confi.log --with-guile=/usr

config.log (text/plain), 65.09 KB, created by David Kredba on 2016-08-16 18:04:17 UTC

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

It was created by coot configure 0.8.2, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/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/coot-0.8.2-r1 --enable-shared --disable-static --with-goocanvas-prefix=/usr --with-guile=/usr --with-python=/usr --with-guile-gtk --with-pygtk=/usr --with-sqlite3 --with-boost=/usr

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

hostname = srv5
uname -m = x86_64
uname -r = 4.6.4-gentoo
uname -s = Linux
uname -v = #1 SMP PREEMPT Thu Jul 14 21:34:35 CEST 2016

/usr/bin/uname -p = Intel(R) Core(TM)2 Quad CPU Q9550 @ 2.83GHz
/bin/uname -X     = unknown

/bin/arch              = x86_64
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/temp/python2.7/bin
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/4.9.4
PATH: /opt/eagle/bin


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

configure:2672: checking for a BSD-compatible install
configure:2740: result: /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c
configure:2751: checking whether build environment is sane
configure:2806: result: yes
configure:2957: checking for a thread-safe mkdir -p
configure:2996: result: /bin/mkdir -p
configure:3003: checking for gawk
configure:3019: found /usr/bin/gawk
configure:3030: result: gawk
configure:3041: checking whether make sets $(MAKE)
configure:3063: result: yes
configure:3092: checking whether make supports nested variables
configure:3109: result: yes
configure:3264: checking for style of include used by make
configure:3292: result: GNU
configure:3323: checking for x86_64-pc-linux-gnu-gcc
configure:3339: found /usr/bin/x86_64-pc-linux-gnu-gcc
configure:3350: result: x86_64-pc-linux-gnu-gcc
configure:3619: checking for C compiler version
configure:3628: x86_64-pc-linux-gnu-gcc --version >&5
x86_64-pc-linux-gnu-gcc (Gentoo 4.9.4) 4.9.4 20160708 (prerelease)
Copyright (C) 2015 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:3639: $? = 0
configure:3628: x86_64-pc-linux-gnu-gcc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.4/x86_64-pc-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.9.4/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.9.4/work/gcc-4.9.4/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.4 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/include/g++-v4 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/python --enable-languages=c,c++,java,objc,obj-c++,fortran,ada --enable-obsolete --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.9.4' --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 --enable-libcilkrts --enable-vtable-verify --enable-libvtv --enable-lto --with-cloog --disable-isl-version-check --enable-libsanitizer
Thread model: posix
gcc version 4.9.4 20160708 (prerelease) (Gentoo 4.9.4) 
configure:3639: $? = 0
configure:3628: 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:3639: $? = 1
configure:3628: 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:3639: $? = 1
configure:3659: checking whether the C compiler works
configure:3681: x86_64-pc-linux-gnu-gcc -O2 -march=core2 -ggdb -pipe  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:3685: $? = 0
configure:3733: result: yes
configure:3736: checking for C compiler default output file name
configure:3738: result: a.out
configure:3744: checking for suffix of executables
configure:3751: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:3755: $? = 0
configure:3777: result: 
configure:3799: checking whether we are cross compiling
configure:3807: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:3811: $? = 0
configure:3818: ./conftest
configure:3822: $? = 0
configure:3837: result: no
configure:3842: checking for suffix of object files
configure:3864: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:3868: $? = 0
configure:3889: result: o
configure:3893: checking whether we are using the GNU C compiler
configure:3912: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:3912: $? = 0
configure:3921: result: yes
configure:3930: checking whether x86_64-pc-linux-gnu-gcc accepts -g
configure:3950: x86_64-pc-linux-gnu-gcc -c -g  conftest.c >&5
configure:3950: $? = 0
configure:3991: result: yes
configure:4008: checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89
configure:4071: x86_64-pc-linux-gnu-gcc  -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:4071: $? = 0
configure:4084: result: none needed
configure:4109: checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together
configure:4131: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o
configure:4134: $? = 0
configure:4131: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o
configure:4134: $? = 0
configure:4146: result: yes
configure:4165: checking dependency style of x86_64-pc-linux-gnu-gcc
configure:4276: result: none
configure:4292: checking for library containing strerror
configure:4323: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:4323: $? = 0
configure:4340: result: none required
configure:4356: checking for x86_64-pc-linux-gnu-gcc
configure:4383: result: x86_64-pc-linux-gnu-gcc
configure:4652: checking for C compiler version
configure:4661: x86_64-pc-linux-gnu-gcc --version >&5
x86_64-pc-linux-gnu-gcc (Gentoo 4.9.4) 4.9.4 20160708 (prerelease)
Copyright (C) 2015 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:4672: $? = 0
configure:4661: x86_64-pc-linux-gnu-gcc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.4/x86_64-pc-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.9.4/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.9.4/work/gcc-4.9.4/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.4 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/include/g++-v4 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/python --enable-languages=c,c++,java,objc,obj-c++,fortran,ada --enable-obsolete --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.9.4' --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 --enable-libcilkrts --enable-vtable-verify --enable-libvtv --enable-lto --with-cloog --disable-isl-version-check --enable-libsanitizer
Thread model: posix
gcc version 4.9.4 20160708 (prerelease) (Gentoo 4.9.4) 
configure:4672: $? = 0
configure:4661: 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:4672: $? = 1
configure:4661: 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:4672: $? = 1
configure:4676: checking whether we are using the GNU C compiler
configure:4704: result: yes
configure:4713: checking whether x86_64-pc-linux-gnu-gcc accepts -g
configure:4774: result: yes
configure:4791: checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89
configure:4867: result: none needed
