diff --git a/config.log b/config.log
index fe797562..d6313eec 100644
--- a/config.log
+++ b/config.log
@@ -4,61 +4,38 @@ running configure, to aid debugging if configure makes a mistake.
 It was created by Gubbins configure 0.1, which was
 generated by GNU Autoconf 2.61.  Invocation command line was
 
-  $ ./configure 
+  $ ./configure --no-create --no-recursion
 
 ## --------- ##
 ## Platform. ##
 ## --------- ##
 
-hostname = mib100408i.local
-uname -m = i386
-uname -r = 9.8.0
-uname -s = Darwin
-uname -v = Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386
+hostname = SillyFace
+uname -m = x86_64
+uname -r = 3.5.3-1.fc17.x86_64
+uname -s = Linux
+uname -v = #1 SMP Wed Aug 29 18:46:34 UTC 2012
 
-/usr/bin/uname -p = i386
+/usr/bin/uname -p = x86_64
 /bin/uname -X     = unknown
 
-/bin/arch              = unknown
+/bin/arch              = x86_64
 /usr/bin/arch -k       = unknown
 /usr/convex/getsysinfo = unknown
-/usr/bin/hostinfo      = Mach kernel version:
-	 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386
-Kernel configured for up to 2 processors.
-2 processors are physically available.
-2 processors are logically available.
-Processor type: i486 (Intel 80486)
-Processors active: 0 1
-Primary memory available: 4.00 gigabytes
-Default processor set: 99 tasks, 444 threads, 2 processors
-Load average: 1.14, Mach factor: 1.13
+/usr/bin/hostinfo      = unknown
 /bin/machine           = unknown
 /usr/bin/oslevel       = unknown
 /bin/universe          = unknown
 
-PATH: /usr/local/share/python
-PATH: /usr/local/Cellar/python/2.7.2/bin
-PATH: /usr/local/lib/python2.7/site-packages
-PATH: /Users/ap13/perl5/perlbrew/bin
-PATH: /Users/ap13/.rvm/gems/ruby-1.9.3-p125/bin
-PATH: /Users/ap13/.rvm/gems/ruby-1.9.3-p125@global/bin
-PATH: /Users/ap13/.rvm/rubies/ruby-1.9.3-p125/bin
-PATH: /Users/ap13/.rvm/bin
 PATH: /usr/local/bin
-PATH: /usr/local/mysql/bin
 PATH: /usr/bin
 PATH: /bin
+PATH: /usr/local/sbin
 PATH: /usr/sbin
-PATH: /sbin
-PATH: /usr/local/bin
-PATH: /usr/X11/bin
-PATH: /opt/local/bin
-PATH: /usr/local/git/bin
-PATH: /Library/instantclient
-PATH: /sw/bin
-PATH: /usr/local/mysql-5.1.38-osx10.5-x86/bin
-PATH: ~/bin
-PATH: /Library/instantclient
+PATH: /home/aidan/.cabal/bin
+PATH: /home/aidan/bin
+PATH: /home/aidan/AndroidSDK/android-sdk-linux_x86/
+PATH: /home/aidan/AndroidSDK/android-sdk-linux_x86/tools
 
