFLAGS='-I/usr/include/postgresql-9.0'
POSTGRESQL_LDFLAGS='-L/usr/lib64/postgresql-9.0/lib64 -lpq'
POSTGRESQL_VERSION='9.0.18'
PURIFY_FALSE=''
PURIFY_TRUE=''
RANLIB='x86_64-pc-linux-gnu-ranlib'
SED='/bin/sed'
SET_MAKE=''
SHELL='/bin/sh'
STRIP='x86_64-pc-linux-gnu-strip'
VERSION='6.6.0'
WARN_CFLAGS=''
XLIB=' -lX11 '
XMKMF=''
X_CFLAGS=''
X_EXTRA_LIBS=''
X_LIBS=''
X_PRE_LIBS=' -lSM -lICE'
ZLIB_CFLAGS=''
ZLIB_LIBS='-lz '
ac_ct_AR=''
ac_ct_CC=''
ac_ct_CXX=''
ac_ct_DUMPBIN=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE='#'
am__fastdepCXX_FALSE=''
am__fastdepCXX_TRUE='#'
am__include='include'
am__isrc=' -I$(srcdir)'
am__leading_dot='.'
am__nodep=''
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-pc-linux-gnu'
build_alias='x86_64-pc-linux-gnu'
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='pc'
datadir='/usr/share'
datarootdir='${prefix}/share'
docdir='/usr/share/doc/emboss-6.6.0'
dvidir='${docdir}'
exec_prefix='NONE'
host='x86_64-pc-linux-gnu'
host_alias='x86_64-pc-linux-gnu'
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='pc'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='/usr/share/info'
install_sh='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0/install-sh'
libdir='/usr/lib64'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='/var/lib'
mandir='/usr/share/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "EMBOSS"
#define PACKAGE_TARNAME "EMBOSS"
#define PACKAGE_VERSION "6.6.0"
#define PACKAGE_STRING "EMBOSS 6.6.0"
#define PACKAGE_BUGREPORT "[e-mail]"
#define PACKAGE_URL "http://emboss.open-bio.org/"
#define PACKAGE "EMBOSS"
#define VERSION "6.6.0"
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_DLFCN_H 1
#define LT_OBJDIR ".libs/"
#define HAVE_DIRENT_H 1
#define STDC_HEADERS 1
#define HAVE_UNISTD_H 1
#define GETPGRP_VOID 1
#define HAVE_STRFTIME 1
#define HAVE_FORK 1
#define HAVE_VFORK 1
#define HAVE_WORKING_VFORK 1
#define HAVE_WORKING_FORK 1
#define HAVE_VPRINTF 1
#define HAVE_MEMMOVE 1
#define PLD_xwin 1
#define HAVE_LIBM 1
#define PLD_pdf 1
#define PLD_png 1
#define HAVE_MYSQL 1
#define HAVE_POSTGRESQL 1

configure: exit 1