configure:4892: checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together
configure:4929: result: yes
configure:4948: checking dependency style of x86_64-pc-linux-gnu-gcc
configure:5059: result: none
configure:5082: checking for x86_64-pc-linux-gnu-gcc
configure:5109: result: x86_64-pc-linux-gnu-gcc
configure:5378: checking for C compiler version
configure:5387: x86_64-pc-linux-gnu-gcc --version >&5
x86_64-pc-linux-gnu-gcc (Gentoo 4.9.4) 4.9.4 20160708 (prerelease)
Copyright (C) 2015 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:5398: $? = 0
configure:5387: x86_64-pc-linux-gnu-gcc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.4/x86_64-pc-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.9.4/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.9.4/work/gcc-4.9.4/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.4 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/include/g++-v4 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/python --enable-languages=c,c++,java,objc,obj-c++,fortran,ada --enable-obsolete --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.9.4' --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 --enable-libcilkrts --enable-vtable-verify --enable-libvtv --enable-lto --with-cloog --disable-isl-version-check --enable-libsanitizer
Thread model: posix
gcc version 4.9.4 20160708 (prerelease) (Gentoo 4.9.4) 
configure:5398: $? = 0
configure:5387: 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:5398: $? = 1
configure:5387: 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:5398: $? = 1
configure:5402: checking whether we are using the GNU C compiler
configure:5430: result: yes
configure:5439: checking whether x86_64-pc-linux-gnu-gcc accepts -g
configure:5500: result: yes
configure:5517: checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89
configure:5593: result: none needed
configure:5618: checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together
configure:5655: result: yes
configure:5674: checking dependency style of x86_64-pc-linux-gnu-gcc
configure:5785: result: none
configure:5807: checking how to run the C preprocessor
configure:5838: x86_64-pc-linux-gnu-gcc -E  conftest.c
configure:5838: $? = 0
configure:5852: x86_64-pc-linux-gnu-gcc -E  conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:5852: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "coot"
| #define PACKAGE_TARNAME "coot"
| #define PACKAGE_VERSION "0.8.2"
| #define PACKAGE_STRING "coot 0.8.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "coot"
| #define VERSION "0.8.2"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:5877: result: x86_64-pc-linux-gnu-gcc -E
configure:5897: x86_64-pc-linux-gnu-gcc -E  conftest.c
configure:5897: $? = 0
configure:5911: x86_64-pc-linux-gnu-gcc -E  conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:5911: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "coot"
| #define PACKAGE_TARNAME "coot"
| #define PACKAGE_VERSION "0.8.2"
| #define PACKAGE_STRING "coot 0.8.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "coot"
| #define VERSION "0.8.2"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:5940: checking for grep that handles long lines and -e
configure:5998: result: /bin/grep
configure:6003: checking for egrep
configure:6065: result: /bin/grep -E
configure:6070: checking for ANSI C header files
configure:6090: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:6090: $? = 0
configure:6163: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
configure:6163: $? = 0
configure:6163: ./conftest
configure:6163: $? = 0
configure:6174: result: yes
configure:6197: checking for x86_64-pc-linux-gnu-g++
configure:6213: found /usr/bin/x86_64-pc-linux-gnu-g++
configure:6224: result: x86_64-pc-linux-gnu-g++
configure:6295: checking for C++ compiler version
configure:6304: x86_64-pc-linux-gnu-g++ --version >&5
x86_64-pc-linux-gnu-g++ (Gentoo 4.9.4) 4.9.4 20160708 (prerelease)
Copyright (C) 2015 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:6315: $? = 0
configure:6304: x86_64-pc-linux-gnu-g++ -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.4/x86_64-pc-linux-gnu-g++
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.9.4/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.9.4/work/gcc-4.9.4/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.4 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/include/g++-v4 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/python --enable-languages=c,c++,java,objc,obj-c++,fortran,ada --enable-obsolete --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.9.4' --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 --enable-libcilkrts --enable-vtable-verify --enable-libvtv --enable-lto --with-cloog --disable-isl-version-check --enable-libsanitizer
Thread model: posix
gcc version 4.9.4 20160708 (prerelease) (Gentoo 4.9.4) 
configure:6315: $? = 0
configure:6304: 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:6315: $? = 1
configure:6304: 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:6315: $? = 1
configure:6319: checking whether we are using the GNU C++ compiler
configure:6338: x86_64-pc-linux-gnu-g++ -c -O2 -march=core2 -ggdb -pipe  conftest.cpp >&5
configure:6338: $? = 0
configure:6347: result: yes
configure:6356: checking whether x86_64-pc-linux-gnu-g++ accepts -g
configure:6376: x86_64-pc-linux-gnu-g++ -c -g  conftest.cpp >&5
configure:6376: $? = 0
configure:6417: result: yes
configure:6442: checking dependency style of x86_64-pc-linux-gnu-g++
configure:6553: result: none
configure:6598: checking build system type
configure:6612: result: x86_64-pc-linux-gnu
configure:6632: checking host system type
configure:6645: result: x86_64-pc-linux-gnu
configure:6686: checking how to print strings
configure:6713: result: printf
configure:6734: checking for a sed that does not truncate output
configure:6798: result: /bin/sed
configure:6816: checking for fgrep
configure:6878: result: /bin/grep -F
configure:6913: checking for ld used by x86_64-pc-linux-gnu-gcc
configure:6980: result: /usr/x86_64-pc-linux-gnu/bin/ld
configure:6987: checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld
configure:7002: result: yes
configure:7014: checking for BSD- or MS-compatible name lister (nm)
configure:7068: result: /usr/bin/x86_64-pc-linux-gnu-nm -B
configure:7198: checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface
configure:7205: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:7208: /usr/bin/x86_64-pc-linux-gnu-nm -B "conftest.o"
configure:7211: output
0000000000000000 B some_variable
configure:7218: result: BSD nm
configure:7221: checking whether ln -s works
configure:7225: result: yes
configure:7233: checking the maximum length of command line arguments
configure:7364: result: 1572864
configure:7412: checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format