 
 ## ----------- ##
@@ -70,22 +47,16 @@ configure:2031: result: /usr/bin/install -c
 configure:2042: checking whether build environment is sane
 configure:2085: result: yes
 configure:2113: checking for a thread-safe mkdir -p
-configure:2152: result: ./install-sh -c -d
+configure:2152: result: /usr/bin/mkdir -p
 configure:2165: checking for gawk
-configure:2195: result: no
-configure:2165: checking for mawk
-configure:2195: result: no
-configure:2165: checking for nawk
-configure:2195: result: no
-configure:2165: checking for awk
-configure:2181: found /usr/bin/awk
-configure:2192: result: awk
+configure:2181: found /usr/bin/gawk
+configure:2192: result: gawk
 configure:2203: checking whether make sets $(MAKE)
 configure:2224: result: yes
 configure:2494: checking build system type
-configure:2512: result: i386-apple-darwin9.8.0
+configure:2512: result: x86_64-unknown-linux-gnu
 configure:2534: checking host system type
-configure:2549: result: i386-apple-darwin9.8.0
+configure:2549: result: x86_64-unknown-linux-gnu
 configure:2583: checking for style of include used by make
 configure:2611: result: GNU
 configure:2681: checking for gcc
@@ -93,22 +64,26 @@ configure:2697: found /usr/bin/gcc
 configure:2708: result: gcc
 configure:2946: checking for C compiler version
 configure:2953: gcc --version >&5
-i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5493)
-Copyright (C) 2005 Free Software Foundation, Inc.
+gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
+Copyright (C) 2012 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:2956: $? = 0
 configure:2963: gcc -v >&5
 Using built-in specs.
-Target: i686-apple-darwin9
-Configured with: /var/tmp/gcc/gcc-5493~1/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9
+COLLECT_GCC=gcc
+COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.7.0/lto-wrapper
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --disable-build-with-cxx --disable-build-poststage1-with-cxx --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
 Thread model: posix
-gcc version 4.0.1 (Apple Inc. build 5493)
+gcc version 4.7.0 20120507 (Red Hat 4.7.0-5) (GCC) 
 configure:2966: $? = 0
 configure:2973: gcc -V >&5
-gcc-4.0: argument to `-V' is missing
-configure:2976: $? = 1
+gcc: error: unrecognized command line option '-V'
+gcc: fatal error: no input files
+compilation terminated.
+configure:2976: $? = 4
 configure:2999: checking for C compiler default output file name
 configure:3026: gcc    conftest.c  >&5
 configure:3029: $? = 0
@@ -148,22 +123,25 @@ configure:3791: result: /usr/bin/grep
 configure:3796: checking for egrep
 configure:3874: result: /usr/bin/grep -E
 configure:3890: checking for ld used by gcc
-configure:3957: result: /usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld
-configure:3966: checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) is GNU ld
-configure:3981: result: no
-configure:3986: checking for /usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld option to reload object files
+configure:3957: result: /usr/bin/ld
+configure:3966: checking if the linker (/usr/bin/ld) is GNU ld
+configure:3981: result: yes
+configure:3986: checking for /usr/bin/ld option to reload object files
 configure:3993: result: -r
 configure:4011: checking for BSD-compatible nm
-configure:4060: result: /usr/bin/nm -p
+configure:4060: result: /usr/bin/nm -B
 configure:4064: checking whether ln -s works
 configure:4068: result: yes
 configure:4075: checking how to recognise dependent libraries
 configure:4251: result: pass_all
+configure:4339: gcc -c -g -O2  conftest.c >&5
+configure:4342: $? = 0
 configure:4485: checking how to run the C preprocessor
 configure:4525: gcc -E  conftest.c
 configure:4531: $? = 0
 configure:4562: gcc -E  conftest.c
-conftest.c:10:28: error: ac_nonexistent.h: No such file or directory
+conftest.c:10:28: fatal error: ac_nonexistent.h: No such file or directory
+compilation terminated.
 configure:4568: $? = 1
 configure: failed program was:
 | /* confdefs.h.  */
@@ -180,7 +158,8 @@ configure:4601: result: gcc -E
 configure:4630: gcc -E  conftest.c
 configure:4636: $? = 0
 configure:4667: gcc -E  conftest.c
-conftest.c:10:28: error: ac_nonexistent.h: No such file or directory
+conftest.c:10:28: fatal error: ac_nonexistent.h: No such file or directory
+compilation terminated.
 configure:4673: $? = 1
 configure: failed program was:
 | /* confdefs.h.  */
@@ -252,22 +231,26 @@ configure:5168: found /usr/bin/g++
 configure:5179: result: g++
 configure:5210: checking for C++ compiler version
 configure:5217: g++ --version >&5
-i686-apple-darwin9-g++-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5493)
-Copyright (C) 2005 Free Software Foundation, Inc.
+g++ (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
+Copyright (C) 2012 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:5220: $? = 0
 configure:5227: g++ -v >&5
 Using built-in specs.
-Target: i686-apple-darwin9
-Configured with: /var/tmp/gcc/gcc-5493~1/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9
+COLLECT_GCC=g++
+COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.7.0/lto-wrapper
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --disable-build-with-cxx --disable-build-poststage1-with-cxx --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
 Thread model: posix
-gcc version 4.0.1 (Apple Inc. build 5493)
+gcc version 4.7.0 20120507 (Red Hat 4.7.0-5) (GCC) 
 configure:5230: $? = 0
 configure:5237: g++ -V >&5
-g++-4.0: argument to `-V' is missing
-configure:5240: $? = 1
+g++: error: unrecognized command line option '-V'
+g++: fatal error: no input files
+compilation terminated.
+configure:5240: $? = 4
 configure:5243: checking whether we are using the GNU C++ compiler
 configure:5272: g++ -c   conftest.cpp >&5
 configure:5278: $? = 0
@@ -282,7 +265,8 @@ configure:5576: checking how to run the C++ preprocessor
 configure:5612: g++ -E  conftest.cpp
 configure:5618: $? = 0
 configure:5649: g++ -E  conftest.cpp
-conftest.cpp:21:28: error: ac_nonexistent.h: No such file or directory
+conftest.cpp:21:28: fatal error: ac_nonexistent.h: No such file or directory
+compilation terminated.
 configure:5655: $? = 1
 configure: failed program was:
 | /* confdefs.h.  */
@@ -310,7 +294,8 @@ configure:5688: result: g++ -E
 configure:5717: g++ -E  conftest.cpp
 configure:5723: $? = 0
 configure:5754: g++ -E  conftest.cpp
-conftest.cpp:21:28: error: ac_nonexistent.h: No such file or directory
+conftest.cpp:21:28: fatal error: ac_nonexistent.h: No such file or directory
+compilation terminated.
 configure:5760: $? = 1
 configure: failed program was:
 | /* confdefs.h.  */
@@ -363,48 +348,64 @@ configure:5883: result: no
 configure:5853: checking for epcf90
 configure:5883: result: no
 configure:5853: checking for gfortran
-configure:5869: found /usr/local/bin/gfortran
-configure:5880: result: gfortran
+configure:5883: result: no
+configure:5853: checking for g95
+configure:5883: result: no
+configure:5853: checking for xlf95
+configure:5883: result: no
+configure:5853: checking for f95
+configure:5883: result: no
+configure:5853: checking for fort
+configure:5883: result: no
+configure:5853: checking for ifort
+configure:5883: result: no
+configure:5853: checking for ifc
+configure:5883: result: no
+configure:5853: checking for efc
+configure:5883: result: no
+configure:5853: checking for pgf95
+configure:5883: result: no
+configure:5853: checking for lf95
+configure:5883: result: no
+configure:5853: checking for ftn
+configure:5883: result: no
 configure:5910: checking for Fortran 77 compiler version
-configure:5917: gfortran --version >&5
-GNU Fortran (GCC) 4.2.3
-Copyright (C) 2007 Free Software Foundation, Inc.
-
-GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
-You may redistribute copies of GNU Fortran
-under the terms of the GNU General Public License.
-For more information about these matters, see the file named COPYING
-
-configure:5920: $? = 0
-configure:5927: gfortran -v >&5
-Using built-in specs.
-Target: i686-apple-darwin8
-Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/local --mandir=/share/man --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --build=i686-apple-darwin8 --host=i686-apple-darwin8 --target=i686-apple-darwin8 --enable-languages=fortran
-Thread model: posix
-gcc version 4.2.3
-configure:5930: $? = 0
-configure:5937: gfortran -V >&5
-gfortran: argument to `-V' is missing
-configure:5940: $? = 1
+configure:5917:  --version >&5
+./configure: line 5918: --version: command not found
+configure:5920: $? = 127
+configure:5927:  -v >&5
+./configure: line 5928: -v: command not found
+configure:5930: $? = 127
+configure:5937:  -V >&5
+./configure: line 5938: -V: command not found
+configure:5940: $? = 127
 configure:5948: checking whether we are using the GNU Fortran 77 compiler
-configure:5967: gfortran -c  conftest.F >&5
-configure:5973: $? = 0
-configure:5990: result: yes
-configure:5996: checking whether gfortran accepts -g
-configure:6013: gfortran -c -g conftest.f >&5
-configure:6019: $? = 0
-configure:6035: result: yes
+configure:5967:  -c  conftest.F >&5
+./configure: line 5968: -c: command not found
+configure:5973: $? = 127
+configure: failed program was:
+|       program main
+| #ifndef __GNUC__
+|        choke me
+| #endif
+| 
+|       end
+configure:5990: result: no
+configure:5996: checking whether  accepts -g
+configure:6013:  -c -g conftest.f >&5
+./configure: line 6014: -c: command not found
+configure:6019: $? = 127
+configure: failed program was:
+|       program main
+| 
+|       end
+configure:6035: result: no
 configure:6065: checking the maximum length of command line arguments
-configure:6174: result: 196608
-configure:6185: checking command to parse /usr/bin/nm -p output from gcc object
+configure:6174: result: 32768
+configure:6185: checking command to parse /usr/bin/nm -B output from gcc object
 configure:6290: gcc -c -g -O2  conftest.c >&5
 configure:6293: $? = 0
-configure:6297: /usr/bin/nm -p conftest.o \| sed -n -e 's/^.*[ 	]\([BCDEGRST][BCDEGRST]*\)[ 	][ 	]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
-configure:6300: $? = 0
-cannot find nm_test_var in conftest.nm
-configure:6290: gcc -c -g -O2  conftest.c >&5
-configure:6293: $? = 0
-configure:6297: /usr/bin/nm -p conftest.o \| sed -n -e 's/^.*[ 	]\([BCDEGRST][BCDEGRST]*\)[ 	][ 	]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p' \> conftest.nm
+configure:6297: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ 	]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ 	][ 	]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
 configure:6300: $? = 0
 configure:6352: gcc -o conftest -g -O2   conftest.c conftstm.o >&5
 configure:6355: $? = 0
@@ -422,13 +423,13 @@ configure:6712: found /usr/bin/strip
 configure:6723: result: strip
 configure:7009: checking if gcc supports -fno-rtti -fno-exceptions
 configure:7027: gcc -c -g -O2  -fno-rtti -fno-exceptions conftest.c >&5
-cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C
+cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C [enabled by default]
 configure:7031: $? = 0
 configure:7044: result: no
 configure:7059: checking for gcc option to produce PIC
-configure:7269: result: -fno-common
-configure:7277: checking if gcc PIC flag -fno-common works
-configure:7295: gcc -c -g -O2  -fno-common -DPIC conftest.c >&5
+configure:7269: result: -fPIC
+configure:7277: checking if gcc PIC flag -fPIC works
+configure:7295: gcc -c -g -O2  -fPIC -DPIC conftest.c >&5
 configure:7299: $? = 0
 configure:7312: result: yes
 configure:7340: checking if gcc static flag -static works
@@ -437,14 +438,20 @@ configure:7378: checking if gcc supports -c -o file.o
 configure:7399: gcc -c -g -O2  -o out/conftest2.o conftest.c >&5
 configure:7403: $? = 0
 configure:7425: result: yes
-configure:7451: checking whether the gcc linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared libraries
+configure:7451: checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
 configure:8405: result: yes
+configure:8426: checking whether -lc should be explicitly linked in
+configure:8431: gcc -c -g -O2  conftest.c >&5
+configure:8434: $? = 0
+configure:8449: gcc -shared conftest.o  -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| grep  -lc  \>/dev/null 2\>\&1
+configure:8452: $? = 0
+configure:8464: result: no
 configure:8472: checking dynamic linker characteristics
-configure:9060: result: darwin9.8.0 dyld
+configure:9060: result: GNU/Linux ld.so
 configure:9069: checking how to hardcode library paths into programs
 configure:9094: result: immediate
 configure:9108: checking whether stripping libraries is possible
-configure:9121: result: yes
+configure:9113: result: yes
 configure:9914: checking if libtool supports shared libraries
 configure:9916: result: yes
 configure:9919: checking whether to build shared libraries
@@ -453,17 +460,17 @@ configure:9943: checking whether to build static libraries
 configure:9947: result: yes
 configure:10039: creating libtool
 configure:10627: checking for ld used by g++
-configure:10694: result: /usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld
-configure:10703: checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) is GNU ld
-configure:10718: result: no
-configure:10769: checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared libraries
+configure:10694: result: /usr/bin/ld -m elf_x86_64
+configure:10703: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld
+configure:10718: result: yes
+configure:10769: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
 configure:11703: result: yes
 configure:11721: g++ -c -g -O2  conftest.cpp >&5
 configure:11724: $? = 0
 configure:11843: checking for g++ option to produce PIC
-configure:12117: result: -fno-common
-configure:12125: checking if g++ PIC flag -fno-common works
-configure:12143: g++ -c -g -O2  -fno-common -DPIC conftest.cpp >&5
+configure:12117: result: -fPIC
+configure:12125: checking if g++ PIC flag -fPIC works
+configure:12143: g++ -c -g -O2  -fPIC -DPIC conftest.cpp >&5
 configure:12147: $? = 0
 configure:12160: result: yes
 configure:12188: checking if g++ static flag -static works
@@ -472,56 +479,36 @@ configure:12226: checking if g++ supports -c -o file.o
 configure:12247: g++ -c -g -O2  -o out/conftest2.o conftest.cpp >&5
 configure:12251: $? = 0
 configure:12273: result: yes
-configure:12299: checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared libraries
+configure:12299: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
 configure:12324: result: yes
 configure:12391: checking dynamic linker characteristics
-configure:12979: result: darwin9.8.0 dyld
+configure:12979: result: GNU/Linux ld.so
 configure:12988: checking how to hardcode library paths into programs
 configure:13013: result: immediate
-configure:13539: checking if libtool supports shared libraries
-configure:13541: result: yes
-configure:13544: checking whether to build shared libraries
-configure:13564: result: yes
-configure:13567: checking whether to build static libraries
-configure:13571: result: yes
-configure:13581: checking for gfortran option to produce PIC
-configure:13791: result: -fno-common
-configure:13799: checking if gfortran PIC flag -fno-common works
-configure:13817: gfortran -c -g -O2 -fno-common conftest.f >&5
-configure:13821: $? = 0
-configure:13834: result: yes
-configure:13862: checking if gfortran static flag -static works
-configure:13890: result: no
-configure:13900: checking if gfortran supports -c -o file.o
-configure:13921: gfortran -c -g -O2 -o out/conftest2.o conftest.f >&5
-configure:13925: $? = 0
-configure:13947: result: yes
-configure:13973: checking whether the gfortran linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared libraries
-configure:14907: result: yes
-configure:14974: checking dynamic linker characteristics
-configure:15562: result: darwin9.8.0 dyld
-configure:15571: checking how to hardcode library paths into programs
-configure:15596: result: immediate
 configure:19201: checking for gcc
 configure:19228: result: gcc
 configure:19466: checking for C compiler version
 configure:19473: gcc --version >&5
-i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5493)
-Copyright (C) 2005 Free Software Foundation, Inc.
+gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
+Copyright (C) 2012 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:19476: $? = 0
 configure:19483: gcc -v >&5
 Using built-in specs.
-Target: i686-apple-darwin9
-Configured with: /var/tmp/gcc/gcc-5493~1/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9
+COLLECT_GCC=gcc
+COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.7.0/lto-wrapper
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --disable-build-with-cxx --disable-build-poststage1-with-cxx --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
 Thread model: posix
-gcc version 4.0.1 (Apple Inc. build 5493)
+gcc version 4.7.0 20120507 (Red Hat 4.7.0-5) (GCC) 
 configure:19486: $? = 0
 configure:19493: gcc -V >&5
-gcc-4.0: argument to `-V' is missing
-configure:19496: $? = 1
+gcc: error: unrecognized command line option '-V'
+gcc: fatal error: no input files
+compilation terminated.
+configure:19496: $? = 4
 configure:19499: checking whether we are using the GNU C compiler
 configure:19551: result: yes
 configure:19556: checking whether gcc accepts -g
@@ -532,22 +519,26 @@ configure:19831: checking dependency style of gcc
 configure:19922: result: gcc3
 configure:20053: checking for C++ compiler version
 configure:20060: g++ --version >&5
-i686-apple-darwin9-g++-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5493)
-Copyright (C) 2005 Free Software Foundation, Inc.
+g++ (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
+Copyright (C) 2012 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:20063: $? = 0
 configure:20070: g++ -v >&5
 Using built-in specs.
-Target: i686-apple-darwin9
-Configured with: /var/tmp/gcc/gcc-5493~1/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9
+COLLECT_GCC=g++
+COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.7.0/lto-wrapper
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --disable-build-with-cxx --disable-build-poststage1-with-cxx --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
 Thread model: posix
-gcc version 4.0.1 (Apple Inc. build 5493)
+gcc version 4.7.0 20120507 (Red Hat 4.7.0-5) (GCC) 
 configure:20073: $? = 0
 configure:20080: g++ -V >&5
-g++-4.0: argument to `-V' is missing
-configure:20083: $? = 1
+g++: error: unrecognized command line option '-V'
+g++: fatal error: no input files
+compilation terminated.
+configure:20083: $? = 4
 configure:20086: checking whether we are using the GNU C++ compiler
 configure:20138: result: yes
 configure:20143: checking whether g++ accepts -g
@@ -555,26 +546,6 @@ configure:20278: result: yes
 configure:20303: checking dependency style of g++
 configure:20394: result: gcc3
 configure:20550: creating ./config.status
-
-## ---------------------- ##
-## Running config.status. ##
-## ---------------------- ##
-
-This file was extended by Gubbins config.status 0.1, which was
-generated by GNU Autoconf 2.61.  Invocation command line was
-
-  CONFIG_FILES    = 
-  CONFIG_HEADERS  = 
-  CONFIG_LINKS    = 
-  CONFIG_COMMANDS = 
-  $ ./config.status 
-
-on mib100408i.local
-
-config.status:662: creating Makefile
-config.status:662: creating src/Makefile
-config.status:662: creating config.h
-config.status:935: executing depfiles commands
 configure:21840: checking zlib.h usability
 configure:21857: gcc -c -g -O2  conftest.c >&5
 configure:21863: $? = 0
@@ -600,7 +571,7 @@ configure:21952: result: yes
 ## Cache variables. ##
 ## ---------------- ##
 
