--- /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 kinfold configure 1.3, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ $ ./configure --disable-option-checking --prefix=/usr/local --cache-file=/dev/null --srcdir=.
+
+## --------- ##
+## 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
+PATH: /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/tcoffee/t_coffee_source
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+configure:2162: checking whether make supports nested variables
+configure:2179: result: yes
+configure:2235: checking for a BSD-compatible install
+configure:2303: result: /usr/bin/install -c
+configure:2314: checking whether build environment is sane
+configure:2364: result: yes
+configure:2505: checking for a thread-safe mkdir -p
+configure:2544: result: /bin/mkdir -p
+configure:2557: checking for gawk
+configure:2573: found /bin/gawk
+configure:2584: result: gawk
+configure:2595: checking whether make sets $(MAKE)
+configure:2617: result: yes
+configure:2698: checking if malloc debugging is wanted
+configure:2716: result: no
+configure:2770: checking for gcc
+configure:2786: found /usr/bin/gcc
+configure:2797: result: gcc
+configure:3026: checking for C compiler version
+configure:3035: 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:3046: $? = 0
+configure:3035: 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:3046: $? = 0
+configure:3035: gcc -V >&5
+gcc: '-V' option must have argument
+configure:3046: $? = 1
+configure:3035: gcc -qversion >&5
+gcc: unrecognized option '-qversion'
+gcc: no input files
+configure:3046: $? = 1
+configure:3066: checking whether the C compiler works
+configure:3088: gcc conftest.c >&5
+configure:3092: $? = 0
+configure:3140: result: yes
+configure:3143: checking for C compiler default output file name
+configure:3145: result: a.out
+configure:3151: checking for suffix of executables
+configure:3158: gcc -o conftest conftest.c >&5
+configure:3162: $? = 0
+configure:3184: result:
+configure:3206: checking whether we are cross compiling
+configure:3214: gcc -o conftest conftest.c >&5
+configure:3218: $? = 0
+configure:3225: ./conftest
+configure:3229: $? = 0
+configure:3244: result: no
+configure:3249: checking for suffix of object files
+configure:3271: gcc -c conftest.c >&5
+configure:3275: $? = 0
+configure:3296: result: o
+configure:3300: checking whether we are using the GNU C compiler
+configure:3319: gcc -c conftest.c >&5
+configure:3319: $? = 0
+configure:3328: result: yes
+configure:3337: checking whether gcc accepts -g
+configure:3357: gcc -c -g conftest.c >&5
+configure:3357: $? = 0
+configure:3398: result: yes
+configure:3415: checking for gcc option to accept ISO C89
+configure:3479: gcc -c -g -O2 conftest.c >&5
+configure:3479: $? = 0
+configure:3492: result: none needed
+configure:3523: checking for style of include used by make
+configure:3551: result: GNU
+configure:3577: checking dependency style of gcc
+configure:3688: result: gcc3
+configure:3716: checking build system type
+configure:3730: result: x86_64-unknown-linux-gnu
+configure:3750: checking host system type
+configure:3763: result: x86_64-unknown-linux-gnu
+configure:3788: checking for strdup
+configure:3788: gcc -o conftest -g -O2 conftest.c >&5
+conftest.c:34: warning: conflicting types for built-in function 'strdup'
+configure:3788: $? = 0
+configure:3788: result: yes
+configure:3788: checking for memset
+configure:3788: gcc -o conftest -g -O2 conftest.c >&5
+conftest.c:35: warning: conflicting types for built-in function 'memset'
+configure:3788: $? = 0
+configure:3788: result: yes
+configure:3788: checking for strchr
+configure:3788: gcc -o conftest -g -O2 conftest.c >&5
