--- /dev/null
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by Clustal Omega configure 1.2.4, which was
+generated by GNU Autoconf 2.63. Invocation command line was
+
+ $ ./configure
+
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = ningal.cluster.lifesci.dundee.ac.uk
+uname -m = x86_64
+uname -r = 2.6.32-642.6.1.el6.x86_64
+uname -s = Linux
+uname -v = #1 SMP Wed Oct 5 00:36:12 UTC 2016
+
+/usr/bin/uname -p = unknown
+/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: /gridware/sge/bin/lx-amd64
+PATH: /homes/fmmarquesmadeira/.local/anaconda/envs/python3/bin
+PATH: /gridware/sge/bin/lx-amd64
+PATH: /usr/lib64/qt-3.3/bin
+PATH: /usr/local/bin
+PATH: /bin
+PATH: /usr/bin
+PATH: /usr/local/sbin
+PATH: /usr/sbin
+PATH: /sbin
+PATH: /opt/dell/srvadmin/bin
+PATH: /homes/fmmarquesmadeira/.local/anaconda/bin
+PATH: /homes/fmmarquesmadeira/.local/bin/stamp4.4.2/bin/linux
+PATH: /homes/fmmarquesmadeira/.local/bin/mustang3.2.2/bin
+PATH: /homes/fmmarquesmadeira/.local/bin/mafft7.273/bin
+PATH: /homes/fmmarquesmadeira/.local/bin/foldx_Linux/bin
+PATH: /homes/fmmarquesmadeira/NOBACK/lib/oxbench_1_3//bin
+PATH: /homes/fmmarquesmadeira/.local/bin/Intellij/bin
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+configure:2083:
+
+ Welcome to Clustal Omega - version 1.2.4 (AndreaGiacomo)
+
+ +NMMMMMMMMMS=
+ MMMMM? :MMMMM8
+ IMMMMS MMMMM,
+ ~MMMMN ,MMMMM
+ =MMMMM MMMMM
+ ?MMMMM +MMMMM
+ MMMMMS MMMMM
+ MMMMM MMMMM:
+ MMMMM MMMMM+
+ MMMMM MMMMM~
+ MMMMM MMMMM
+ MMMMMZ MMMMM
+ MMMMM ,MMMMZ
+ MMMM8 MMMM+
+ MMMMS MMMM,
+ MMMMO MMMM
+ ,N SMMM MMM8 +8
+ ,M7 M+ M+ :M8
+ ,MMMMMMMMMMMMI MMMMMMMMMMMM8
+ ,MMMMMMMMMMMM8 MMMMMMMMMMMM8
+ ,MMMMMMMMMMMMN MMMMMMMMMMMM8
+
+
+configure:2194: checking for a BSD-compatible install
+configure:2262: result: /usr/bin/install -c
+configure:2273: checking whether build environment is sane
+configure:2316: result: yes
+configure:2341: checking for a thread-safe mkdir -p
+configure:2380: result: /bin/mkdir -p
+configure:2393: checking for gawk
+configure:2409: found /bin/gawk
+configure:2420: result: gawk
+configure:2431: checking whether make sets $(MAKE)
+configure:2453: result: yes
+configure:2669: checking for style of include used by make
+configure:2697: result: GNU
+configure:2767: checking for gcc
+configure:2783: found /usr/bin/gcc
+configure:2794: result: gcc
+configure:3026: checking for C compiler version
+configure:3034: gcc --version >&5
+gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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:3038: $? = 0
+configure:3045: gcc -v >&5
+Using built-in specs.
+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 --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --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 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:3049: $? = 0
+configure:3056: gcc -V >&5
+gcc: '-V' option must have argument
+configure:3060: $? = 1
+configure:3083: checking for C compiler default output file name
+configure:3105: gcc conftest.c >&5
+configure:3109: $? = 0
+configure:3147: result: a.out
+configure:3166: checking whether the C compiler works
+configure:3176: ./a.out
+configure:3180: $? = 0
+configure:3199: result: yes
+configure:3206: checking whether we are cross compiling
+configure:3208: result: no
+configure:3211: checking for suffix of executables
+configure:3218: gcc -o conftest conftest.c >&5
+configure:3222: $? = 0
+configure:3248: result:
+configure:3254: checking for suffix of object files
+configure:3280: gcc -c conftest.c >&5
+configure:3284: $? = 0
+configure:3309: result: o
+configure:3313: checking whether we are using the GNU C compiler
+configure:3342: gcc -c conftest.c >&5
+configure:3349: $? = 0
+configure:3366: result: yes
+configure:3375: checking whether gcc accepts -g
+configure:3405: gcc -c -g conftest.c >&5
+configure:3412: $? = 0
+configure:3513: result: yes
+configure:3530: checking for gcc option to accept ISO C89
+configure:3604: gcc -c -g -O2 conftest.c >&5
+configure:3611: $? = 0
+configure:3634: result: none needed
+configure:3654: checking dependency style of gcc
+configure:3745: result: gcc3
+configure:3766: checking how to run the C preprocessor
+configure:3806: gcc -E conftest.c
+configure:3813: $? = 0
+configure:3844: gcc -E conftest.c
+conftest.c:10:28: error: ac_nonexistent.h: No such file or directory
+configure:3851: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:3884: result: gcc -E
+configure:3913: gcc -E conftest.c
+configure:3920: $? = 0
+configure:3951: gcc -E conftest.c
+conftest.c:10:28: error: ac_nonexistent.h: No such file or directory
+configure:3958: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:3998: checking for grep that handles long lines and -e
+configure:4058: result: /bin/grep
+configure:4063: checking for egrep
+configure:4127: result: /bin/grep -E
+configure:4132: checking for ANSI C header files
+configure:4162: gcc -c -g -O2 conftest.c >&5
+configure:4169: $? = 0
+configure:4268: gcc -o conftest -g -O2 conftest.c >&5
+configure:4272: $? = 0
+configure:4278: ./conftest
+configure:4282: $? = 0
+configure:4300: result: yes
+configure:4324: checking for sys/types.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for sys/stat.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for stdlib.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for string.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for memory.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for strings.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for inttypes.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for stdint.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for unistd.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4394: checking minix/config.h usability
+configure:4411: gcc -c -g -O2 conftest.c >&5