-ac_cv_build=i386-apple-darwin9.8.0
+ac_cv_build=x86_64-unknown-linux-gnu
 ac_cv_c_compiler_gnu=yes
 ac_cv_cxx_compiler_gnu=yes
 ac_cv_env_CCC_set=
@@ -633,7 +604,7 @@ ac_cv_env_host_alias_set=
 ac_cv_env_host_alias_value=
 ac_cv_env_target_alias_set=
 ac_cv_env_target_alias_value=
-ac_cv_f77_compiler_gnu=yes
+ac_cv_f77_compiler_gnu=no
 ac_cv_header_dlfcn_h=yes
 ac_cv_header_inttypes_h=yes
 ac_cv_header_math_h=yes
@@ -647,24 +618,24 @@ ac_cv_header_sys_stat_h=yes
 ac_cv_header_sys_types_h=yes
 ac_cv_header_unistd_h=yes
 ac_cv_header_zlib_h=yes
-ac_cv_host=i386-apple-darwin9.8.0
+ac_cv_host=x86_64-unknown-linux-gnu
 ac_cv_objext=o
 ac_cv_path_EGREP='/usr/bin/grep -E'
 ac_cv_path_GREP=/usr/bin/grep
 ac_cv_path_install='/usr/bin/install -c'
-ac_cv_prog_AWK=awk
+ac_cv_path_mkdir=/usr/bin/mkdir
+ac_cv_prog_AWK=gawk
 ac_cv_prog_CPP='gcc -E'
 ac_cv_prog_CXXCPP='g++ -E'
 ac_cv_prog_ac_ct_AR=ar
 ac_cv_prog_ac_ct_CC=gcc
 ac_cv_prog_ac_ct_CXX=g++
-ac_cv_prog_ac_ct_F77=gfortran
 ac_cv_prog_ac_ct_RANLIB=ranlib
 ac_cv_prog_ac_ct_STRIP=strip
 ac_cv_prog_cc_c89=
 ac_cv_prog_cc_g=yes
 ac_cv_prog_cxx_g=yes
-ac_cv_prog_f77_g=yes
+ac_cv_prog_f77_g=no
 ac_cv_prog_make_make_set=yes
 am_cv_CC_dependencies_compiler_type=gcc3
 am_cv_CXX_dependencies_compiler_type=gcc3
@@ -673,24 +644,22 @@ lt_cv_file_magic_cmd='$MAGIC_CMD'
 lt_cv_file_magic_test_file=
 lt_cv_ld_reload_flag=-r
 lt_cv_objdir=.libs
-lt_cv_path_LD=/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld
-lt_cv_path_LDCXX=/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld
-lt_cv_path_NM='/usr/bin/nm -p'
+lt_cv_path_LD=/usr/bin/ld
+lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64'
+lt_cv_path_NM='/usr/bin/nm -B'
 lt_cv_path_SED=/usr/bin/sed
 lt_cv_prog_compiler_c_o=yes
 lt_cv_prog_compiler_c_o_CXX=yes
-lt_cv_prog_compiler_c_o_F77=yes
 lt_cv_prog_compiler_rtti_exceptions=no
-lt_cv_prog_gnu_ld=no
-lt_cv_prog_gnu_ldcxx=no
-lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ 	]\([BCDEGRST][BCDEGRST]*\)[ 	][ 	]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p'\'''
+lt_cv_prog_gnu_ld=yes
+lt_cv_prog_gnu_ldcxx=yes
+lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ 	]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ 	][ 	]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'''
 lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/  {\"\1\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \([^ ]*\) \([^ ]*\)$/  {"\2", (lt_ptr) \&\2},/p'\'''
 lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^. .* \(.*\)$/extern int \1;/p'\'''
-lt_cv_sys_max_cmd_len=196608
+lt_cv_sys_max_cmd_len=32768
 lt_lt_cv_prog_compiler_c_o='"yes"'
 lt_lt_cv_prog_compiler_c_o_CXX='"yes"'
-lt_lt_cv_prog_compiler_c_o_F77='"yes"'
-lt_lt_cv_sys_global_symbol_pipe='"sed -n -e '\''s/^.*[ 	]\\([BCDEGRST][BCDEGRST]*\\)[ 	][ 	]*_\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 _\\2 \\2/p'\''"'
+lt_lt_cv_sys_global_symbol_pipe='"sed -n -e '\''s/^.*[ 	]\\([ABCDGIRSTW][ABCDGIRSTW]*\\)[ 	][ 	]*\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 \\2 \\2/p'\''"'
 lt_lt_cv_sys_global_symbol_to_c_name_address='"sed -n -e '\''s/^: \\([^ ]*\\) \$/  {\\\"\\1\\\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \\([^ ]*\\) \\([^ ]*\\)\$/  {\"\\2\", (lt_ptr) \\&\\2},/p'\''"'
 lt_lt_cv_sys_global_symbol_to_cdecl='"sed -n -e '\''s/^. .* \\(.*\\)\$/extern int \\1;/p'\''"'
 
@@ -698,16 +667,16 @@ lt_lt_cv_sys_global_symbol_to_cdecl='"sed -n -e '\''s/^. .* \\(.*\\)\$/extern in
 ## Output variables. ##
 ## ----------------- ##
 