configure:7452: result: func_convert_file_noop
configure:7459: checking how to convert x86_64-pc-linux-gnu file names to toolchain format
configure:7479: result: func_convert_file_noop
configure:7486: checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files
configure:7493: result: -r
configure:7527: checking for x86_64-pc-linux-gnu-objdump
configure:7543: found /usr/bin/x86_64-pc-linux-gnu-objdump
configure:7554: result: x86_64-pc-linux-gnu-objdump
configure:7626: checking how to recognize dependent libraries
configure:7826: result: pass_all
configure:7871: checking for x86_64-pc-linux-gnu-dlltool
configure:7901: result: no
configure:7911: checking for dlltool
configure:7941: result: no
configure:7971: checking how to associate runtime and link libraries
configure:7998: result: printf %s\n
configure:8014: checking for x86_64-pc-linux-gnu-ar
configure:8030: found /usr/bin/x86_64-pc-linux-gnu-ar
configure:8041: result: x86_64-pc-linux-gnu-ar
configure:8122: checking for archiver @FILE support
configure:8139: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:8139: $? = 0
configure:8142: x86_64-pc-linux-gnu-ar cru libconftest.a @conftest.lst >&5
configure:8145: $? = 0
configure:8150: 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:8153: $? = 1
configure:8165: result: @
configure:8183: checking for x86_64-pc-linux-gnu-strip
configure:8199: found /usr/bin/x86_64-pc-linux-gnu-strip
configure:8210: result: x86_64-pc-linux-gnu-strip
configure:8282: checking for x86_64-pc-linux-gnu-ranlib
configure:8298: found /usr/bin/x86_64-pc-linux-gnu-ranlib
configure:8309: result: x86_64-pc-linux-gnu-ranlib
configure:8451: checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object
configure:8604: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:8607: $? = 0
configure:8611: /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:8614: $? = 0
configure:8680: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe  -Wl,-O1 -Wl,--as-needed conftest.c conftstm.o >&5
configure:8683: $? = 0
configure:8721: result: ok
configure:8768: checking for sysroot
configure:8798: result: no
configure:8805: checking for a working dd
configure:8843: result: /bin/dd
configure:8847: checking how to truncate binary pipes
configure:8862: result: /bin/dd bs=4096 count=1
configure:8998: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9001: $? = 0
configure:9151: checking for x86_64-pc-linux-gnu-mt
configure:9181: result: no
configure:9191: checking for mt
configure:9207: found /usr/sbin/mt
configure:9218: result: mt
configure:9241: checking if mt is a manifest tool
configure:9247: mt '-?'
usage: mt [-v] [--version] [-h] [ -f device ] command [ count ]
configure:9255: result: no
configure:9932: checking for sys/types.h
configure:9932: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9932: $? = 0
configure:9932: result: yes
configure:9932: checking for sys/stat.h
configure:9932: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9932: $? = 0
configure:9932: result: yes
configure:9932: checking for stdlib.h
configure:9932: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9932: $? = 0
configure:9932: result: yes
configure:9932: checking for string.h
configure:9932: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9932: $? = 0
configure:9932: result: yes
configure:9932: checking for memory.h
configure:9932: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9932: $? = 0
configure:9932: result: yes
configure:9932: checking for strings.h
configure:9932: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9932: $? = 0
configure:9932: result: yes
configure:9932: checking for inttypes.h
configure:9932: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9932: $? = 0
configure:9932: result: yes
configure:9932: checking for stdint.h
configure:9932: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9932: $? = 0
configure:9932: result: yes
configure:9932: checking for unistd.h
configure:9932: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9932: $? = 0
configure:9932: result: yes
configure:9946: checking for dlfcn.h
configure:9946: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:9946: $? = 0
configure:9946: result: yes
configure:10213: checking for objdir
configure:10228: result: .libs
configure:10492: checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions
configure:10510: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -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:10514: $? = 0
configure:10527: result: no
configure:10885: checking for x86_64-pc-linux-gnu-gcc option to produce PIC
configure:10892: result: -fPIC -DPIC
configure:10900: checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works
configure:10918: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  -fPIC -DPIC -DPIC conftest.c >&5
configure:10922: $? = 0
configure:10935: result: yes
configure:10964: checking if x86_64-pc-linux-gnu-gcc static flag -static works
configure:10992: result: yes
configure:11007: checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o
configure:11028: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  -o out/conftest2.o conftest.c >&5
configure:11032: $? = 0
configure:11054: result: yes
configure:11062: checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o
configure:11109: result: yes
configure:11142: 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:12401: result: yes
configure:12438: checking whether -lc should be explicitly linked in
configure:12446: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe  conftest.c >&5
configure:12449: $? = 0
configure:12464: 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:12467: $? = 0
configure:12481: result: no
configure:12641: checking dynamic linker characteristics
configure:13235: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe  -Wl,-O1 -Wl,--as-needed -Wl,-rpath -Wl,/foo conftest.c  >&5
configure:13235: $? = 0
configure:13472: result: GNU/Linux ld.so
configure:13594: checking how to hardcode library paths into programs
configure:13619: result: immediate
configure:14167: checking whether stripping libraries is possible
configure:14172: result: yes
configure:14207: checking if libtool supports shared libraries
configure:14209: result: yes
configure:14212: checking whether to build shared libraries
configure:14237: result: yes
configure:14240: checking whether to build static libraries
configure:14244: result: no
configure:14267: checking how to run the C++ preprocessor
configure:14294: x86_64-pc-linux-gnu-g++ -E  conftest.cpp
configure:14294: $? = 0
configure:14308: 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:14308: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "coot"
| #define PACKAGE_TARNAME "coot"
| #define PACKAGE_VERSION "0.8.2"