+conftest.c:53:26: error: minix/config.h: No such file or directory
+configure:4418: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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
+| /* 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 <minix/config.h>
+configure:4432: result: no
+configure:4436: checking minix/config.h presence
+configure:4451: gcc -E conftest.c
+conftest.c:20:26: error: minix/config.h: No such file or directory
+configure:4458: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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
+| /* end confdefs.h. */
+| #include <minix/config.h>
+configure:4472: result: no
+configure:4505: checking for minix/config.h
+configure:4512: result: no
+configure:4543: checking whether it is safe to define __EXTENSIONS__
+configure:4571: gcc -c -g -O2 conftest.c >&5
+configure:4578: $? = 0
+configure:4593: result: yes
+configure:4627: checking build system type
+configure:4645: result: x86_64-unknown-linux-gnu
+configure:4667: checking host system type
+configure:4682: result: x86_64-unknown-linux-gnu
+configure:4708: checking whether make sets $(MAKE)
+configure:4730: result: yes
+configure:4770: checking for a sed that does not truncate output
+configure:4836: result: /bin/sed
+configure:4854: checking for fgrep
+configure:4918: result: /bin/grep -F
+configure:4953: checking for ld used by gcc
+configure:5020: result: /usr/bin/ld
+configure:5029: checking if the linker (/usr/bin/ld) is GNU ld
+configure:5044: result: yes
+configure:5056: checking for BSD- or MS-compatible name lister (nm)
+configure:5105: result: /usr/bin/nm -B
+configure:5223: checking the name lister (/usr/bin/nm -B) interface
+configure:5230: gcc -c -g -O2 conftest.c >&5
+configure:5233: /usr/bin/nm -B "conftest.o"
+configure:5236: output
+0000000000000000 B some_variable
+configure:5243: result: BSD nm
+configure:5246: checking whether ln -s works
+configure:5250: result: yes
+configure:5258: checking the maximum length of command line arguments
+configure:5378: result: 1966080
+configure:5395: checking whether the shell understands some XSI constructs
+configure:5405: result: yes
+configure:5409: checking whether the shell understands "+="
+configure:5415: result: yes
+configure:5450: checking for /usr/bin/ld option to reload object files
+configure:5457: result: -r
+configure:5526: checking for objdump
+configure:5542: found /usr/bin/objdump
+configure:5553: result: objdump
+configure:5585: checking how to recognize dependent libraries
+configure:5781: result: pass_all
+configure:5841: checking for ar
+configure:5857: found /usr/bin/ar
+configure:5868: result: ar
+configure:5946: checking for strip
+configure:5962: found /usr/bin/strip
+configure:5973: result: strip
+configure:6045: checking for ranlib
+configure:6061: found /usr/bin/ranlib
+configure:6072: result: ranlib
+configure:6162: checking command to parse /usr/bin/nm -B output from gcc object
+configure:6280: gcc -c -g -O2 conftest.c >&5
+configure:6283: $? = 0
+configure:6287: /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:6290: $? = 0
+configure:6344: gcc -o conftest -g -O2 conftest.c conftstm.o >&5
+configure:6347: $? = 0
+configure:6385: result: ok
+configure:6480: gcc -c -g -O2 conftest.c >&5
+configure:6483: $? = 0
+configure:7250: checking for dlfcn.h
+configure:7271: gcc -c -g -O2 conftest.c >&5
+configure:7278: $? = 0
+configure:7295: result: yes
+configure:7481: checking for objdir
+configure:7496: result: .libs
+configure:7792: checking if gcc supports -fno-rtti -fno-exceptions
+configure:7810: 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
+configure:7814: $? = 0
+configure:7827: result: no
+configure:7847: checking for gcc option to produce PIC
+configure:8119: result: -fPIC -DPIC
+configure:8131: checking if gcc PIC flag -fPIC -DPIC works
+configure:8149: gcc -c -g -O2 -fPIC -DPIC -DPIC conftest.c >&5
+configure:8153: $? = 0
+configure:8166: result: yes
+configure:8190: checking if gcc static flag -static works
+configure:8218: result: yes
+configure:8233: checking if gcc supports -c -o file.o
+configure:8254: gcc -c -g -O2 -o out/conftest2.o conftest.c >&5
+configure:8258: $? = 0
+configure:8280: result: yes
+configure:8288: checking if gcc supports -c -o file.o
+configure:8335: result: yes
+configure:8368: checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
+configure:9443: result: yes
+configure:9480: checking whether -lc should be explicitly linked in
+configure:9485: gcc -c -g -O2 conftest.c >&5
+configure:9488: $? = 0
+configure:9503: gcc -shared conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /bin/grep -lc \>/dev/null 2\>\&1
+configure:9506: $? = 0
+configure:9518: result: no
+configure:9682: checking dynamic linker characteristics
+configure:10125: gcc -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.c >&5
+configure:10132: $? = 0
+configure:10377: result: GNU/Linux ld.so
+configure:10479: checking how to hardcode library paths into programs
+configure:10504: result: immediate
+configure:11337: checking whether stripping libraries is possible
+configure:11342: result: yes
+configure:11377: checking if libtool supports shared libraries
+configure:11379: result: yes
+configure:11382: checking whether to build shared libraries
+configure:11403: result: yes
+configure:11406: checking whether to build static libraries
+configure:11410: result: yes
+configure:11462: checking for a BSD-compatible install
+configure:11530: result: /usr/bin/install -c
+configure:11598: checking for gcc
+configure:11625: result: gcc
+configure:11857: checking for C compiler version
+configure:11865: gcc --version >&5
+gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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:11869: $? = 0
+configure:11876: gcc -v >&5
+Using built-in specs.