-ACLOCAL='${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run aclocal-1.10'
+ACLOCAL='${SHELL} /home/aidan/tmp/gubbins/missing --run aclocal-1.10'
 AMDEPBACKSLASH='\'
 AMDEP_FALSE='#'
 AMDEP_TRUE=''
-AMTAR='${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run tar'
+AMTAR='${SHELL} /home/aidan/tmp/gubbins/missing --run tar'
 AR='ar'
-AUTOCONF='${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run autoconf'
-AUTOHEADER='${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run autoheader'
-AUTOMAKE='${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run automake-1.10'
-AWK='awk'
+AUTOCONF='${SHELL} /home/aidan/tmp/gubbins/missing --run autoconf'
+AUTOHEADER='${SHELL} /home/aidan/tmp/gubbins/missing --run autoheader'
+AUTOMAKE='${SHELL} /home/aidan/tmp/gubbins/missing --run automake-1.10'
+AWK='gawk'
 CC='gcc'
 CCDEPMODE='depmode=gcc3'
 CFLAGS='-g -O2'
@@ -720,13 +689,14 @@ CXXFLAGS='-g -O2'
 CYGPATH_W='echo'
 DEFS='-DHAVE_CONFIG_H'
 DEPDIR='.deps'
-ECHO='/bin/echo'
-ECHO_C='ECHO_N=''
+ECHO='echo'
+ECHO_C=''
+ECHO_N='-n'
 ECHO_T=''
 EGREP='/usr/bin/grep -E'
 EXEEXT=''
-F77='gfortran'
-FFLAGS='-g -O2'
+F77=''
+FFLAGS=''
 GREP='/usr/bin/grep'
 INSTALL_DATA='${INSTALL} -m 644'
 INSTALL_PROGRAM='${INSTALL}'
@@ -738,7 +708,7 @@ LIBS=''
 LIBTOOL='$(SHELL) $(top_builddir)/libtool'
 LN_S='ln -s'
 LTLIBOBJS=''
-MAKEINFO='${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run makeinfo'
+MAKEINFO='${SHELL} /home/aidan/tmp/gubbins/missing --run makeinfo'
 OBJEXT='o'
 PACKAGE='gubbins'
 PACKAGE_BUGREPORT=''
@@ -754,7 +724,7 @@ STRIP='strip'
 VERSION='0.1'
 ac_ct_CC='gcc'
 ac_ct_CXX='g++'
-ac_ct_F77='gfortran'
+ac_ct_F77=''
 am__fastdepCC_FALSE='#'
 am__fastdepCC_TRUE=''
 am__fastdepCXX_FALSE='#'
@@ -766,31 +736,31 @@ am__quote=''
 am__tar='${AMTAR} chof - "$$tardir"'
 am__untar='${AMTAR} xf -'
 bindir='${exec_prefix}/bin'
-build='i386-apple-darwin9.8.0'
+build='x86_64-unknown-linux-gnu'
 build_alias=''
-build_cpu='i386'
-build_os='darwin9.8.0'
-build_vendor='apple'
+build_cpu='x86_64'
+build_os='linux-gnu'
+build_vendor='unknown'
 datadir='${datarootdir}'
 datarootdir='${prefix}/share'
 docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
 dvidir='${docdir}'
 exec_prefix='${prefix}'
-host='i386-apple-darwin9.8.0'
+host='x86_64-unknown-linux-gnu'
 host_alias=''
-host_cpu='i386'
-host_os='darwin9.8.0'
-host_vendor='apple'
+host_cpu='x86_64'
+host_os='linux-gnu'
+host_vendor='unknown'
 htmldir='${docdir}'
 includedir='${prefix}/include'
 infodir='${datarootdir}/info'
-install_sh='$(SHELL) /Users/ap13/pathogens/multi_fasta_to_vcf/install-sh'
+install_sh='$(SHELL) /home/aidan/tmp/gubbins/install-sh'
 libdir='${exec_prefix}/lib'
 libexecdir='${exec_prefix}/libexec'
 localedir='${datarootdir}/locale'
 localstatedir='${prefix}/var'
 mandir='${datarootdir}/man'
-mkdir_p='$(top_builddir)/./install-sh -c -d'
+mkdir_p='/usr/bin/mkdir -p'
 oldincludedir='/usr/include'
 pdfdir='${docdir}'
 prefix='/usr/local'
@@ -839,9 +809,30 @@ generated by GNU Autoconf 2.61.  Invocation command line was
   CONFIG_HEADERS  = 
   CONFIG_LINKS    = 
   CONFIG_COMMANDS = 
-  $ ./config.status src/Makefile depfiles
+  $ ./config.status 
 
-on mib100408i.internal.sanger.ac.uk
+on SillyFace
 
+config.status:662: creating Makefile
 config.status:662: creating src/Makefile
+config.status:662: creating config.h
+config.status:889: config.h is unchanged
 config.status:935: executing depfiles commands
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by Gubbins config.status 0.1, which was
+generated by GNU Autoconf 2.61.  Invocation command line was
+
+  CONFIG_FILES    = 
+  CONFIG_HEADERS  = 
+  CONFIG_LINKS    = 
+  CONFIG_COMMANDS = 
+  $ ./config.status config.h
+
+on SillyFace
+
+config.status:662: creating config.h
+config.status:889: config.h is unchanged
diff --git a/config.status b/config.status
index c49d3f0b..0f52ac88 100755
--- a/config.status
+++ b/config.status
@@ -341,10 +341,10 @@ Copyright (C) 2006 Free Software Foundation, Inc.
 This config.status script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it."
 
-ac_pwd='/Users/ap13/pathogens/multi_fasta_to_vcf'
+ac_pwd='/home/aidan/tmp/gubbins'
 srcdir='.'
 INSTALL='/usr/bin/install -c'
-MKDIR_P='./install-sh -c -d'
+MKDIR_P='/usr/bin/mkdir -p'
 # If no file are specified by the user, then we need to provide default
 # value.  By we need to know if files were specified by the user.
 ac_need_defaults=:
@@ -526,8 +526,8 @@ s,@libdir@,|#_!!_#|${exec_prefix}/lib,g
 s,@localedir@,|#_!!_#|${datarootdir}/locale,g
 s,@mandir@,|#_!!_#|${datarootdir}/man,g
 s,@DEFS@,|#_!!_#|-DHAVE_CONFIG_H,g
-s,@ECHO_C@,|#_!!_#|\\c,g
-s,@ECHO_N@,|#_!!_#|,g
+s,@ECHO_C@,|#_!!_#|,g
+s,@ECHO_N@,|#_!!_#|-n,g
 s,@ECHO_T@,|#_!!_#|,g
 s,@LIBS@,|#_!!_#|,g
 s,@build_alias@,|#_!!_#|,g
@@ -540,29 +540,29 @@ s,@am__isrc@,|#_!!_#|,g
 s,@CYGPATH_W@,|#_!!_#|echo,g
 s,@PACKAGE@,|#_!!_#|gubbins,g
 s,@VERSION@,|#_!!_#|0.1,g
-s,@ACLOCAL@,|#_!!_#|${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run aclocal-1.10,g
-s,@AUTOCONF@,|#_!!_#|${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run autoconf,g
-s,@AUTOMAKE@,|#_!!_#|${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run automake-1.10,g
-s,@AUTOHEADER@,|#_!!_#|${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run autoheader,g
-s,@MAKEINFO@,|#_!!_#|${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run makeinfo,g
-s,@install_sh@,|#_!!_#|$(SHELL) /Users/ap13/pathogens/multi_fasta_to_vcf/install-sh,g
+s,@ACLOCAL@,|#_!!_#|${SHELL} /home/aidan/tmp/gubbins/missing --run aclocal-1.10,g
+s,@AUTOCONF@,|#_!!_#|${SHELL} /home/aidan/tmp/gubbins/missing --run autoconf,g
+s,@AUTOMAKE@,|#_!!_#|${SHELL} /home/aidan/tmp/gubbins/missing --run automake-1.10,g
+s,@AUTOHEADER@,|#_!!_#|${SHELL} /home/aidan/tmp/gubbins/missing --run autoheader,g
+s,@MAKEINFO@,|#_!!_#|${SHELL} /home/aidan/tmp/gubbins/missing --run makeinfo,g
+s,@install_sh@,|#_!!_#|$(SHELL) /home/aidan/tmp/gubbins/install-sh,g
 s,@STRIP@,|#_!!_#|strip,g
 s,@INSTALL_STRIP_PROGRAM@,|#_!!_#|$(install_sh) -c -s,g
-s,@mkdir_p@,|#_!!_#|$(top_builddir)/./install-sh -c -d,g
-s,@AWK@,|#_!!_#|awk,g
+s,@mkdir_p@,|#_!!_#|/usr/bin/mkdir -p,g
+s,@AWK@,|#_!!_#|gawk,g
 s,@SET_MAKE@,|#_!!_#|,g
 s,@am__leading_dot@,|#_!!_#|.,g
-s,@AMTAR@,|#_!!_#|${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run tar,g
+s,@AMTAR@,|#_!!_#|${SHELL} /home/aidan/tmp/gubbins/missing --run tar,g
 s,@am__tar@,|#_!!_#|${AMTAR} chof - "$$tardir",g
 s,@am__untar@,|#_!!_#|${AMTAR} xf -,g
-s,@build@,|#_!!_#|i386-apple-darwin9.8.0,g
-s,@build_cpu@,|#_!!_#|i386,g
-s,@build_vendor@,|#_!!_#|apple,g
-s,@build_os@,|#_!!_#|darwin9.8.0,g
-s,@host@,|#_!!_#|i386-apple-darwin9.8.0,g
-s,@host_cpu@,|#_!!_#|i386,g
-s,@host_vendor@,|#_!!_#|apple,g
-s,@host_os@,|#_!!_#|darwin9.8.0,g
+s,@build@,|#_!!_#|x86_64-unknown-linux-gnu,g
+s,@build_cpu@,|#_!!_#|x86_64,g
+s,@build_vendor@,|#_!!_#|unknown,g
+s,@build_os@,|#_!!_#|linux-gnu,g
+s,@host@,|#_!!_#|x86_64-unknown-linux-gnu,g
+s,@host_cpu@,|#_!!_#|x86_64,g
+s,@host_vendor@,|#_!!_#|unknown,g
+s,@host_os@,|#_!!_#|linux-gnu,g
 s,@CC@,|#_!!_#|gcc,g
 s,@CFLAGS@,|#_!!_#|-g -O2,g
 s,@LDFLAGS@,|#_!!_#|,g
@@ -582,7 +582,7 @@ s,@am__fastdepCC_FALSE@,|#_!!_#|#,g
 s,@GREP@,|#_!!_#|/usr/bin/grep,g
 s,@EGREP@,|#_!!_#|/usr/bin/grep -E,g
 s,@LN_S@,|#_!!_#|ln -s,g
-s,@ECHO@,|#_!!_#|/bin/echo,g
+s,@ECHO@,|#_!!_#|echo,g
 s,@AR@,|#_!!_#|ar,g
 s,@RANLIB@,|#_!!_#|ranlib,g
 s,@CPP@,|#_!!_#|gcc -E,g
@@ -596,9 +596,9 @@ s,@CXXCPP@,|#_!!_#|g++ -E,g
 CEOF
 cat >"$tmp/subs-2.sed" <<\CEOF
 /@[a-zA-Z_][a-zA-Z_0-9]*@/!b end
-s,@F77@,|#_!!_#|gfortran,g
-s,@FFLAGS@,|#_!!_#|-g -O2,g
-s,@ac_ct_F77@,|#_!!_#|gfortran,g
+s,@F77@,|#_!!_#|,g
+s,@FFLAGS@,|#_!!_#|,g
+s,@ac_ct_F77@,|#_!!_#|,g
 s,@LIBTOOL@,|#_!!_#|$(SHELL) $(top_builddir)/libtool,g
 s,@LIBOBJS@,|#_!!_#|,g
 s,@LTLIBOBJS@,|#_!!_#|,g
diff --git a/libtool b/libtool
index 6f2aa266..93420e0b 100755
--- a/libtool
+++ b/libtool
@@ -40,11 +40,11 @@ Xsed="/usr/bin/sed -e 1s/^X//"
 (unset CDPATH) >/dev/null 2>&1 && unset CDPATH
 