| #define PACKAGE_STRING "coot 0.8.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "coot"
| #define VERSION "0.8.2"
| #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:14333: result: x86_64-pc-linux-gnu-g++ -E
configure:14353: x86_64-pc-linux-gnu-g++ -E  conftest.cpp
configure:14353: $? = 0
configure:14367: 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:14367: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "coot"
| #define PACKAGE_TARNAME "coot"
| #define PACKAGE_VERSION "0.8.2"
| #define PACKAGE_STRING "coot 0.8.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "coot"
| #define VERSION "0.8.2"
| #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:14529: checking for ld used by x86_64-pc-linux-gnu-g++
configure:14596: result: /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
configure:14603: checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld
configure:14618: result: yes
configure:14673: 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:15746: result: yes
configure:15782: x86_64-pc-linux-gnu-g++ -c -O2 -march=core2 -ggdb -pipe  conftest.cpp >&5
configure:15785: $? = 0
configure:16266: checking for x86_64-pc-linux-gnu-g++ option to produce PIC
configure:16273: result: -fPIC -DPIC
configure:16281: checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works
configure:16299: x86_64-pc-linux-gnu-g++ -c -O2 -march=core2 -ggdb -pipe  -fPIC -DPIC -DPIC conftest.cpp >&5
configure:16303: $? = 0
configure:16316: result: yes
configure:16339: checking if x86_64-pc-linux-gnu-g++ static flag -static works
configure:16367: result: yes
configure:16379: checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o
configure:16400: x86_64-pc-linux-gnu-g++ -c -O2 -march=core2 -ggdb -pipe  -o out/conftest2.o conftest.cpp >&5
configure:16404: $? = 0
configure:16426: result: yes
configure:16431: checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o
configure:16478: result: yes
configure:16508: 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:16548: result: yes
configure:16689: checking dynamic linker characteristics
configure:17447: result: GNU/Linux ld.so
configure:17512: checking how to hardcode library paths into programs
configure:17537: result: immediate
configure:17601: checking which libtool initialization strategy to adopt
configure:17603: result: AC-PROG-LIBTOOL
configure:17616: checking what warning flags to pass to the C compiler
configure:17637: result: -Wall -Wunused
configure:17648: checking what language compliance flags to pass to the C compiler
configure:17664: result: 
configure:17681: checking what warning flags to pass to the C++ compiler
configure:17701: result: -Wall -Wno-unused
configure:17712: checking what language compliance flags to pass to the C++ compiler
configure:17728: result: 
configure:17739: checking sys/stdtypes.h usability
configure:17739: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe -Wall -Wunused   conftest.c >&5
conftest.c:56:26: fatal error: sys/stdtypes.h: No such file or directory
 #include <sys/stdtypes.h>
                          ^
compilation terminated.
configure:17739: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "coot"
| #define PACKAGE_TARNAME "coot"
| #define PACKAGE_VERSION "0.8.2"
| #define PACKAGE_STRING "coot 0.8.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "coot"
| #define VERSION "0.8.2"
| #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 <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 <sys/stdtypes.h>
configure:17739: result: no
configure:17739: checking sys/stdtypes.h presence
configure:17739: x86_64-pc-linux-gnu-gcc -E  conftest.c
conftest.c:23:26: fatal error: sys/stdtypes.h: No such file or directory
 #include <sys/stdtypes.h>
                          ^
compilation terminated.
configure:17739: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "coot"
| #define PACKAGE_TARNAME "coot"
| #define PACKAGE_VERSION "0.8.2"
| #define PACKAGE_STRING "coot 0.8.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "coot"
| #define VERSION "0.8.2"
| #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 <sys/stdtypes.h>
configure:17739: result: no
configure:17739: checking for sys/stdtypes.h
configure:17739: result: no
configure:17754: checking for OpenMP flag of C compiler
configure:17794: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wunused  -fopenmp  -Wl,-O1 -Wl,--as-needed conftest.c  >&5
conftest.c: In function 'main':
conftest.c:31:10: warning: variable 'arr' set but not used [-Wunused-but-set-variable]
   int i, arr[N];
          ^
configure:17794: $? = 0
configure:17803: result: -fopenmp
configure:17854: checking for x86_64-pc-linux-gnu-pkg-config
configure:17872: found /usr/bin/x86_64-pc-linux-gnu-pkg-config
configure:17884: result: /usr/bin/x86_64-pc-linux-gnu-pkg-config
configure:17952: checking pkg-config is at least version 0.9.0
configure:17955: result: yes
configure:17965: checking for GLIB
configure:17972: $PKG_CONFIG --exists --print-errors "glib-2.0"
configure:17975: $? = 0
configure:17989: $PKG_CONFIG --exists --print-errors "glib-2.0"
configure:17992: $? = 0
configure:18050: result: yes
configure:18058: checking if this is MINGW on Windows
configure:18093: result: no
configure:18307: checking for SQLite3
configure:18320: result: yes
configure:18456: checking for mmdb2
configure:18467: result: yes
configure:18496: x86_64-pc-linux-gnu-g++ -c -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused    conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:28:37: error: 'class mmdb::Link' has no member named 'dist'
 mmdb::Link *l; mmdb::realtype ll=l->dist
                                     ^
configure:18496: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "coot"
| #define PACKAGE_TARNAME "coot"
| #define PACKAGE_VERSION "0.8.2"
| #define PACKAGE_STRING "coot 0.8.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "coot"
| #define VERSION "0.8.2"
| #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_OPENMP 1
| /* end confdefs.h.  */
| #include <mmdb2/mmdb_manager.h>
| int
| main ()
| {
| mmdb::Link *l; mmdb::realtype ll=l->dist
|   ;
|   return 0;
| }
configure:18523: checking for ssm
configure:18536: result: yes
configure:18605: result: no
configure:18632: checking for prefixed single-precision FFTW2 (sfftw.h)
configure:18662: x86_64-pc-linux-gnu-g++ -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused    -Wl,-O1 -Wl,--as-needed conftest.cpp  -lsrfftw -lsfftw  >&5
configure:18662: $? = 0
configure:18669: result: yes
configure:18722: checking for Clipper
configure:18733: result: yes
configure:19025: checking for gsl-config
configure:19043: found /usr/bin/gsl-config
configure:19056: result: /usr/bin/gsl-config
configure:19065: checking for GSL - version >= 1.3