+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 --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --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 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:11880: $? = 0
+configure:11887: gcc -V >&5
+gcc: '-V' option must have argument
+configure:11891: $? = 1
+configure:11894: checking whether we are using the GNU C compiler
+configure:11947: result: yes
+configure:11956: checking whether gcc accepts -g
+configure:12094: result: yes
+configure:12111: checking for gcc option to accept ISO C89
+configure:12215: result: none needed
+configure:12235: checking dependency style of gcc
+configure:12326: result: gcc3
+configure:12347: checking how to run the C preprocessor
+configure:12465: result: gcc -E
+configure:12494: gcc -E conftest.c
+configure:12501: $? = 0
+configure:12532: gcc -E conftest.c
+conftest.c:27:28: error: ac_nonexistent.h: No such file or directory
+configure:12539: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:12641: checking for g++
+configure:12657: found /usr/bin/g++
+configure:12668: result: g++
+configure:12695: checking for C++ compiler version
+configure:12703: g++ --version >&5
+g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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:12707: $? = 0
+configure:12714: g++ -v >&5
+Using built-in specs.
+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 --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --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 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:12718: $? = 0
+configure:12725: g++ -V >&5
+g++: '-V' option must have argument
+configure:12729: $? = 1
+configure:12732: checking whether we are using the GNU C++ compiler
+configure:12761: g++ -c conftest.cpp >&5
+configure:12768: $? = 0
+configure:12785: result: yes
+configure:12794: checking whether g++ accepts -g
+configure:12824: g++ -c -g conftest.cpp >&5
+configure:12831: $? = 0
+configure:12932: result: yes
+configure:12957: checking dependency style of g++
+configure:13048: result: gcc3
+configure:13176: checking for C++ compiler version
+configure:13184: g++ --version >&5
+g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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:13188: $? = 0
+configure:13195: g++ -v >&5
+Using built-in specs.
+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 --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --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 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:13199: $? = 0
+configure:13206: g++ -V >&5
+g++: '-V' option must have argument
+configure:13210: $? = 1
+configure:13213: checking whether we are using the GNU C++ compiler
+configure:13266: result: yes
+configure:13275: checking whether g++ accepts -g
+configure:13413: result: yes
+configure:13438: checking dependency style of g++
+configure:13529: result: gcc3
+configure:13552: checking how to run the C++ preprocessor
+configure:13588: g++ -E conftest.cpp
+configure:13595: $? = 0
+configure:13626: g++ -E conftest.cpp
+conftest.cpp:27:28: error: ac_nonexistent.h: No such file or directory
+configure:13633: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:13666: result: g++ -E
+configure:13695: g++ -E conftest.cpp
+configure:13702: $? = 0
+configure:13733: g++ -E conftest.cpp
+conftest.cpp:27:28: error: ac_nonexistent.h: No such file or directory
+configure:13740: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:13916: checking for ld used by g++
+configure:13983: result: /usr/bin/ld -m elf_x86_64
+configure:13992: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld
+configure:14007: result: yes
+configure:14062: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
+configure:15037: result: yes
+configure:15065: g++ -c -g -O2 conftest.cpp >&5
+configure:15068: $? = 0
+configure:15250: checking for g++ option to produce PIC
+configure:15567: result: -fPIC -DPIC
+configure:15576: checking if g++ PIC flag -fPIC -DPIC works
+configure:15594: g++ -c -g -O2 -fPIC -DPIC -DPIC conftest.cpp >&5
+configure:15598: $? = 0
+configure:15611: result: yes
+configure:15632: checking if g++ static flag -static works
+configure:15660: result: yes
+configure:15672: checking if g++ supports -c -o file.o
+configure:15693: g++ -c -g -O2 -o out/conftest2.o conftest.cpp >&5
+configure:15697: $? = 0
+configure:15719: result: yes
+configure:15724: checking if g++ supports -c -o file.o
+configure:15771: result: yes
+configure:15801: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
+configure:15830: result: yes
+configure:15967: checking dynamic linker characteristics
+configure:16358: g++ -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.cpp >&5
+configure:16365: $? = 0
+configure:16610: result: GNU/Linux ld.so
+configure:16661: checking how to hardcode library paths into programs
+configure:16686: result: immediate
+configure:16731: checking how to run the C++ preprocessor
+configure:16845: result: g++ -E
+configure:16874: g++ -E conftest.cpp
+configure:16881: $? = 0
+configure:16912: g++ -E conftest.cpp
+conftest.cpp:27:28: error: ac_nonexistent.h: No such file or directory
+configure:16919: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:17113: checking for ANSI C header files
+configure:17281: result: yes
+configure:17319: checking assert.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking assert.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for assert.h
+configure:17439: result: yes
+configure:17319: checking ctype.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking ctype.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for ctype.h
+configure:17439: result: yes
+configure:17319: checking float.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking float.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for float.h