+conftest.c:36: warning: conflicting types for built-in function 'strchr'
+configure:3788: $? = 0
+configure:3788: result: yes
+configure:3819: checking for gcc option to support OpenMP
+configure:3834: gcc -o conftest -g -O2 conftest.c >&5
+conftest.c:16: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'me'
+In file included from conftest.c:18:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:76: error: expected ')' before '*' token
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:77: error: expected ')' before '*' token
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:78: error: expected ')' before '*' token
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:79: error: expected ')' before '*' token
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:80: error: expected ')' before '*' token
+configure:3834: $? = 1
+configure: failed program was:
+| /* confdefs.h */
+| #define PACKAGE_NAME "kinfold"
+| #define PACKAGE_TARNAME "Kinfold"
+| #define PACKAGE_VERSION "1.3"
+| #define PACKAGE_STRING "kinfold 1.3"
+| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at"
+| #define PACKAGE_URL ""
+| #define PACKAGE "Kinfold"
+| #define VERSION "1.3"
+| #define HAVE_STRDUP 1
+| #define HAVE_MEMSET 1
+| #define HAVE_STRCHR 1
+| /* end confdefs.h. */
+|
+| #ifndef _OPENMP
+| choke me
+| #endif
+| #include <omp.h>
+| int main () { return omp_get_num_threads (); }
+|
+configure:3851: gcc -o conftest -g -O2 -fopenmp conftest.c >&5
+configure:3851: $? = 0
+configure:3865: result: -fopenmp
+configure:3877: checking for ViennaRNA package
+configure:3920: result: headers in "../H" and library... "../lib"
+configure:3930: checking how to run the C preprocessor
+configure:3961: gcc -E -I../H conftest.c
+configure:3961: $? = 0
+configure:3975: gcc -E -I../H conftest.c
+conftest.c:14:28: error: ac_nonexistent.h: No such file or directory
+configure:3975: $? = 1
+configure: failed program was:
+| /* confdefs.h */
+| #define PACKAGE_NAME "kinfold"
+| #define PACKAGE_TARNAME "Kinfold"
+| #define PACKAGE_VERSION "1.3"
+| #define PACKAGE_STRING "kinfold 1.3"
+| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at"
+| #define PACKAGE_URL ""
+| #define PACKAGE "Kinfold"
+| #define VERSION "1.3"
+| #define HAVE_STRDUP 1
+| #define HAVE_MEMSET 1
+| #define HAVE_STRCHR 1
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:4000: result: gcc -E
+configure:4020: gcc -E -I../H conftest.c
+configure:4020: $? = 0
+configure:4034: gcc -E -I../H conftest.c
+conftest.c:14:28: error: ac_nonexistent.h: No such file or directory
+configure:4034: $? = 1
+configure: failed program was:
+| /* confdefs.h */
+| #define PACKAGE_NAME "kinfold"
+| #define PACKAGE_TARNAME "Kinfold"
+| #define PACKAGE_VERSION "1.3"
+| #define PACKAGE_STRING "kinfold 1.3"
+| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at"
+| #define PACKAGE_URL ""
+| #define PACKAGE "Kinfold"
+| #define VERSION "1.3"
+| #define HAVE_STRDUP 1
+| #define HAVE_MEMSET 1
+| #define HAVE_STRCHR 1
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:4063: checking for grep that handles long lines and -e
+configure:4121: result: /bin/grep
+configure:4126: checking for egrep
+configure:4188: result: /bin/grep -E
+configure:4193: checking for ANSI C header files
+configure:4213: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4213: $? = 0
+configure:4286: gcc -o conftest -g -O2 -I../H -L../lib conftest.c >&5
+configure:4286: $? = 0
+configure:4286: ./conftest
+configure:4286: $? = 0
+configure:4297: result: yes
+configure:4310: checking for sys/types.h
+configure:4310: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4310: $? = 0
+configure:4310: result: yes
+configure:4310: checking for sys/stat.h