configure:19159: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wunused  -I/usr/include   -Wl,-O1 -Wl,--as-needed conftest.c  -L/usr/lib64 -lgsl -lgslcblas -lm >&5
configure:19159: $? = 0
configure:19159: ./conftest
configure:19159: $? = 0
configure:19173: result: yes
configure:19242: checking for GTK
configure:19249: $PKG_CONFIG --exists --print-errors "gtk+-2.0 >= 2.4.12"
configure:19252: $? = 0
configure:19266: $PKG_CONFIG --exists --print-errors "gtk+-2.0 >= 2.4.12"
configure:19269: $? = 0
configure:19327: result: yes
configure:19333: checking for GNOME_CANVAS
configure:19340: $PKG_CONFIG --exists --print-errors "libgnomecanvas-2.0 >= 0.15.0"
configure:19343: $? = 0
configure:19357: $PKG_CONFIG --exists --print-errors "libgnomecanvas-2.0 >= 0.15.0"
configure:19360: $? = 0
configure:19418: result: yes
configure:19452: checking for pkg-config
configure:19483: result: /usr/bin/x86_64-pc-linux-gnu-pkg-config
configure:19505: checking for GtkGLExt - version >= 1.0.0
configure:19624: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wunused  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2   -Wl,-O1 -Wl,--as-needed conftest.c -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGL -lGLU -lGL -lXmu -lXt -lSM -lICE -lgdk-x11-2.0 -lpangox-1.0 -lX11 -Wl,--export-dynamic -lgmodule-2.0 -pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype  >&5
configure:19624: $? = 0
configure:19624: ./conftest
configure:19624: $? = 0
configure:19638: result: yes (version 1.2.0)
configure:19750: checking for glLineWidth in -lGL
configure:19775: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wunused    -Wl,-O1 -Wl,--as-needed conftest.c -lGL   >&5
configure:19775: $? = 0
configure:19784: result: yes
configure:19811: checking for GLUT
configure:19941: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wunused     -Wl,-O1 -Wl,--as-needed conftest.c  -lglut  -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype >&5
configure:19941: $? = 0
configure:19949: result: yes
configure:19977: checking for Python
configure:20117: checking Python.h usability
configure:20117: x86_64-pc-linux-gnu-gcc -c -O2 -march=core2 -ggdb -pipe -Wall -Wunused    -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 conftest.c >&5
In file included from /usr/include/python2.7/Python.h:8:0,
                 from conftest.c:58:
/usr/include/python2.7/pyconfig.h:1193:0: warning: "_POSIX_C_SOURCE" redefined
 #define _POSIX_C_SOURCE 200112L
 ^
In file included from /usr/include/stdio.h:27:0,
                 from conftest.c:25:
/usr/include/features.h:225:0: note: this is the location of the previous definition
 # define _POSIX_C_SOURCE 200809L
 ^
configure:20117: $? = 0
configure:20117: result: yes
configure:20117: checking Python.h presence
configure:20117: x86_64-pc-linux-gnu-gcc -E   -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 conftest.c
configure:20117: $? = 0
configure:20117: result: yes
configure:20117: checking for Python.h
configure:20117: result: yes
configure:20153: checking for PYGTK
configure:20160: $PKG_CONFIG --exists --print-errors "pygtk-2.0"
configure:20163: $? = 0
configure:20177: $PKG_CONFIG --exists --print-errors "pygtk-2.0"
configure:20180: $? = 0
configure:20218: result: yes
configure:20326: checking for python version
configure:20333: result: 2.7
configure:20350: checking for python platform
configure:20357: result: linux2
configure:20364: checking for python script directory
configure:20396: result: ${prefix}/lib64/python2.7/site-packages
configure:20405: checking for python extension module directory
configure:20437: result: ${exec_prefix}/lib64/python2.7/site-packages
configure:20484: checking for guile-gtk
configure:20515: result: 
configure:20570: checking for boostlib >= 1.20.0
configure:20650: x86_64-pc-linux-gnu-g++ -c -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused    -I/usr/include conftest.cpp >&5
configure:20650: $? = 0
configure:20652: result: yes
configure:20847: checking for python2.7
configure:20877: result: /usr/bin/python2.7
configure:20894: checking for a version of Python >= '2.1.0'
configure:20920: result: yes
configure:20951: checking for the distutils Python package
configure:20955: result: yes
configure:20969: checking for Python include path
configure:20985: result: -I/usr/include/python2.7
configure:20992: checking for Python library path
configure:21073: result: -L/usr/lib64 -lpython2.7
configure:21080: checking for Python site-packages path
configure:21086: result: /usr/lib64/python2.7/site-packages
configure:21093: checking python extra libraries
configure:21100: result: -lpthread -ldl  -lutil -lm
configure:21107: checking python extra linking flags
configure:21115: result: -Xlinker -export-dynamic
configure:21122: checking consistency of all components of python development environment
configure:21148: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wunused    -I/usr/include/python2.7 -Wl,-O1 -Wl,--as-needed conftest.c  -L/usr/lib64 -lpython2.7 -Xlinker -export-dynamic -lpthread -ldl  -lutil -lm >&5
configure:21148: $? = 0
configure:21165: result: yes
configure:21190: checking whether the Boost::Python library is available
configure:21223: x86_64-pc-linux-gnu-g++ -c -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -I/usr/include -I/usr/include/python2.7   conftest.cpp >&5
configure:21223: $? = 0
configure:21238: result: yes
configure:21257: checking for exit in -lboost_python-2.7-mt
configure:21282: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wunused    -Wl,-O1 -Wl,--as-needed conftest.c -lboost_python-2.7-mt -L/usr/lib64 -lpython2.7  >&5
conftest.c:35:6: warning: conflicting types for built-in function 'exit'
 char exit ();
      ^
configure:21282: $? = 0
configure:21292: result: yes
configure:21337: checking libglade
configure:21380: x86_64-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wunused  -I/usr/include/libglade-2.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_LIBGLADE   -Wl,-O1 -Wl,--as-needed conftest.c  -lglade-2.0 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype >&5
conftest.c: In function 'main':
conftest.c:32:11: warning: unused variable 'xml' [-Wunused-variable]
 GladeXML *xml = glade_xml_new("x",NULL,NULL);
           ^
configure:21380: $? = 0
configure:21391: result: yes
configure:21471: checking for Goocanvas
configure:21497: x86_64-pc-linux-gnu-g++ -o conftest -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2   -Wl,-O1 -Wl,--as-needed conftest.cpp  -L/usr/lib -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype >&5
configure:21497: $? = 0
configure:21511: result: yes
configure:21647: checking for curl >= 7.9.7
configure:21658: result: 7.50.1
configure:21693: result: Gentoo-Linux-python2.7-gtk2
configure:21852: checking that generated files are newer than configure
configure:21858: result: done
configure:21913: creating ./config.status