 # The names of the tagged configurations supported by this script.
-available_tags=" CXX F77"
+available_tags=" CXX"
 
 # ### BEGIN LIBTOOL CONFIG
 
-# Libtool was configured on host mib100408i.local:
+# Libtool was configured on host SillyFace:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -62,20 +62,20 @@ build_libtool_need_lc=no
 allow_libtool_libs_with_static_runtimes=no
 
 # Whether or not to optimize for fast installation.
-fast_install=needless
+fast_install=yes
 
 # The host system.
 host_alias=
-host=i386-apple-darwin9.8.0
-host_os=darwin9.8.0
+host=x86_64-unknown-linux-gnu
+host_os=linux-gnu
 
 # The build system.
 build_alias=
-build=i386-apple-darwin9.8.0
-build_os=darwin9.8.0
+build=x86_64-unknown-linux-gnu
+build_os=linux-gnu
 
 # An echo program that does not interpret backslashes.
-echo="/bin/echo"
+echo="echo"
 
 # The archiver.
 AR="ar"
@@ -97,13 +97,13 @@ with_gcc=yes
 EGREP="/usr/bin/grep -E"
 
 # The linker used to build libraries.
-LD="/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld"
+LD="/usr/bin/ld -m elf_x86_64"
 
 # Whether we need hard or soft links.
 LN_S="ln -s"
 
 # A BSD-compatible nm program.
-NM="/usr/bin/nm -p"
+NM="/usr/bin/nm -B"
 
 # A symbol stripping program
 STRIP="strip"
@@ -125,7 +125,7 @@ objdir=.libs
 
 # How to create reloadable object files.
 reload_flag=" -r"
-reload_cmds="\$LTCC \$LTCFLAGS -nostdlib \${wl}-r -o \$output\$reload_objs"
+reload_cmds="\$LD\$reload_flag -o \$output\$reload_objs"
 
 # How to pass a linker flag through the compiler.
 wl="-Wl,"
@@ -137,17 +137,17 @@ objext="o"
 libext="a"
 
 # Shared library suffix (normally ".so").
-shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+shrext_cmds='.so'
 
 # Executable file suffix (normally "").
 exeext=""
 
 # Additional compiler flags for building library objects.
-pic_flag=" -fno-common -DPIC"
+pic_flag=" -fPIC -DPIC"
 pic_mode=default
 
 # What is the maximum length of a command?
-max_cmd_len=196608
+max_cmd_len=32768
 
 # Does compiler simultaneously support -c and -o options?
 compiler_c_o="yes"
@@ -177,26 +177,26 @@ link_static_flag=""
 no_builtin_flag=" -fno-builtin"
 
 # Compiler flag to allow reflexive dlopens.
-export_dynamic_flag_spec=""
+export_dynamic_flag_spec="\${wl}--export-dynamic"
 
 # Compiler flag to generate shared objects directly from archives.
-whole_archive_flag_spec=""
+whole_archive_flag_spec="\${wl}--whole-archive\$convenience \${wl}--no-whole-archive"
 
 # Compiler flag to generate thread-safe objects.
 thread_safe_flag_spec=""
 
 # Library versioning type.
-version_type=darwin
+version_type=linux
 
 # Format of library name prefix.
 libname_spec="lib\$name"
 
 # List of archive names.  First name is the real one, the rest are links.
 # The last name is the one that the linker finds with -lNAME.
-library_names_spec="\${libname}\${release}\${major}\$shared_ext \${libname}\$shared_ext \${libname}\${release}\${versuffix}\$shared_ext"
+library_names_spec="\${libname}\${release}\${shared_ext}\$versuffix \${libname}\${release}\${shared_ext}\$major \$libname\${shared_ext}"
 
 # The coded name of the library, if different from the real name.
-soname_spec="\${libname}\${release}\${major}\$shared_ext"
+soname_spec="\${libname}\${release}\${shared_ext}\$major"
 
 # Commands used to build and install an old-style archive.
 RANLIB="ranlib"
@@ -211,18 +211,21 @@ old_archive_from_new_cmds=""
 old_archive_from_expsyms_cmds=""
 
 # Commands used to build and install a shared archive.
-archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring"
-archive_expsym_cmds="sed -e \\\"s,#.*,,\\\" -e \\\"s,^[    ]*,,\\\" -e \\\"s,^\\\\(..*\\\\),_&,\\\" < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring~nmedit -s \$output_objdir/\${libname}-symbols.expsym \${lib}"
+archive_cmds="\$CC -shared \$libobjs \$deplibs \$compiler_flags \${wl}-soname \$wl\$soname -o \$lib"
+archive_expsym_cmds="\$echo \\\"{ global:\\\" > \$output_objdir/\$libname.ver~
+  cat \$export_symbols | sed -e \\\"s/\\\\(.*\\\\)/\\\\1;/\\\" >> \$output_objdir/\$libname.ver~
+  \$echo \\\"local: *; };\\\" >> \$output_objdir/\$libname.ver~
+	  \$CC -shared \$libobjs \$deplibs \$compiler_flags \${wl}-soname \$wl\$soname \${wl}-version-script \${wl}\$output_objdir/\$libname.ver -o \$lib"
 postinstall_cmds=""
 postuninstall_cmds=""
 
 # Commands used to build a loadable module (assumed same as above if empty)
-module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs\$compiler_flags"
-module_expsym_cmds="sed -e \\\"s,#.*,,\\\" -e \\\"s,^[    ]*,,\\\" -e \\\"s,^\\\\(..*\\\\),_&,\\\" < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag  -o \$lib -bundle \$libobjs \$deplibs\$compiler_flags~nmedit -s \$output_objdir/\${libname}-symbols.expsym \${lib}"
+module_cmds=""
+module_expsym_cmds=""
 
 # Commands to strip libraries.
-old_striplib=""
-striplib="strip -x"
+old_striplib="strip --strip-debug"
+striplib="strip --strip-unneeded"
 
 # Dependencies to place before the objects being linked to create a
 # shared library.
@@ -251,19 +254,19 @@ deplibs_check_method="pass_all"
 file_magic_cmd="\$MAGIC_CMD"
 
 # Flag that allows shared libraries with undefined symbols to be built.
-allow_undefined_flag="\${wl}-flat_namespace \${wl}-undefined \${wl}suppress"
+allow_undefined_flag=""
 
 # Flag that forces no undefined symbols.
 no_undefined_flag=""
 
 # Commands used to finish a libtool library installation in a directory.
-finish_cmds=""
+finish_cmds="PATH=\\\"\\\$PATH:/sbin\\\" ldconfig -n \$libdir"
 
 # Same as above, but a single script fragment to be evaled but not shown.
 finish_eval=""
 
 # Take the output of nm and produce a listing of raw symbols and C names.
-global_symbol_pipe="sed -n -e 's/^.*[ 	]\\([BCDEGRST][BCDEGRST]*\\)[ 	][ 	]*_\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 _\\2 \\2/p'"
+global_symbol_pipe="sed -n -e 's/^.*[ 	]\\([ABCDGIRSTW][ABCDGIRSTW]*\\)[ 	][ 	]*\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 \\2 \\2/p'"
 
 # Transform the output of nm in a proper C declaration
 global_symbol_to_cdecl="sed -n -e 's/^. .* \\(.*\\)\$/extern int \\1;/p'"
@@ -272,23 +275,23 @@ global_symbol_to_cdecl="sed -n -e 's/^. .* \\(.*\\)\$/extern int \\1;/p'"
 global_symbol_to_c_name_address="sed -n -e 's/^: \\([^ ]*\\) \$/  {\\\"\\1\\\", (lt_ptr) 0},/p' -e 's/^[BCDEGRST] \\([^ ]*\\) \\([^ ]*\\)\$/  {\"\\2\", (lt_ptr) \\&\\2},/p'"
 
 # This is the shared library runtime path variable.
-runpath_var=
+runpath_var=LD_RUN_PATH
 
 # This is the shared library path variable.
-shlibpath_var=DYLD_LIBRARY_PATH
+shlibpath_var=LD_LIBRARY_PATH
 
 # Is shlibpath searched before the hard-coded library search path?
-shlibpath_overrides_runpath=yes
+shlibpath_overrides_runpath=no
 
 # How to hardcode a shared library path into an executable.
 hardcode_action=immediate
 
 # Whether we should hardcode library paths into libraries.
-hardcode_into_libs=no
+hardcode_into_libs=yes
 
 # Flag to hardcode $libdir into a binary during linking.
 # This must work even if $libdir does not exist.
-hardcode_libdir_flag_spec=""
+hardcode_libdir_flag_spec="\${wl}--rpath \${wl}\$libdir"
 
 # If ld is used when linking, flag to hardcode $libdir into
 # a binary during linking. This must work even if $libdir does
@@ -312,20 +315,20 @@ hardcode_shlibpath_var=unsupported
 
 # Set to yes if building a shared library automatically hardcodes DIR into the library
 # and all subsequent libraries and executables linked against it.
-hardcode_automatic=yes
+hardcode_automatic=no
 
 # Variables whose values should be saved in libtool wrapper scripts and
 # restored at relink time.
-variables_saved_for_relink="PATH DYLD_LIBRARY_PATH  GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
 