+configure:17439: result: yes
+configure:17319: checking limits.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking limits.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for limits.h
+configure:17439: result: yes
+configure:17319: checking math.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking math.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for math.h
+configure:17439: result: yes
+configure:17308: checking for memory.h
+configure:17315: result: yes
+configure:17319: checking stdarg.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking stdarg.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for stdarg.h
+configure:17439: result: yes
+configure:17319: checking stdio.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking stdio.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for stdio.h
+configure:17439: result: yes
+configure:17308: checking for stdlib.h
+configure:17315: result: yes
+configure:17308: checking for string.h
+configure:17315: result: yes
+configure:17319: checking time.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking time.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for time.h
+configure:17439: result: yes
+configure:17308: checking for unistd.h
+configure:17315: result: yes
+configure:17457: checking for an ANSI C-conforming const
+configure:17532: gcc -c -g -O2 conftest.c >&5
+configure:17539: $? = 0
+configure:17554: result: yes
+configure:17564: checking for size_t
+configure:17592: gcc -c -g -O2 conftest.c >&5
+configure:17599: $? = 0
+configure:17626: gcc -c -g -O2 conftest.c >&5
+conftest.c: In function 'main':
+conftest.c:79: error: expected expression before ')' token
+configure:17633: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| /* end confdefs.h. */
+| #include <stdio.h>
+| #ifdef HAVE_SYS_TYPES_H
+| # include <sys/types.h>
+| #endif
+| #ifdef HAVE_SYS_STAT_H
+| # include <sys/stat.h>
+| #endif
+| #ifdef STDC_HEADERS
+| # include <stdlib.h>
+| # include <stddef.h>
+| #else
+| # ifdef HAVE_STDLIB_H
+| # include <stdlib.h>
+| # endif
+| #endif
+| #ifdef HAVE_STRING_H
+| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+| # include <memory.h>
+| # endif
+| # include <string.h>
+| #endif
+| #ifdef HAVE_STRINGS_H
+| # include <strings.h>
+| #endif
+| #ifdef HAVE_INTTYPES_H
+| # include <inttypes.h>
+| #endif
+| #ifdef HAVE_STDINT_H
+| # include <stdint.h>
+| #endif
+| #ifdef HAVE_UNISTD_H
+| # include <unistd.h>
+| #endif
+| int
+| main ()
+| {
+| if (sizeof ((size_t)))
+| return 0;
+| ;
+| return 0;
+| }
+configure:17656: result: yes
+configure:17668: checking for inline
+configure:17694: gcc -c -g -O2 conftest.c >&5
+configure:17701: $? = 0
+configure:17719: result: inline
+configure:17746: checking for log in -lm
+configure:17781: gcc -o conftest -g -O2 conftest.c -lm >&5
+conftest.c:50: warning: conflicting types for built-in function 'log'
+configure:17788: $? = 0
+configure:17809: result: yes
+configure:17824: checking for log2 in -lm
+configure:17859: gcc -o conftest -g -O2 conftest.c -lm -lm >&5
+conftest.c:51: warning: conflicting types for built-in function 'log2'
+configure:17866: $? = 0
+configure:17887: result: yes
+configure:17918: checking argtable2.h usability
+configure:17935: gcc -c -g -O2 conftest.c >&5
+configure:17942: $? = 0
+configure:17956: result: yes
+configure:17960: checking argtable2.h presence
+configure:17975: gcc -E conftest.c
+configure:17982: $? = 0
+configure:17996: result: yes
+configure:18029: checking for argtable2.h
+configure:18038: result: yes
+configure:18058: checking for arg_parse in -largtable2
+configure:18093: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:18100: $? = 0
+configure:18121: result: yes
+configure:18274: checking for OpenMP flag of C compiler
+configure:18320: gcc -o conftest -g -O2 -fopenmp conftest.c -largtable2 -lm >&5
+configure:18327: $? = 0
+configure:18350: result: -fopenmp
+configure:18399: checking whether byte ordering is bigendian
+configure:18424: gcc -c -g -O2 conftest.c >&5
+conftest.c:49: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'a'
+configure:18431: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| /* end confdefs.h. */
+| #ifndef __APPLE_CC__
+| not a universal capable compiler
+| #endif
+| typedef int dummy;
+|
+configure:18481: gcc -c -g -O2 conftest.c >&5
+configure:18488: $? = 0
+configure:18520: gcc -c -g -O2 conftest.c >&5
+conftest.c: In function 'main':
+conftest.c:55: error: 'not' undeclared (first use in this function)
+conftest.c:55: error: (Each undeclared identifier is reported only once
+conftest.c:55: error: for each function it appears in.)
+conftest.c:55: error: expected ';' before 'big'
+configure:18527: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| /* end confdefs.h. */
+| #include <sys/types.h>
+| #include <sys/param.h>
+|
+| int
+| main ()
+| {
+| #if BYTE_ORDER != BIG_ENDIAN
+| not big endian
+| #endif
+|
+| ;
+| return 0;
+| }
+configure:18779: result: no
+configure:18809: checking for ntohs
+configure:18865: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:18872: $? = 0
+configure:18894: result: yes
+configure:18809: checking for ntohl
+configure:18865: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:18872: $? = 0
+configure:18894: result: yes
+configure:18809: checking for ntons
+configure:18865: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/ccMjUguw.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:84: undefined reference to `ntons'
+collect2: ld returned 1 exit status
+configure:18872: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| /* end confdefs.h. */
+| /* Define ntons to an innocuous variant, in case <limits.h> declares ntons.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define ntons innocuous_ntons
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char ntons (); below.
+| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+| <limits.h> exists even on freestanding compilers. */
+|
+| #ifdef __STDC__
+| # include <limits.h>
+| #else
+| # include <assert.h>
+| #endif
+|
+| #undef ntons
+|
+| /* Override any GCC internal prototype to avoid an error.
+| Use char because int might match the return type of a GCC
+| builtin and then its argument prototype would still apply. */
+| #ifdef __cplusplus
+| extern "C"
+| #endif
+| char ntons ();
+| /* The GNU C library defines this for functions which it implements
+| to always fail with ENOSYS. Some functions are actually named
+| something starting with __ and the normal name is an alias. */
+| #if defined __stub_ntons || defined __stub___ntons
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return ntons ();
+| ;
+| return 0;
+| }
+configure:18894: result: no
+configure:18809: checking for ntonl
+configure:18865: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/ccc48aZC.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:84: undefined reference to `ntonl'
+collect2: ld returned 1 exit status
+configure:18872: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| /* end confdefs.h. */
+| /* Define ntonl to an innocuous variant, in case <limits.h> declares ntonl.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define ntonl innocuous_ntonl
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char ntonl (); below.
+| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+| <limits.h> exists even on freestanding compilers. */
+|
+| #ifdef __STDC__
+| # include <limits.h>
+| #else
+| # include <assert.h>
+| #endif
+|
+| #undef ntonl
+|
+| /* Override any GCC internal prototype to avoid an error.
+| Use char because int might match the return type of a GCC
+| builtin and then its argument prototype would still apply. */
+| #ifdef __cplusplus
+| extern "C"
+| #endif
+| char ntonl ();
+| /* The GNU C library defines this for functions which it implements
+| to always fail with ENOSYS. Some functions are actually named
+| something starting with __ and the normal name is an alias. */
+| #if defined __stub_ntonl || defined __stub___ntonl
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return ntonl ();
+| ;
+| return 0;
+| }
+configure:18894: result: no
+configure:18911: checking size of unsigned short
+configure:19216: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:19220: $? = 0
+configure:19226: ./conftest
+configure:19230: $? = 0
+configure:19256: result: 2
+configure:19270: checking size of unsigned int
+configure:19575: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:19579: $? = 0
+configure:19585: ./conftest
+configure:19589: $? = 0
+configure:19615: result: 4
+configure:19629: checking size of unsigned long
+configure:19934: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:19938: $? = 0
+configure:19944: ./conftest
+configure:19948: $? = 0
+configure:19974: result: 8
+configure:19988: checking size of unsigned long long
+configure:20293: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20297: $? = 0
+configure:20303: ./conftest
+configure:20307: $? = 0
+configure:20333: result: 8
+configure:20349: checking for stroul
+configure:20405: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/ccLKPuKy.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:88: undefined reference to `stroul'
+collect2: ld returned 1 exit status
+configure:20412: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| #define SIZEOF_UNSIGNED_SHORT 2
+| #define SIZEOF_UNSIGNED_INT 4
+| #define SIZEOF_UNSIGNED_LONG 8
+| #define SIZEOF_UNSIGNED_LONG_LONG 8
+| /* end confdefs.h. */
+| /* Define stroul to an innocuous variant, in case <limits.h> declares stroul.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define stroul innocuous_stroul
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char stroul (); below.
+| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+| <limits.h> exists even on freestanding compilers. */
+|
+| #ifdef __STDC__
+| # include <limits.h>
+| #else
+| # include <assert.h>
+| #endif
+|
+| #undef stroul
+|
+| /* Override any GCC internal prototype to avoid an error.
+| Use char because int might match the return type of a GCC
+| builtin and then its argument prototype would still apply. */
+| #ifdef __cplusplus
+| extern "C"
+| #endif
+| char stroul ();
+| /* The GNU C library defines this for functions which it implements
+| to always fail with ENOSYS. Some functions are actually named
+| something starting with __ and the normal name is an alias. */
+| #if defined __stub_stroul || defined __stub___stroul
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return stroul ();
+| ;
+| return 0;
+| }
+configure:20434: result: no
+configure:20349: checking for strtoull
+configure:20405: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20412: $? = 0
+configure:20434: result: yes
+configure:20451: checking for ftello
+configure:20507: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20514: $? = 0
+configure:20536: result: yes
+configure:20451: checking for fseeko
+configure:20507: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20514: $? = 0
+configure:20536: result: yes
+configure:20553: checking for ftello64
+configure:20609: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20616: $? = 0
+configure:20638: result: yes
+configure:20553: checking for fseeko64
+configure:20609: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20616: $? = 0
+configure:20638: result: yes
+configure:20655: checking for ftell64
+configure:20711: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/ccIKIivi.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:93: undefined reference to `ftell64'
+collect2: ld returned 1 exit status
+configure:20718: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| #define SIZEOF_UNSIGNED_SHORT 2
+| #define SIZEOF_UNSIGNED_INT 4
+| #define SIZEOF_UNSIGNED_LONG 8
+| #define SIZEOF_UNSIGNED_LONG_LONG 8
+| #define HAVE_STRTOULL 1
+| #define HAVE_FTELLO 1
+| #define HAVE_FSEEKO 1
+| #define HAVE_FTELLO64 1
+| #define HAVE_FSEEKO64 1
+| /* end confdefs.h. */
+| /* Define ftell64 to an innocuous variant, in case <limits.h> declares ftell64.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define ftell64 innocuous_ftell64
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char ftell64 (); below.
+| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+| <limits.h> exists even on freestanding compilers. */
+|
+| #ifdef __STDC__
+| # include <limits.h>
+| #else
+| # include <assert.h>
+| #endif
+|
+| #undef ftell64
+|
+| /* Override any GCC internal prototype to avoid an error.
+| Use char because int might match the return type of a GCC
+| builtin and then its argument prototype would still apply. */
+| #ifdef __cplusplus
+| extern "C"
+| #endif
+| char ftell64 ();
+| /* The GNU C library defines this for functions which it implements
+| to always fail with ENOSYS. Some functions are actually named
+| something starting with __ and the normal name is an alias. */
+| #if defined __stub_ftell64 || defined __stub___ftell64
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return ftell64 ();
+| ;
+| return 0;
+| }
+configure:20740: result: no
+configure:20655: checking for fseek64
+configure:20711: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/cc95kpLo.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:93: undefined reference to `fseek64'
+collect2: ld returned 1 exit status
+configure:20718: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| #define SIZEOF_UNSIGNED_SHORT 2
+| #define SIZEOF_UNSIGNED_INT 4
+| #define SIZEOF_UNSIGNED_LONG 8
+| #define SIZEOF_UNSIGNED_LONG_LONG 8
+| #define HAVE_STRTOULL 1
+| #define HAVE_FTELLO 1
+| #define HAVE_FSEEKO 1
+| #define HAVE_FTELLO64 1
+| #define HAVE_FSEEKO64 1
+| /* end confdefs.h. */
+| /* Define fseek64 to an innocuous variant, in case <limits.h> declares fseek64.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define fseek64 innocuous_fseek64
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char fseek64 (); below.
+| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+| <limits.h> exists even on freestanding compilers. */
+|
+| #ifdef __STDC__
+| # include <limits.h>
+| #else
+| # include <assert.h>
+| #endif
+|
+| #undef fseek64
+|
+| /* Override any GCC internal prototype to avoid an error.
+| Use char because int might match the return type of a GCC
+| builtin and then its argument prototype would still apply. */
+| #ifdef __cplusplus
+| extern "C"
+| #endif
+| char fseek64 ();
+| /* The GNU C library defines this for functions which it implements
+| to always fail with ENOSYS. Some functions are actually named
+| something starting with __ and the normal name is an alias. */
+| #if defined __stub_fseek64 || defined __stub___fseek64
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return fseek64 ();
+| ;
+| return 0;
+| }
+configure:20740: result: no
+configure:20753: checking for off_t
+configure:20781: gcc -c -g -O2 conftest.c >&5
+configure:20788: $? = 0
+configure:20815: gcc -c -g -O2 conftest.c >&5
+conftest.c: In function 'main':
+conftest.c:95: error: expected expression before ')' token
+configure:20822: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #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 __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| #define SIZEOF_UNSIGNED_SHORT 2
+| #define SIZEOF_UNSIGNED_INT 4
+| #define SIZEOF_UNSIGNED_LONG 8
+| #define SIZEOF_UNSIGNED_LONG_LONG 8
+| #define HAVE_STRTOULL 1
+| #define HAVE_FTELLO 1
+| #define HAVE_FSEEKO 1
+| #define HAVE_FTELLO64 1
+| #define HAVE_FSEEKO64 1
+| /* end confdefs.h. */
+| #include <stdio.h>
+| #ifdef HAVE_SYS_TYPES_H
+| # include <sys/types.h>
+| #endif
+| #ifdef HAVE_SYS_STAT_H
+| # include <sys/stat.h>
+| #endif
+| #ifdef STDC_HEADERS
+| # include <stdlib.h>
+| # include <stddef.h>
+| #else
+| # ifdef HAVE_STDLIB_H
+| # include <stdlib.h>
+| # endif
+| #endif
+| #ifdef HAVE_STRING_H
+| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+| # include <memory.h>
+| # endif
+| # include <string.h>
+| #endif
+| #ifdef HAVE_STRINGS_H
+| # include <strings.h>
+| #endif
+| #ifdef HAVE_INTTYPES_H
+| # include <inttypes.h>
+| #endif
+| #ifdef HAVE_STDINT_H
+| # include <stdint.h>
+| #endif
+| #ifdef HAVE_UNISTD_H
+| # include <unistd.h>
+| #endif
+| int
+| main ()
+| {
+| if (sizeof ((off_t)))
+| return 0;
+| ;
+| return 0;
+| }
+configure:20845: result: yes
+configure:20861: checking size of fpos_t
+configure:21166: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:21170: $? = 0
+configure:21176: ./conftest