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by coot config.status 0.8.2, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  CONFIG_FILES    = 
  CONFIG_HEADERS  = 
  CONFIG_LINKS    = 
  CONFIG_COMMANDS = 
  $ ./config.status 

on srv5

config.status:1236: creating Makefile
config.status:1236: creating macros/Makefile
config.status:1236: creating pdb-templates/Makefile
config.status:1236: creating scheme/Makefile
config.status:1236: creating python/Makefile
config.status:1236: creating compat/Makefile
config.status:1236: creating utils/Makefile
config.status:1236: creating coot-utils/Makefile
config.status:1236: creating protein_db/Makefile
config.status:1236: creating ccp4mg-utils/Makefile
config.status:1236: creating coords/Makefile
config.status:1236: creating db-main/Makefile
config.status:1236: creating density-contour/Makefile
config.status:1236: creating surface/Makefile
config.status:1236: creating coot-surface/Makefile
config.status:1236: creating angles/Makefile
config.status:1236: creating mini-mol/Makefile
config.status:1236: creating skeleton/Makefile
config.status:1236: creating ligand/Makefile
config.status:1236: creating geometry/Makefile
config.status:1236: creating ideal/Makefile
config.status:1236: creating build/Makefile
config.status:1236: creating analysis/Makefile
config.status:1236: creating high-res/Makefile
config.status:1236: creating tw/Makefile
config.status:1236: creating cootaneer/Makefile
config.status:1236: creating cootilus/Makefile
config.status:1236: creating greg-tests/Makefile
config.status:1236: creating python-tests/Makefile
config.status:1236: creating lidia-core/Makefile
config.status:1236: creating libgtkgraph/Makefile
config.status:1236: creating goograph/Makefile
config.status:1236: creating lbg/Makefile
config.status:1236: creating doc/Makefile
config.status:1236: creating src/Makefile
config.status:1236: creating src/coot
config.status:1236: creating python/coot_load_modules.py
config.status:1236: creating data/Makefile
config.status:1236: creating pixmaps/Makefile
config.status:1236: creating pixmaps/icons/Makefile
config.status:1236: creating rama-data/Makefile
config.status:1236: creating pyrogen/Makefile
config.status:1236: creating pyrogen/pyrogen
config.status:1236: creating auxil/Makefile
config.status:1236: creating auxil/catcheck/Makefile
config.status:1236: creating auxil/rama/Makefile
config.status:1236: creating auxil/sec-str/Makefile
config.status:1236: creating auxil/strand-analysis/Makefile
config.status:1236: creating auxil/vectors/Makefile
config.status:1236: creating rcrane/Makefile
config.status:1408: executing depfiles commands
config.status:1408: executing libtool commands