 # Whether libtool must link a program against all its dependency libraries.
-link_all_deplibs=yes
+link_all_deplibs=unknown
 
 # Compile-time system search path for libraries
-sys_lib_search_path_spec=" /lib/i686-apple-darwin9/4.0.1/ /lib/ /usr/lib/i686-apple-darwin9/4.0.1/ /usr/lib/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/../../../../i686-apple-darwin9/lib/i686-apple-darwin9/4.0.1/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/../../../../i686-apple-darwin9/lib/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/../../../i686-apple-darwin9/4.0.1/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/../../../  /lib /usr/lib /usr/local/lib"
+sys_lib_search_path_spec=" /usr/lib/gcc/x86_64-redhat-linux/4.7.0/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../x86_64-redhat-linux/lib/x86_64-redhat-linux/4.7.0/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../x86_64-redhat-linux/lib/../lib64/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../x86_64-redhat-linux/4.7.0/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../lib64/ /lib/x86_64-redhat-linux/4.7.0/ /lib/../lib64/ /usr/lib/x86_64-redhat-linux/4.7.0/ /usr/lib/../lib64/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../x86_64-redhat-linux/lib/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../ /lib/ /usr/lib/"
 
 # Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/usr/local/lib /lib /usr/lib"
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib64/atlas /usr/lib64/llvm /usr/lib64/tracker-0.14 /usr/lib64/xulrunner-2 "
 
 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""
@@ -7212,7 +7215,7 @@ disable_libs=static
 # End:
 # ### BEGIN LIBTOOL TAG CONFIG: CXX
 
-# Libtool was configured on host mib100408i.local:
+# Libtool was configured on host SillyFace:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -7230,20 +7233,20 @@ build_libtool_need_lc=no
 allow_libtool_libs_with_static_runtimes=no
 
 # Whether or not to optimize for fast installation.
-fast_install=needless
+fast_install=yes
 
 # The host system.
 host_alias=
-host=i386-apple-darwin9.8.0
-host_os=darwin9.8.0
+host=x86_64-unknown-linux-gnu
+host_os=linux-gnu
 
 # The build system.
 build_alias=
-build=i386-apple-darwin9.8.0
-build_os=darwin9.8.0
+build=x86_64-unknown-linux-gnu
+build_os=linux-gnu
 
 # An echo program that does not interpret backslashes.
-echo="/bin/echo"
+echo="echo"
 
 # The archiver.
 AR="ar"
@@ -7265,13 +7268,13 @@ with_gcc=yes
 EGREP="/usr/bin/grep -E"
 
 # The linker used to build libraries.
-LD="/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld"
+LD="/usr/bin/ld -m elf_x86_64"
 
 # Whether we need hard or soft links.
 LN_S="ln -s"
 
 # A BSD-compatible nm program.
-NM="/usr/bin/nm -p"
+NM="/usr/bin/nm -B"
 
 # A symbol stripping program
 STRIP="strip"
@@ -7293,7 +7296,7 @@ objdir=.libs
 
 # How to create reloadable object files.
 reload_flag=" -r"
-reload_cmds="\$LTCC \$LTCFLAGS -nostdlib \${wl}-r -o \$output\$reload_objs"
+reload_cmds="\$LD\$reload_flag -o \$output\$reload_objs"
 
 # How to pass a linker flag through the compiler.
 wl="-Wl,"
@@ -7305,17 +7308,17 @@ objext="o"
 libext="a"
 
 # Shared library suffix (normally ".so").
-shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+shrext_cmds='.so'
 
 # Executable file suffix (normally "").
 exeext=""
 
 # Additional compiler flags for building library objects.
-pic_flag=" -fno-common -DPIC"
+pic_flag=" -fPIC -DPIC"
 pic_mode=default
 
 # What is the maximum length of a command?
-max_cmd_len=196608
+max_cmd_len=32768
 
 # Does compiler simultaneously support -c and -o options?
 compiler_c_o="yes"
@@ -7345,26 +7348,26 @@ link_static_flag=""
 no_builtin_flag=" -fno-builtin"
 
 # Compiler flag to allow reflexive dlopens.
-export_dynamic_flag_spec=""
+export_dynamic_flag_spec="\${wl}--export-dynamic"
 
 # Compiler flag to generate shared objects directly from archives.
-whole_archive_flag_spec=""
+whole_archive_flag_spec="\${wl}--whole-archive\$convenience \${wl}--no-whole-archive"
 
 # Compiler flag to generate thread-safe objects.
 thread_safe_flag_spec=""
 
 # Library versioning type.
-version_type=darwin
+version_type=linux
 
 # Format of library name prefix.
 libname_spec="lib\$name"
 
 # List of archive names.  First name is the real one, the rest are links.
 # The last name is the one that the linker finds with -lNAME.
-library_names_spec="\${libname}\${release}\${major}\$shared_ext \${libname}\$shared_ext \${libname}\${release}\${versuffix}\$shared_ext"
+library_names_spec="\${libname}\${release}\${shared_ext}\$versuffix \${libname}\${release}\${shared_ext}\$major \$libname\${shared_ext}"
 
 # The coded name of the library, if different from the real name.
-soname_spec="\${libname}\${release}\${major}\$shared_ext"
+soname_spec="\${libname}\${release}\${shared_ext}\$major"
 
 # Commands used to build and install an old-style archive.
 RANLIB="ranlib"
@@ -7379,26 +7382,26 @@ old_archive_from_new_cmds=""
 old_archive_from_expsyms_cmds=""
 
 # Commands used to build and install a shared archive.
-archive_cmds="\$CC -dynamiclib -single_module \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring"
-archive_expsym_cmds="sed -e \\\"s,#.*,,\\\" -e \\\"s,^[    ]*,,\\\" -e \\\"s,^\\\\(..*\\\\),_&,\\\" < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib -single_module \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring~nmedit -s \$output_objdir/\${libname}-symbols.expsym \${lib}"
+archive_cmds="\$CC -shared -nostdlib \$predep_objects \$libobjs \$deplibs \$postdep_objects \$compiler_flags \${wl}-soname \$wl\$soname -o \$lib"
+archive_expsym_cmds="\$CC -shared -nostdlib \$predep_objects \$libobjs \$deplibs \$postdep_objects \$compiler_flags \${wl}-soname \$wl\$soname \${wl}-retain-symbols-file \$wl\$export_symbols -o \$lib"
 postinstall_cmds=""
 postuninstall_cmds=""
 
 # Commands used to build a loadable module (assumed same as above if empty)
-module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs\$compiler_flags"
-module_expsym_cmds="sed -e \\\"s,#.*,,\\\" -e \\\"s,^[    ]*,,\\\" -e \\\"s,^\\\\(..*\\\\),_&,\\\" < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag  -o \$lib -bundle \$libobjs \$deplibs\$compiler_flags~nmedit -s \$output_objdir/\${libname}-symbols.expsym \${lib}"
+module_cmds=""
+module_expsym_cmds=""
 
 # Commands to strip libraries.
-old_striplib=""
-striplib="strip -x"
+old_striplib="strip --strip-debug"
+striplib="strip --strip-unneeded"
 
 # Dependencies to place before the objects being linked to create a
 # shared library.
-predep_objects=""
+predep_objects="/usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.7.0/crtbeginS.o"
 
 # Dependencies to place after the objects being linked to create a
 # shared library.
-postdep_objects=""
+postdep_objects="/usr/lib/gcc/x86_64-redhat-linux/4.7.0/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../lib64/crtn.o"
 
 # Dependencies to place before the objects being linked to create a
 # shared library.
@@ -7406,11 +7409,11 @@ predeps=""
 
 # Dependencies to place after the objects being linked to create a
 # shared library.
-postdeps=""
+postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
 
 # The library search path used internally by the compiler when linking
 # a shared library.
-compiler_lib_search_path=""
+compiler_lib_search_path="-L/usr/lib/gcc/x86_64-redhat-linux/4.7.0 -L/usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../.."
 
 # Method to check whether dependent libraries are shared objects.
 deplibs_check_method="pass_all"
@@ -7419,19 +7422,19 @@ deplibs_check_method="pass_all"
 file_magic_cmd="\$MAGIC_CMD"
 
 # Flag that allows shared libraries with undefined symbols to be built.
-allow_undefined_flag="\${wl}-flat_namespace \${wl}-undefined \${wl}suppress"
+allow_undefined_flag=""
 
 # Flag that forces no undefined symbols.
 no_undefined_flag=""
 
 # Commands used to finish a libtool library installation in a directory.
-finish_cmds=""
+finish_cmds="PATH=\\\"\\\$PATH:/sbin\\\" ldconfig -n \$libdir"
 
 # Same as above, but a single script fragment to be evaled but not shown.
 finish_eval=""
 
 # Take the output of nm and produce a listing of raw symbols and C names.
-global_symbol_pipe="sed -n -e 's/^.*[ 	]\\([BCDEGRST][BCDEGRST]*\\)[ 	][ 	]*_\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 _\\2 \\2/p'"
+global_symbol_pipe="sed -n -e 's/^.*[ 	]\\([ABCDGIRSTW][ABCDGIRSTW]*\\)[ 	][ 	]*\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 \\2 \\2/p'"
 
 # Transform the output of nm in a proper C declaration
 global_symbol_to_cdecl="sed -n -e 's/^. .* \\(.*\\)\$/extern int \\1;/p'"
@@ -7440,23 +7443,23 @@ global_symbol_to_cdecl="sed -n -e 's/^. .* \\(.*\\)\$/extern int \\1;/p'"
 global_symbol_to_c_name_address="sed -n -e 's/^: \\([^ ]*\\) \$/  {\\\"\\1\\\", (lt_ptr) 0},/p' -e 's/^[BCDEGRST] \\([^ ]*\\) \\([^ ]*\\)\$/  {\"\\2\", (lt_ptr) \\&\\2},/p'"
 