+configure:21180: $? = 0
+configure:21206: result: 16
+configure:21249: checking if malloc debugging is wanted
+configure:21269: result: no
+configure:21293: checking whether to build with debug information
+configure:21302: result: no
+configure:21476: creating ./config.status
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by Clustal Omega config.status 1.2.4, which was
+generated by GNU Autoconf 2.63. Invocation command line was
+
+ CONFIG_FILES =
+ CONFIG_HEADERS =
+ CONFIG_LINKS =
+ CONFIG_COMMANDS =
+ $ ./config.status
+
+on ningal.cluster.lifesci.dundee.ac.uk
+
+config.status:1097: creating Makefile
+config.status:1097: creating src/Makefile
+config.status:1097: creating clustalo.pc
+config.status:1097: creating Doxyfile
+config.status:1097: creating src/clustal/Makefile
+config.status:1097: creating src/hhalign/Makefile
+config.status:1097: creating src/kmpp/Makefile
+config.status:1097: creating src/squid/Makefile
+config.status:1097: creating src/config.h
+config.status:1319: src/config.h is unchanged
+config.status:1371: executing src/clustal-omega-config.h commands
+config.status:1411: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines
+config.status:1433: src/clustal-omega-config.h is unchanged
+config.status:1371: executing depfiles commands
+config.status:1371: executing libtool commands
+
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+
+ac_cv_build=x86_64-unknown-linux-gnu
+ac_cv_c_bigendian=no
+ac_cv_c_compiler_gnu=yes
+ac_cv_c_const=yes
+ac_cv_c_inline=inline
+ac_cv_cxx_compiler_gnu=yes
+ac_cv_env_CCC_set=
+ac_cv_env_CCC_value=
+ac_cv_env_CC_set=
+ac_cv_env_CC_value=
+ac_cv_env_CFLAGS_set=
+ac_cv_env_CFLAGS_value=
+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=
+ac_cv_env_CXXFLAGS_value=
+ac_cv_env_CXX_set=
+ac_cv_env_CXX_value=
+ac_cv_env_LDFLAGS_set=
+ac_cv_env_LDFLAGS_value=
+ac_cv_env_LIBS_set=
+ac_cv_env_LIBS_value=
+ac_cv_env_build_alias_set=
+ac_cv_env_build_alias_value=
+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_func_fseek64=no
+ac_cv_func_fseeko64=yes
+ac_cv_func_fseeko=yes
+ac_cv_func_ftell64=no
+ac_cv_func_ftello64=yes
+ac_cv_func_ftello=yes
+ac_cv_func_ntohl=yes
+ac_cv_func_ntohs=yes
+ac_cv_func_ntonl=no
+ac_cv_func_ntons=no
+ac_cv_func_stroul=no
+ac_cv_func_strtoull=yes
+ac_cv_header_argtable2_h=yes
+ac_cv_header_assert_h=yes
+ac_cv_header_ctype_h=yes
+ac_cv_header_dlfcn_h=yes
+ac_cv_header_float_h=yes
+ac_cv_header_inttypes_h=yes
+ac_cv_header_limits_h=yes
+ac_cv_header_math_h=yes
+ac_cv_header_memory_h=yes
+ac_cv_header_minix_config_h=no
+ac_cv_header_stdarg_h=yes
+ac_cv_header_stdc=yes
+ac_cv_header_stdint_h=yes
+ac_cv_header_stdio_h=yes
+ac_cv_header_stdlib_h=yes
+ac_cv_header_string_h=yes
+ac_cv_header_strings_h=yes
+ac_cv_header_sys_stat_h=yes
+ac_cv_header_sys_types_h=yes
+ac_cv_header_time_h=yes
+ac_cv_header_unistd_h=yes
+ac_cv_host=x86_64-unknown-linux-gnu
+ac_cv_lib_argtable2_arg_parse=yes
+ac_cv_lib_m_log2=yes
+ac_cv_lib_m_log=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_SED=/bin/sed
+ac_cv_path_install='/usr/bin/install -c'
+ac_cv_path_mkdir=/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_OBJDUMP=objdump
+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_make_make_set=yes
+ac_cv_safe_to_define___extensions__=yes
+ac_cv_sizeof_fpos_t=16
+ac_cv_sizeof_unsigned_int=4
+ac_cv_sizeof_unsigned_long=8
+ac_cv_sizeof_unsigned_long_long=8
+ac_cv_sizeof_unsigned_short=2
+ac_cv_type_off_t=yes
+ac_cv_type_size_t=yes
+am_cv_CC_dependencies_compiler_type=gcc3
+am_cv_CXX_dependencies_compiler_type=gcc3
+ax_cv_c_openmp=-fopenmp
+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/bin/ld
+lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64'
+lt_cv_path_NM='/usr/bin/nm -B'
+lt_cv_prog_compiler_c_o=yes
+lt_cv_prog_compiler_c_o_CXX=yes
+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_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\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\'''
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\'''
+lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
+lt_cv_sys_max_cmd_len=1966080
+
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+
+ACLOCAL='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run aclocal-1.10'
+AMDEPBACKSLASH='\'
+AMDEP_FALSE='#'