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

ac_cv_boost_python=yes
ac_cv_build=x86_64-pc-linux-gnu
ac_cv_build_alias=x86_64-pc-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CCP4_CFLAGS_set=
ac_cv_env_CCP4_CFLAGS_value=
ac_cv_env_CCP4_LIBS_set=
ac_cv_env_CCP4_LIBS_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-O2 -march=core2 -ggdb -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='-O2 -march=core2 -ggdb -pipe'
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_GLIB_CFLAGS_set=
ac_cv_env_GLIB_CFLAGS_value=
ac_cv_env_GLIB_LIBS_set=
ac_cv_env_GLIB_LIBS_value=
ac_cv_env_GNOME_CANVAS_CFLAGS_set=
ac_cv_env_GNOME_CANVAS_CFLAGS_value=
ac_cv_env_GNOME_CANVAS_LIBS_set=
ac_cv_env_GNOME_CANVAS_LIBS_value=
ac_cv_env_GTK_CFLAGS_set=
ac_cv_env_GTK_CFLAGS_value=
ac_cv_env_GTK_LIBS_set=
ac_cv_env_GTK_LIBS_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_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=/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/temp/python2.7/pkgconfig
ac_cv_env_PKG_CONFIG_set=
ac_cv_env_PKG_CONFIG_value=
ac_cv_env_PYGTK_CFLAGS_set=
ac_cv_env_PYGTK_CFLAGS_value=
ac_cv_env_PYGTK_LIBS_set=
ac_cv_env_PYGTK_LIBS_value=
ac_cv_env_PYTHON_VERSION_set=
ac_cv_env_PYTHON_VERSION_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_header_Python_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_stdtypes_h=no
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-pc-linux-gnu
ac_cv_lib_GL_glLineWidth=yes
ac_cv_lib_boost_python_2_7_mt___exit=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_GSL_CONFIG=/usr/bin/gsl-config
ac_cv_path_PKG_CONFIG=/usr/bin/x86_64-pc-linux-gnu-pkg-config
ac_cv_path_PYTHON=/usr/bin/python2.7
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_strerror='none required'
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
am_cv_prog_cc_stdc=
am_cv_python_platform=linux2
am_cv_python_pyexecdir='${exec_prefix}/lib64/python2.7/site-packages'
am_cv_python_pythondir='${prefix}/lib64/python2.7/site-packages'
am_cv_python_version=2.7
ax_cv_c_openmp=-fopenmp
coot_cv_curl_vers=7.50.1
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=no
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_GLIB_CFLAGS='-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include'
pkg_cv_GLIB_LIBS=-lglib-2.0
pkg_cv_GNOME_CANVAS_CFLAGS='-pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2'
pkg_cv_GNOME_CANVAS_LIBS='-lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype'
pkg_cv_GTK_CFLAGS='-pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2'
pkg_cv_GTK_LIBS='-lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype'
pkg_cv_PYGTK_CFLAGS='-pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2'
pkg_cv_PYGTK_LIBS='-lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype'