 # This is the shared library runtime path variable.
-runpath_var=
+runpath_var=LD_RUN_PATH
 
 # This is the shared library path variable.
-shlibpath_var=DYLD_LIBRARY_PATH
+shlibpath_var=LD_LIBRARY_PATH
 
 # Is shlibpath searched before the hard-coded library search path?
-shlibpath_overrides_runpath=yes
+shlibpath_overrides_runpath=no
 
 # How to hardcode a shared library path into an executable.
 hardcode_action=immediate
 
 # Whether we should hardcode library paths into libraries.
-hardcode_into_libs=no
+hardcode_into_libs=yes
 
 # Flag to hardcode $libdir into a binary during linking.
 # This must work even if $libdir does not exist.
-hardcode_libdir_flag_spec=""
+hardcode_libdir_flag_spec="\${wl}--rpath \${wl}\$libdir"
 
 # If ld is used when linking, flag to hardcode $libdir into
 # a binary during linking. This must work even if $libdir does
@@ -7480,20 +7483,20 @@ hardcode_shlibpath_var=unsupported
 
 # Set to yes if building a shared library automatically hardcodes DIR into the library
 # and all subsequent libraries and executables linked against it.
-hardcode_automatic=yes
+hardcode_automatic=no
 
 # Variables whose values should be saved in libtool wrapper scripts and
 # restored at relink time.
-variables_saved_for_relink="PATH DYLD_LIBRARY_PATH  GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
 
 # Whether libtool must link a program against all its dependency libraries.
-link_all_deplibs=yes
+link_all_deplibs=unknown
 
 # Compile-time system search path for libraries
-sys_lib_search_path_spec=" /lib/i686-apple-darwin9/4.0.1/ /lib/ /usr/lib/i686-apple-darwin9/4.0.1/ /usr/lib/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/../../../../i686-apple-darwin9/lib/i686-apple-darwin9/4.0.1/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/../../../../i686-apple-darwin9/lib/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/../../../i686-apple-darwin9/4.0.1/ /usr/lib/gcc/i686-apple-darwin9/4.0.1/../../../  /lib /usr/lib /usr/local/lib"
+sys_lib_search_path_spec=" /usr/lib/gcc/x86_64-redhat-linux/4.7.0/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../x86_64-redhat-linux/lib/x86_64-redhat-linux/4.7.0/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../x86_64-redhat-linux/lib/../lib64/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../x86_64-redhat-linux/4.7.0/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../lib64/ /lib/x86_64-redhat-linux/4.7.0/ /lib/../lib64/ /usr/lib/x86_64-redhat-linux/4.7.0/ /usr/lib/../lib64/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../../x86_64-redhat-linux/lib/ /usr/lib/gcc/x86_64-redhat-linux/4.7.0/../../../ /lib/ /usr/lib/"
 
 # Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/usr/local/lib /lib /usr/lib"
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib64/atlas /usr/lib64/llvm /usr/lib64/tracker-0.14 /usr/lib64/xulrunner-2 "
 
 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""
@@ -7515,308 +7518,3 @@ include_expsyms=""
 