+AMDEP_TRUE=''
+AMTAR='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run tar'
+AM_CFLAGS=' -O3'
+AM_CXXFLAGS=' -O3'
+AM_LDFLAGS=''
+AR='ar'
+AUTOCONF='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoconf'
+AUTOHEADER='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoheader'
+AUTOMAKE='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run automake-1.10'
+AWK='gawk'
+CC='gcc'
+CCDEPMODE='depmode=gcc3'
+CFLAGS='-g -O2'
+CPP='gcc -E'
+CPPFLAGS=''
+CXX='g++'
+CXXCPP='g++ -E'
+CXXDEPMODE='depmode=gcc3'
+CXXFLAGS='-g -O2'
+CYGPATH_W='echo'
+DEFS='-DHAVE_CONFIG_H'
+DEPDIR='.deps'
+DSYMUTIL=''
+DUMPBIN=''
+ECHO_C=''
+ECHO_N='-n'
+ECHO_T=''
+EGREP='/bin/grep -E'
+EXEEXT=''
+FGREP='/bin/grep -F'
+GREP='/bin/grep'
+INSTALL_DATA='${INSTALL} -m 644'
+INSTALL_PROGRAM='${INSTALL}'
+INSTALL_SCRIPT='${INSTALL}'
+INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
+LD='/usr/bin/ld -m elf_x86_64'
+LDFLAGS=''
+LIBOBJS=''
+LIBS='-largtable2 -lm '
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+LIPO=''
+LN_S='ln -s'
+LTLIBOBJS=''
+MAKEINFO='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run makeinfo'
+MKDIR_P='/bin/mkdir -p'
+NM='/usr/bin/nm -B'
+NMEDIT=''
+OBJDUMP='objdump'
+OBJEXT='o'
+OPENMP_CFLAGS='-fopenmp'
+OPENMP_CXXFLAGS='-fopenmp'
+OTOOL64=''
+OTOOL=''
+PACKAGE='clustal-omega'
+PACKAGE_BUGREPORT='clustalw@ucd.ie'
+PACKAGE_CODENAME='AndreaGiacomo'
+PACKAGE_NAME='Clustal Omega'
+PACKAGE_STRING='Clustal Omega 1.2.4'
+PACKAGE_TARNAME='clustal-omega'
+PACKAGE_VERSION='1.2.4'
+PATH_SEPARATOR=':'
+RANLIB='ranlib'
+SED='/bin/sed'
+SET_MAKE=''
+SHELL='/bin/sh'
+STRIP='strip'
+VERSION='1.2.4'
+ac_ct_CC='gcc'
+ac_ct_CXX='g++'
+ac_ct_DUMPBIN=''
+am__fastdepCC_FALSE='#'
+am__fastdepCC_TRUE=''
+am__fastdepCXX_FALSE='#'
+am__fastdepCXX_TRUE=''
+am__include='include'
+am__isrc=''
+am__leading_dot='.'
+am__quote=''
+am__tar='${AMTAR} chof - "$$tardir"'
+am__untar='${AMTAR} xf -'
+bindir='${exec_prefix}/bin'
+build='x86_64-unknown-linux-gnu'
+build_alias=''
+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='x86_64-unknown-linux-gnu'
+host_alias=''
+host_cpu='x86_64'
+host_os='linux-gnu'
+host_vendor='unknown'
+htmldir='${docdir}'
+includedir='${prefix}/include'
+infodir='${datarootdir}/info'
+install_sh='$(SHELL) /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/install-sh'
+libdir='${exec_prefix}/lib'
+libexecdir='${exec_prefix}/libexec'
+localedir='${datarootdir}/locale'
+localstatedir='${prefix}/var'
+lt_ECHO='echo'
+mandir='${datarootdir}/man'
+mkdir_p='/bin/mkdir -p'
+oldincludedir='/usr/include'
+pdfdir='${docdir}'
+prefix='/usr/local'
+program_transform_name='s,x,x,'
+psdir='${docdir}'
+sbindir='${exec_prefix}/sbin'
+sharedstatedir='${prefix}/com'
+sysconfdir='${prefix}/etc'
+target_alias=''
+
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+
+#define PACKAGE_NAME "Clustal Omega"
+#define PACKAGE_TARNAME "clustal-omega"
+#define PACKAGE_VERSION "1.2.4"
+#define PACKAGE_STRING "Clustal Omega 1.2.4"
+#define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+#define PACKAGE "clustal-omega"
+#define VERSION "1.2.4"
+#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 __EXTENSIONS__ 1
+#define _ALL_SOURCE 1
+#define _GNU_SOURCE 1
+#define _POSIX_PTHREAD_SEMANTICS 1
+#define _TANDEM_SOURCE 1
+#define HAVE_DLFCN_H 1
+#define LT_OBJDIR ".libs/"
+#define CLUSTALO 1
+#define PACKAGE_CODENAME "AndreaGiacomo"
+#define LINUX 1
+#define STDC_HEADERS 1
+#define HAVE_ASSERT_H 1
+#define HAVE_CTYPE_H 1
+#define HAVE_FLOAT_H 1
+#define HAVE_LIMITS_H 1
+#define HAVE_MATH_H 1
+#define HAVE_MEMORY_H 1
+#define HAVE_STDARG_H 1
+#define HAVE_STDIO_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_STRING_H 1
+#define HAVE_TIME_H 1
+#define HAVE_UNISTD_H 1
+#define HAVE_LIBM 1
+#define HAVE_LOG2 1
+#define HAVE_ARGTABLE2_H 1
+#define HAVE_LIBARGTABLE2 1
+#define HAVE_OPENMP 1
+#define HAVE_NTOHS 1
+#define HAVE_NTOHL 1
+#define SIZEOF_UNSIGNED_SHORT 2
+#define SIZEOF_UNSIGNED_INT 4
+#define SIZEOF_UNSIGNED_LONG 8
+#define SIZEOF_UNSIGNED_LONG_LONG 8
+#define HAVE_STRTOULL 1
+#define HAVE_FTELLO 1
+#define HAVE_FSEEKO 1
+#define HAVE_FTELLO64 1
+#define HAVE_FSEEKO64 1
+#define SIZEOF_FPOS_T 16
+#define NDEBUG /**/
+
+configure: exit 0
git://source.jalview.org / jabaws.git / blobdiff