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

ACLOCAL='${SHELL} /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/missing aclocal-1.15 -I macros'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE='#'
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AR='x86_64-pc-linux-gnu-ar'
AUTOCONF='${SHELL} /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/missing autoconf'
AUTOHEADER='${SHELL} /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/missing autoheader'
AUTOMAKE='${SHELL} /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/missing automake-1.15'
AWK='gawk'
BOOST_CPPFLAGS='-I/usr/include'
BOOST_LDFLAGS='-L/usr/lib64'
BOOST_PYTHON_LIB='boost_python-2.7-mt'
CC='x86_64-pc-linux-gnu-gcc'
CCDEPMODE='depmode=none'
CCP4SRS_CXXFLAGS=''
CCP4SRS_LIBS=''
CCP4_CFLAGS=''
CCP4_LIBS=''
CFLAGS='-O2 -march=core2 -ggdb -pipe -Wall -Wunused '
CLIPPER_CXXFLAGS=''
CLIPPER_LIBS='-lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2'
COOT_BUILD_INFO_STRING=''
COOT_GSL_FLAGS='-DHAVE_GSL'
COOT_OPENGL_LIBS='-lGL'
COOT_STDTYPES='-DHAVE_SYS_STDTYPES_H=0'
COOT_SYS_BUILD_TYPE='Gentoo-Linux-python2.7-gtk2'
COOT_USE_GUILE=''
COOT_USE_PYTHON_FALSE='#'
COOT_USE_PYTHON_TRUE=''
COOT_WINDOWS_CFLAGS=''
COOT_WINDOWS_LDFLAGS=''
CPP='x86_64-pc-linux-gnu-gcc -E'
CPPFLAGS=' '
CURL_CFLAGS=''
CURL_LIBS='-lcurl -lidn -lrtmp -lz -lssl -lcrypto -lnettle -lgnutls -llber -lldap -lz'
CXX='x86_64-pc-linux-gnu-g++'
CXXCPP='x86_64-pc-linux-gnu-g++ -E'
CXXDEPMODE='depmode=none'
CXXFLAGS='-O2 -march=core2 -ggdb -pipe -Wall -Wno-unused '
CYGPATH_W='echo'
DEFS='-DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/'
DEPDIR='.deps'
DLLTOOL='false'
DSYMUTIL=''
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
ENHANCED_LIGAND_TOOLS_CFLAGS=''
EXEEXT=''
EXPORT_DYNAMIC_FLAG_SPEC='-Wl,--export-dynamic'
FFTW2_CPPFLAGS=''
FFTW2_LIBS=' -lsrfftw -lsfftw'
FGREP='/bin/grep -F'
GLIB_CFLAGS='-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include'
GLIB_LIBS='-lglib-2.0'
GLOB_CFLAGS=''
GLOB_LIBS=''
GLUT_CFLAGS=''
GLUT_LIBS='-lglut  -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype'
GNOME_CANVAS_CFLAGS='-DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2'
GNOME_CANVAS_LIBS='-lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype'
GOOCANVAS_CFLAGS='-DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0'
GOOCANVAS_LIBS='-L/usr/lib -lgoocanvas'
GREP='/bin/grep'
GSL_CFLAGS='-I/usr/include'
GSL_CONFIG='/usr/bin/gsl-config'
GSL_LIBS='-L/usr/lib64 -lgsl -lgslcblas -lm'
GTKGLEXT_CFLAGS='-pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2'
GTKGLEXT_LIBS='-lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGL -lGLU -lGL -lXmu -lXt -lSM -lICE -lgdk-x11-2.0 -lpangox-1.0 -lX11 -Wl,--export-dynamic -lgmodule-2.0 -pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype'
GTK_CFLAGS='-pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2'
GTK_LIBS='-lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype'
GUILE=''
GUILE_CFLAGS=''
GUILE_CONFIG=''
GUILE_GTK_CFLAGS=''
GUILE_GTK_LIBS='-lguilegtk-2.0'
GUILE_LDFLAGS=''
GUILE_TOOLS=''
GUILE_VERSION=''
INSIDE_GNOME_COMMON_FALSE=''
INSIDE_GNOME_COMMON_TRUE='#'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LD='/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64'
LDFLAGS='-Wl,-O1 -Wl,--as-needed'
LIBGLADE_CFLAGS='-I/usr/include/libglade-2.0'
LIBGLADE_LIBS='-lglade-2.0'
LIBOBJS=''
LIBPNG_CFLAGS='-DUSE_LIBPNG'
LIBPNG_LIBS='-lpng'
LIBS=''
LIBSSM_CXXFLAGS=' -DHAVE_SSMLIB'
LIBSSM_LIBS='-lssm -lmmdb2'
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LIPO=''
LN_S='ln -s'
LTLIBOBJS=''
LT_SYS_LIBRARY_PATH=''
L_BOOST_PYTHON=''
MAKEINFO='${SHELL} /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/missing makeinfo'
MAKE_COOTRC_CMD='sed -e '\''s/\#GTK2 //'\'' '
MAKE_ENHANCED_LIGAND_TOOLS_FALSE=''
MAKE_ENHANCED_LIGAND_TOOLS_TRUE='#'
MANIFEST_TOOL=':'
MKDIR_P='/bin/mkdir -p'
MMDB_CXXFLAGS=''
MMDB_LIBS='-lmmdb2'
MYSQL_CFLAGS=''
MYSQL_LIBS=''
NM='/usr/bin/x86_64-pc-linux-gnu-nm -B'
NMEDIT=''
OBJDUMP='x86_64-pc-linux-gnu-objdump'
OBJEXT='o'
OS_WIN32_FALSE=''
OS_WIN32_TRUE='#'
OTOOL64=''
OTOOL=''
PACKAGE='coot'
PACKAGE_BUGREPORT=''
PACKAGE_NAME='coot'
PACKAGE_STRING='coot 0.8.2'
PACKAGE_TARNAME='coot'
PACKAGE_URL=''
PACKAGE_VERSION='0.8.2'
PATH_SEPARATOR=':'
PKG_CONFIG='/usr/bin/x86_64-pc-linux-gnu-pkg-config'
PKG_CONFIG_LIBDIR=''
PKG_CONFIG_PATH='/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/temp/python2.7/pkgconfig'
PYGTK_CFLAGS='-pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2'
PYGTK_LIBS='-lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype'
PYTHON='/usr/bin/python2.7'
PYTHON_CFLAGS='-DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK'
PYTHON_CPPFLAGS='-I/usr/include/python2.7'
PYTHON_EXEC_PREFIX='${exec_prefix}'
PYTHON_EXTRA_LDFLAGS='-Xlinker -export-dynamic'
PYTHON_EXTRA_LIBS='-lpthread -ldl  -lutil -lm'
PYTHON_LDFLAGS='-L/usr/lib64 -lpython2.7'
PYTHON_LIBS='-lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil'
PYTHON_PLATFORM='linux2'
PYTHON_PREFIX='${prefix}'
PYTHON_SITE_PKG='/usr/lib64/python2.7/site-packages'
PYTHON_VERSION='2.7'
RANLIB='x86_64-pc-linux-gnu-ranlib'
RDKIT_CXXFLAGS=''
RDKIT_LIBS=''
SED='/bin/sed'
SET_MAKE=''
SHARED_LDFLAGS=''
SHELL='/bin/sh'
SQLITE3_CFLAGS='-DUSE_SQLITE3 '
SQLITE3_LIBS='-lsqlite3'
STRIP='x86_64-pc-linux-gnu-strip'
SWIG_FLAGS='-DCOOT_USE_GTK2_INTERFACE'
USE_GUILE_GTK='-DUSE_GUILE_GTK'
USE_LIBCURL='-DUSE_LIBCURL'
USING_GTK2_VERSION_FALSE='#'
USING_GTK2_VERSION_TRUE=''
VERSION='0.8.2'
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=''
am__leading_dot='.'
am__nodep=''
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-pc-linux-gnu'
build_alias='x86_64-pc-linux-gnu'
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='pc'
cflags_set='yes'
cxxflags_set='yes'
datadir='/usr/share'
datarootdir='${prefix}/share'
docdir='/usr/share/doc/coot-0.8.2-r1'
dvidir='${docdir}'
exec_prefix='${prefix}'
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='${SHELL} /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/install-sh'
libdir='/usr/lib64'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='/var/lib'
mandir='/usr/share/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
pkgpyexecdir='${pyexecdir}/coot'
pkgpythondir='${pythondir}/coot'
prefix='/usr'
program_transform_name='s,x,x,'
psdir='${docdir}'
pyexecdir='${exec_prefix}/lib64/python2.7/site-packages'
pythondir='${prefix}/lib64/python2.7/site-packages'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='/etc'
target_alias=''

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

/* confdefs.h */
#define PACKAGE_NAME "coot"
#define PACKAGE_TARNAME "coot"
#define PACKAGE_VERSION "0.8.2"
#define PACKAGE_STRING "coot 0.8.2"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#define PACKAGE "coot"
#define VERSION "0.8.2"
#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_OPENMP 1
#define FFTW2_PREFIX_S 1
#define HAVE_BOOST /**/
#define HAVE_PYTHON "2.7"
#define HAVE_BOOST_PYTHON /**/

configure: exit 0