 # ### END LIBTOOL TAG CONFIG: CXX
 
-# ### BEGIN LIBTOOL TAG CONFIG: F77
-
-# Libtool was configured on host mib100408i.local:
-
-# Shell to use when invoking shell scripts.
-SHELL="/bin/sh"
-
-# Whether or not to build shared libraries.
-build_libtool_libs=yes
-
-# Whether or not to build static libraries.
-build_old_libs=yes
-
-# Whether or not to add -lc for building shared libraries.
-build_libtool_need_lc=no
-
-# Whether or not to disallow shared libs when runtime libs are static
-allow_libtool_libs_with_static_runtimes=no
-
-# Whether or not to optimize for fast installation.
-fast_install=needless
-
-# The host system.
-host_alias=
-host=i386-apple-darwin9.8.0
-host_os=darwin9.8.0
-
-# The build system.
-build_alias=
-build=i386-apple-darwin9.8.0
-build_os=darwin9.8.0
-
-# An echo program that does not interpret backslashes.
-echo="/bin/echo"
-
-# The archiver.
-AR="ar"
-AR_FLAGS="cru"
-
-# A C compiler.
-LTCC="gcc"
-
-# LTCC compiler flags.
-LTCFLAGS="-g -O2"
-
-# A language-specific compiler.
-CC="gfortran"
-
-# Is the compiler the GNU C compiler?
-with_gcc=yes
-
-# An ERE matcher.
-EGREP="/usr/bin/grep -E"
-
-# The linker used to build libraries.
-LD="/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld"
-
-# Whether we need hard or soft links.
-LN_S="ln -s"
-
-# A BSD-compatible nm program.
-NM="/usr/bin/nm -p"
-
-# A symbol stripping program
-STRIP="strip"
-
-# Used to examine libraries when file_magic_cmd begins "file"
-MAGIC_CMD=file
-
-# Used on cygwin: DLL creation program.
-DLLTOOL="dlltool"
-
-# Used on cygwin: object dumper.
-OBJDUMP="objdump"
-
-# Used on cygwin: assembler.
-AS="as"
-
-# The name of the directory that contains temporary libtool files.
-objdir=.libs
-
-# How to create reloadable object files.
-reload_flag=" -r"
-reload_cmds="\$LTCC \$LTCFLAGS -nostdlib \${wl}-r -o \$output\$reload_objs"
-
-# How to pass a linker flag through the compiler.
-wl="-Wl,"
-
-# Object file suffix (normally "o").
-objext="o"
-
-# Old archive suffix (normally "a").
-libext="a"
-
-# Shared library suffix (normally ".so").
-shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
-
-# Executable file suffix (normally "").
-exeext=""
-
-# Additional compiler flags for building library objects.
-pic_flag=" -fno-common"
-pic_mode=default
-
-# What is the maximum length of a command?
-max_cmd_len=196608
-
-# Does compiler simultaneously support -c and -o options?
-compiler_c_o="yes"
-
-# Must we lock files when doing compilation?
-need_locks="no"
-
-# Do we need the lib prefix for modules?
-need_lib_prefix=no
-
-# Do we need a version for libraries?
-need_version=no
-
-# Whether dlopen is supported.
-dlopen_support=unknown
-
-# Whether dlopen of programs is supported.
-dlopen_self=unknown
-
-# Whether dlopen of statically linked programs is supported.
-dlopen_self_static=unknown
-
-# Compiler flag to prevent dynamic linking.
-link_static_flag=""
-
-# Compiler flag to turn off builtin functions.
-no_builtin_flag=""
-
-# Compiler flag to allow reflexive dlopens.
-export_dynamic_flag_spec=""
-
-# Compiler flag to generate shared objects directly from archives.
-whole_archive_flag_spec=""
-
-# Compiler flag to generate thread-safe objects.
-thread_safe_flag_spec=""
-
-# Library versioning type.
-version_type=darwin
-
-# Format of library name prefix.
-libname_spec="lib\$name"
-
-# List of archive names.  First name is the real one, the rest are links.
-# The last name is the one that the linker finds with -lNAME.
-library_names_spec="\${libname}\${release}\${major}\$shared_ext \${libname}\$shared_ext \${libname}\${release}\${versuffix}\$shared_ext"
-
-# The coded name of the library, if different from the real name.
-soname_spec="\${libname}\${release}\${major}\$shared_ext"
-
-# Commands used to build and install an old-style archive.
-RANLIB="ranlib"
-old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs\$old_deplibs~\$RANLIB \$oldlib"
-old_postinstall_cmds="chmod 644 \$oldlib~\$RANLIB \$oldlib"
-old_postuninstall_cmds=""
-
-# Create an old-style archive from a shared archive.
-old_archive_from_new_cmds=""
-
-# Create a temporary old-style archive to link instead of a shared archive.
-old_archive_from_expsyms_cmds=""
-
-# Commands used to build and install a shared archive.
-archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring"
-archive_expsym_cmds="sed -e \\\"s,#.*,,\\\" -e \\\"s,^[    ]*,,\\\" -e \\\"s,^\\\\(..*\\\\),_&,\\\" < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring~nmedit -s \$output_objdir/\${libname}-symbols.expsym \${lib}"
-postinstall_cmds=""
-postuninstall_cmds=""
-
-# Commands used to build a loadable module (assumed same as above if empty)
-module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs\$compiler_flags"
-module_expsym_cmds="sed -e \\\"s,#.*,,\\\" -e \\\"s,^[    ]*,,\\\" -e \\\"s,^\\\\(..*\\\\),_&,\\\" < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag  -o \$lib -bundle \$libobjs \$deplibs\$compiler_flags~nmedit -s \$output_objdir/\${libname}-symbols.expsym \${lib}"
-
-# Commands to strip libraries.
-old_striplib=""
-striplib="strip -x"
-
-# Dependencies to place before the objects being linked to create a
-# shared library.
-predep_objects=""
-
-# Dependencies to place after the objects being linked to create a
-# shared library.
-postdep_objects=""
-
-# Dependencies to place before the objects being linked to create a
-# shared library.
-predeps=""
-
-# Dependencies to place after the objects being linked to create a
-# shared library.
-postdeps=""
-
-# The library search path used internally by the compiler when linking
-# a shared library.
-compiler_lib_search_path=""
-
-# Method to check whether dependent libraries are shared objects.
-deplibs_check_method="pass_all"
-
-# Command to use when deplibs_check_method == file_magic.
-file_magic_cmd="\$MAGIC_CMD"
-
-# Flag that allows shared libraries with undefined symbols to be built.
-allow_undefined_flag="\${wl}-flat_namespace \${wl}-undefined \${wl}suppress"
-
-# Flag that forces no undefined symbols.
-no_undefined_flag=""
-
-# Commands used to finish a libtool library installation in a directory.
-finish_cmds=""
-
-# Same as above, but a single script fragment to be evaled but not shown.
-finish_eval=""
-
-# Take the output of nm and produce a listing of raw symbols and C names.
-global_symbol_pipe="sed -n -e 's/^.*[ 	]\\([BCDEGRST][BCDEGRST]*\\)[ 	][ 	]*_\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 _\\2 \\2/p'"
-
-# Transform the output of nm in a proper C declaration
-global_symbol_to_cdecl="sed -n -e 's/^. .* \\(.*\\)\$/extern int \\1;/p'"
-
-# Transform the output of nm in a C name address pair
-global_symbol_to_c_name_address="sed -n -e 's/^: \\([^ ]*\\) \$/  {\\\"\\1\\\", (lt_ptr) 0},/p' -e 's/^[BCDEGRST] \\([^ ]*\\) \\([^ ]*\\)\$/  {\"\\2\", (lt_ptr) \\&\\2},/p'"
-
-# This is the shared library runtime path variable.
-runpath_var=
-
-# This is the shared library path variable.
-shlibpath_var=DYLD_LIBRARY_PATH
-
-# Is shlibpath searched before the hard-coded library search path?
-shlibpath_overrides_runpath=yes
-
-# How to hardcode a shared library path into an executable.
-hardcode_action=immediate
-
-# Whether we should hardcode library paths into libraries.
-hardcode_into_libs=no
-
-# Flag to hardcode $libdir into a binary during linking.
-# This must work even if $libdir does not exist.
-hardcode_libdir_flag_spec=""
-
-# If ld is used when linking, flag to hardcode $libdir into
-# a binary during linking. This must work even if $libdir does
-# not exist.
-hardcode_libdir_flag_spec_ld=""
-
-# Whether we need a single -rpath flag with a separated argument.
-hardcode_libdir_separator=""
-
-# Set to yes if using DIR/libNAME during linking hardcodes DIR into the
-# resulting binary.
-hardcode_direct=no
-
-# Set to yes if using the -LDIR flag during linking hardcodes DIR into the
-# resulting binary.
-hardcode_minus_L=no
-
-# Set to yes if using SHLIBPATH_VAR=DIR during linking hardcodes DIR into
-# the resulting binary.
-hardcode_shlibpath_var=unsupported
-
-# Set to yes if building a shared library automatically hardcodes DIR into the library
-# and all subsequent libraries and executables linked against it.
-hardcode_automatic=yes
-
-# Variables whose values should be saved in libtool wrapper scripts and
-# restored at relink time.
-variables_saved_for_relink="PATH DYLD_LIBRARY_PATH  GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
-
-# Whether libtool must link a program against all its dependency libraries.
-link_all_deplibs=yes
-
-# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /usr/local/lib/gcc/i686-apple-darwin8/4.2.3/ /usr/lib/gcc/i686-apple-darwin8/4.2.3/ /usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../../../i686-apple-darwin8/lib/i686-apple-darwin8/4.2.3/ /usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../../../i686-apple-darwin8/lib/ /usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../../i686-apple-darwin8/4.2.3/ /usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../../ /lib/i686-apple-darwin8/4.2.3/ /lib/ /usr/lib/i686-apple-darwin8/4.2.3/ /usr/lib/  /lib /usr/lib /usr/local/lib"
-
-# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/usr/local/lib /lib /usr/lib"
-
-# Fix the shell variable $srcfile for the compiler.
-fix_srcfile_path=""
-
-# Set to yes if exported symbols are required.
-always_export_symbols=no
-
-# The commands to list exported symbols.
-export_symbols_cmds="\$NM \$libobjs \$convenience | \$global_symbol_pipe | \$SED 's/.* //' | sort | uniq > \$export_symbols"
-
-# The commands to extract the exported symbol list from a shared archive.
-extract_expsyms_cmds=""
-
-# Symbols that should not be listed in the preloaded symbols.
-exclude_expsyms="_GLOBAL_OFFSET_TABLE_"
-
-# Symbols that must always be exported.
-include_expsyms=""
-
-# ### END LIBTOOL TAG CONFIG: F77
-
diff --git a/src/Makefile b/src/Makefile
index 2e904140..660608d8 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -32,8 +32,8 @@ POST_INSTALL = :
 NORMAL_UNINSTALL = :
 PRE_UNINSTALL = :
 POST_UNINSTALL = :
-build_triplet = i386-apple-darwin9.8.0
-host_triplet = i386-apple-darwin9.8.0
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
 bin_PROGRAMS = gubbins$(EXEEXT)
 check_PROGRAMS = run_all_tests$(EXEEXT)
 subdir = src
@@ -107,13 +107,13 @@ DATA = $(dist_data_DATA)
 ETAGS = etags
 CTAGS = ctags
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run aclocal-1.10
-AMTAR = ${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run tar
+ACLOCAL = ${SHELL} /home/aidan/tmp/gubbins/missing --run aclocal-1.10
+AMTAR = ${SHELL} /home/aidan/tmp/gubbins/missing --run tar
 AR = ar
-AUTOCONF = ${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run autoconf
-AUTOHEADER = ${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run autoheader
-AUTOMAKE = ${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run automake-1.10
-AWK = awk
+AUTOCONF = ${SHELL} /home/aidan/tmp/gubbins/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/aidan/tmp/gubbins/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/aidan/tmp/gubbins/missing --run automake-1.10
+AWK = gawk
 CC = gcc
 CCDEPMODE = depmode=gcc3
 CFLAGS = -g -O2
@@ -126,14 +126,14 @@ CXXFLAGS = -g -O2
 CYGPATH_W = echo
 DEFS = -DHAVE_CONFIG_H
 DEPDIR = .deps
-ECHO = /bin/echo
-ECHO_C = \c
-ECHO_N = 
+ECHO = echo
+ECHO_C = 
+ECHO_N = -n
 ECHO_T = 
 EGREP = /usr/bin/grep -E
 EXEEXT = 
-F77 = gfortran
-FFLAGS = -g -O2
+F77 = 
+FFLAGS = 
 GREP = /usr/bin/grep
 INSTALL = /usr/bin/install -c
 INSTALL_DATA = ${INSTALL} -m 644
@@ -146,8 +146,8 @@ LIBS =
 LIBTOOL = $(SHELL) $(top_builddir)/libtool
 LN_S = ln -s
 LTLIBOBJS = 
-MAKEINFO = ${SHELL} /Users/ap13/pathogens/multi_fasta_to_vcf/missing --run makeinfo
-MKDIR_P = .././install-sh -c -d
+MAKEINFO = ${SHELL} /home/aidan/tmp/gubbins/missing --run makeinfo
+MKDIR_P = /usr/bin/mkdir -p
 OBJEXT = o
 PACKAGE = gubbins
 PACKAGE_BUGREPORT = 
@@ -161,45 +161,45 @@ SET_MAKE =
 SHELL = /bin/sh
 STRIP = strip
 VERSION = 0.1
-abs_builddir = /Users/ap13/pathogens/multi_fasta_to_vcf/src
-abs_srcdir = /Users/ap13/pathogens/multi_fasta_to_vcf/src
-abs_top_builddir = /Users/ap13/pathogens/multi_fasta_to_vcf
-abs_top_srcdir = /Users/ap13/pathogens/multi_fasta_to_vcf
+abs_builddir = /home/aidan/tmp/gubbins/src
+abs_srcdir = /home/aidan/tmp/gubbins/src
+abs_top_builddir = /home/aidan/tmp/gubbins
+abs_top_srcdir = /home/aidan/tmp/gubbins
 ac_ct_CC = gcc
 ac_ct_CXX = g++
-ac_ct_F77 = gfortran
+ac_ct_F77 = 
 am__include = include
 am__leading_dot = .
 am__quote = 
 am__tar = ${AMTAR} chof - "$$tardir"
 am__untar = ${AMTAR} xf -
 bindir = ${exec_prefix}/bin
-build = i386-apple-darwin9.8.0
+build = x86_64-unknown-linux-gnu
 build_alias = 
-build_cpu = i386
-build_os = darwin9.8.0
-build_vendor = apple
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
 builddir = .
 datadir = ${datarootdir}
 datarootdir = ${prefix}/share
 docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
 dvidir = ${docdir}
 exec_prefix = ${prefix}
-host = i386-apple-darwin9.8.0
+host = x86_64-unknown-linux-gnu
 host_alias = 
-host_cpu = i386
-host_os = darwin9.8.0
-host_vendor = apple
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
 htmldir = ${docdir}
 includedir = ${prefix}/include
 infodir = ${datarootdir}/info
-install_sh = $(SHELL) /Users/ap13/pathogens/multi_fasta_to_vcf/install-sh
+install_sh = $(SHELL) /home/aidan/tmp/gubbins/install-sh
 libdir = ${exec_prefix}/lib
 libexecdir = ${exec_prefix}/libexec
 localedir = ${datarootdir}/locale
 localstatedir = ${prefix}/var
 mandir = ${datarootdir}/man
-mkdir_p = $(top_builddir)/./install-sh -c -d
+mkdir_p = /usr/bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
 prefix = /usr/local
diff --git a/src/main.c b/src/main.c
index 2c8243da..4ef586e9 100644
--- a/src/main.c
+++ b/src/main.c
@@ -24,6 +24,7 @@
 #include <unistd.h>
 #include "snp_sites.h"
 #include "gubbins.h"
+#include "../config.h"
 
 #define MAX_FILENAME_SIZE 1024
 const char* program_name;
@@ -47,6 +48,7 @@ int check_file_exists_or_exit(char * filename)
 void print_usage(FILE* stream, int exit_code)
 {
   fprintf (stream, "Usage:  %s [options] alignment_file\n", program_name);
+  fprintf (stream, "Version: %s\n", PACKAGE_VERSION);
   fprintf (stream,
            "  -r    detect recombinations mode\n"
            "  -t    Newick tree file\n"