+configure:4310: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4310: $? = 0
+configure:4310: result: yes
+configure:4310: checking for stdlib.h
+configure:4310: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4310: $? = 0
+configure:4310: result: yes
+configure:4310: checking for string.h
+configure:4310: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4310: $? = 0
+configure:4310: result: yes
+configure:4310: checking for memory.h
+configure:4310: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4310: $? = 0
+configure:4310: result: yes
+configure:4310: checking for strings.h
+configure:4310: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4310: $? = 0
+configure:4310: result: yes
+configure:4310: checking for inttypes.h
+configure:4310: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4310: $? = 0
+configure:4310: result: yes
+configure:4310: checking for stdint.h
+configure:4310: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4310: $? = 0
+configure:4310: result: yes
+configure:4310: checking for unistd.h
+configure:4310: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4310: $? = 0
+configure:4310: result: yes
+configure:4325: checking for stdlib.h
+configure:4325: result: yes
+configure:4325: checking for string.h
+configure:4325: result: yes
+configure:4325: checking for strings.h
+configure:4325: result: yes
+configure:4325: checking for unistd.h
+configure:4325: result: yes
+configure:4325: checking fold.h usability
+configure:4325: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4325: $? = 0
+configure:4325: result: yes
+configure:4325: checking fold.h presence
+configure:4325: gcc -E -I../H conftest.c
+configure:4325: $? = 0
+configure:4325: result: yes
+configure:4325: checking for fold.h
+configure:4325: result: yes
+configure:4336: checking for exp in -lm
+configure:4361: gcc -o conftest -g -O2 -I../H -L../lib conftest.c -lm >&5
+conftest.c:36: warning: conflicting types for built-in function 'exp'
+configure:4361: $? = 0
+configure:4370: result: yes
+configure:4383: checking for stdlib.h
+configure:4383: result: yes
+configure:4393: checking for GNU libc compatible malloc
+configure:4417: gcc -o conftest -g -O2 -I../H -L../lib conftest.c -lm >&5
+configure:4417: $? = 0
+configure:4417: ./conftest
+configure:4417: $? = 0
+configure:4427: result: yes
+configure:4450: checking for stdlib.h
+configure:4450: result: yes
+configure:4460: checking for GNU libc compatible realloc
+configure:4484: gcc -o conftest -g -O2 -I../H -L../lib conftest.c -lm >&5
+configure:4484: $? = 0
+configure:4484: ./conftest
+configure:4484: $? = 0
+configure:4494: result: yes
+configure:4518: checking for an ANSI C-conforming const
+configure:4583: gcc -c -g -O2 -I../H conftest.c >&5
+configure:4583: $? = 0
+configure:4590: result: yes
+configure:4732: creating ./config.status
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by kinfold config.status 1.3, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ CONFIG_FILES =
+ CONFIG_HEADERS =
+ CONFIG_LINKS =
+ CONFIG_COMMANDS =
+ $ ./config.status
+
+on ningal.cluster.lifesci.dundee.ac.uk
+
+config.status:888: creating Example/Makefile
+config.status:888: creating Makefile
+config.status:888: creating config.h
+config.status:1117: executing depfiles commands
+
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+
+ac_cv_build=x86_64-unknown-linux-gnu
+ac_cv_c_compiler_gnu=yes
+ac_cv_c_const=yes
+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_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_malloc_0_nonnull=yes
+ac_cv_func_memset=yes
+ac_cv_func_realloc_0_nonnull=yes
+ac_cv_func_strchr=yes
+ac_cv_func_strdup=yes
+ac_cv_header_fold_h=yes
+ac_cv_header_inttypes_h=yes
+ac_cv_header_memory_h=yes
+ac_cv_header_stdc=yes
+ac_cv_header_stdint_h=yes
+ac_cv_header_stdlib_h=yes
+ac_cv_header_string_h=yes
+ac_cv_header_strings_h=yes
+ac_cv_header_sys_stat_h=yes
+ac_cv_header_sys_types_h=yes
+ac_cv_header_unistd_h=yes
+ac_cv_host=x86_64-unknown-linux-gnu
+ac_cv_lib_m_exp=yes
+ac_cv_objext=o
+ac_cv_path_EGREP='/bin/grep -E'
+ac_cv_path_GREP=/bin/grep
+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_ac_ct_CC=gcc
+ac_cv_prog_c_openmp=-fopenmp
+ac_cv_prog_cc_c89=
+ac_cv_prog_cc_g=yes
+ac_cv_prog_make_make_set=yes
+am_cv_CC_dependencies_compiler_type=gcc3
+am_cv_make_support_nested_variables=yes
+
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+
+ACLOCAL='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/missing --run aclocal-1.11'
+AMDEPBACKSLASH='\'
+AMDEP_FALSE='#'
+AMDEP_TRUE=''
+AMTAR='$${TAR-tar}'
+AM_BACKSLASH='\'
+AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
+AM_DEFAULT_VERBOSITY='0'
+AM_V='$(V)'
+AUTOCONF='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/missing --run autoconf'
+AUTOHEADER='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/missing --run autoheader'
+AUTOMAKE='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/missing --run automake-1.11'
+AWK='gawk'
+CC='gcc'
+CCDEPMODE='depmode=gcc3'
+CFLAGS='-g -O2'
+CPP='gcc -E'
+CPPFLAGS=' -I../H'
+CYGPATH_W='echo'
+DEFS='-DHAVE_CONFIG_H'
+DEPDIR='.deps'
+ECHO_C=''
+ECHO_N='-n'
+ECHO_T=''
+EGREP='/bin/grep -E'
+EXEEXT=''
+GREP='/bin/grep'
+INSTALL_DATA='${INSTALL} -m 644'
+INSTALL_PROGRAM='${INSTALL}'
+INSTALL_SCRIPT='${INSTALL}'
+INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
+ISODATE='2017-04-11'
+LDFLAGS='-L../lib '
+LIBOBJS=''
+LIBS='-lRNA -lm '
+LTLIBOBJS=''
+MAKEINFO='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/missing --run makeinfo'
+MKDIR_P='/bin/mkdir -p'
+OBJEXT='o'
+OPENMP_CFLAGS='-fopenmp'
+PACKAGE='Kinfold'
+PACKAGE_BUGREPORT='rna@tbi.univie.ac.at'
+PACKAGE_NAME='kinfold'
+PACKAGE_STRING='kinfold 1.3'
+PACKAGE_TARNAME='Kinfold'
+PACKAGE_URL=''
+PACKAGE_VERSION='1.3'
+PATH_SEPARATOR=':'
+SET_MAKE=''
+SHELL='/bin/sh'
+STRIP=''
+VERSION='1.3'
+ac_ct_CC='gcc'
+am__EXEEXT_FALSE=''
+am__EXEEXT_TRUE='#'
+am__fastdepCC_FALSE='#'
+am__fastdepCC_TRUE=''
+am__include='include'
+am__isrc=''
+am__leading_dot='.'
+am__nodep='_no'
+am__quote=''
+am__tar='$${TAR-tar} chof - "$$tardir"'
+am__untar='$${TAR-tar} 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='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/install-sh'
+libdir='${exec_prefix}/lib'
+libexecdir='${exec_prefix}/libexec'
+localedir='${datarootdir}/locale'
+localstatedir='${prefix}/var'
+mandir='${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. ##
+## ----------- ##
+
+/* confdefs.h */
+#define PACKAGE_NAME "kinfold"
+#define PACKAGE_TARNAME "Kinfold"
+#define PACKAGE_VERSION "1.3"
+#define PACKAGE_STRING "kinfold 1.3"
+#define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at"
+#define PACKAGE_URL ""
+#define PACKAGE "Kinfold"
+#define VERSION "1.3"
+#define HAVE_STRDUP 1
+#define HAVE_MEMSET 1
+#define HAVE_STRCHR 1
+#define STDC_HEADERS 1
+#define HAVE_SYS_TYPES_H 1
+#define HAVE_SYS_STAT_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_STRING_H 1
+#define HAVE_MEMORY_H 1
+#define HAVE_STRINGS_H 1
+#define HAVE_INTTYPES_H 1
+#define HAVE_STDINT_H 1
+#define HAVE_UNISTD_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_STRING_H 1
+#define HAVE_STRINGS_H 1
+#define HAVE_UNISTD_H 1
+#define HAVE_FOLD_H 1
+#define HAVE_LIBM 1
+#define HAVE_STDLIB_H 1
+#define HAVE_MALLOC 1
+#define HAVE_STDLIB_H 1
+#define HAVE_REALLOC 1
+
+configure: exit 0
git://source.jalview.org / jabaws.git / blobdiff