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 2.63.  Invocation command line was

  $ ./configure --disable-option-checking --prefix=/projects/remc_bigdata/miR/vRNA-2.0.0 --cache-file=/dev/null --srcdir=.

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

hostname = xhost09.bcgsc.ca
uname -m = x86_64
uname -r = 2.6.18-194.3.1.el5
uname -s = Linux
uname -v = #1 SMP Thu May 13 13:08:30 EDT 2010

/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: /home/grobertson/linux_x86_64/EPD/epd-6.2-2-rh5-x86_64/lib/python2.6/site-packages
PATH: /home/grobertson/linux_x86_64/EPD/epd-6.2-2-rh5-x86_64/lib
PATH: /home/grobertson/linux_x86_64/EPD/epd-6.2-2-rh5-x86_64/bin
PATH: /home/grobertson/linux_x86_64/libxml2/libxml2-2.7.3/bin
PATH: /home/grobertson/linux_x86_64/libxml2/libxml2-2.7.3/lib
PATH: /home/grobertson/linux_x86_64/samtools/samtools-0.1.12a
PATH: /home/grobertson/linux_x86_64/ruby/ruby-1.8.7-p302/bin
PATH: /home/grobertson/linux_x86_64/ruby/rubygems-1.3.5/bin
PATH: /home/grobertson/linux_x86_64/Git/git-1.6.5.1/bin
PATH: /home/grobertson/bin/x86_64
PATH: /home/grobertson/linux_x86_64/pysam/pysam-0.2/pysam
PATH: /home/grobertson/linux_x86_64/Pyrex/bin
PATH: /home/grobertson/linux_x86_64/Hg/bin
PATH: /home/grobertson/linux_x86_64/zlib/zlib-1.2.3
PATH: /home/grobertson/Pairagon/gmap-2007-09-28/bin
PATH: /home/grobertson/linux_x86_64/glib/glib-2.20.3/bin
PATH: /home/grobertson/linux_x86_64/Hg/mercurial-1.3.1
PATH: /home/grobertson/linux_x86_64/boost/boost_1_42_0/boost
PATH: /home/grobertson/linux_x86_64/BLAT/blatSrc/bin/x86_64-redhat-linux-gnu
PATH: /home/grobertson/linux_x86_64/perl_5.10/bin
PATH: /usr/lib/pkgconfig
PATH: /home/grobertson/linux_x86_64/R/R-2.12.1/bin
PATH: /home/grobertson/linux_x86_64/R/R-2.12.1/etc
PATH: /home/grobertson/apache-ant-1.7.1/bin
PATH: /home/grobertson/linux_x86_64/Cufflinks/tophat-1.0.13/bin
PATH: /home/grobertson/linux_x86_64/Cufflinks/bowtie-0.12.5
PATH: /home/grobertson/linux_x86_64/Cufflinks/cufflinks-0.8.2.Linux_x86_64
PATH: /home/grobertson/linux_x86_64/gsl/gsl-1.14/bin
PATH: /home/grobertson/linux_x86_64/gsl/gsl-1.14/lib
PATH: /home/grobertson/linux_x86_64/gsl/gsl-1.14/include/gsl
PATH: #{JAVA_HOME}/usr/bin
PATH: /usr/kerberos/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /home/grobertson/bin


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

configure:1900: checking for a BSD-compatible install
configure:1968: result: /usr/bin/install -c
configure:1979: checking whether build environment is sane
configure:2039: result: yes
configure:2180: checking for a thread-safe mkdir -p
configure:2219: result: /bin/mkdir -p
configure:2232: checking for gawk
configure:2248: found /bin/gawk
configure:2259: result: gawk
configure:2270: checking whether make sets $(MAKE)
configure:2292: result: yes
configure:2375: checking if malloc debugging is wanted
configure:2395: result: no
configure:2449: checking for gcc
configure:2465: found /usr/bin/gcc
configure:2476: result: gcc
configure:2708: checking for C compiler version
configure:2716: gcc --version >&5
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
Copyright (C) 2006 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:2720: $? = 0
configure:2727: 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 --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)
configure:2731: $? = 0
configure:2738: gcc -V >&5
gcc: '-V' option must have argument
configure:2742: $? = 1
configure:2765: checking for C compiler default output file name
configure:2787: gcc    conftest.c  >&5
configure:2791: $? = 0
configure:2829: result: a.out
configure:2848: checking whether the C compiler works
configure:2858: ./a.out
configure:2862: $? = 0
configure:2881: result: yes
configure:2888: checking whether we are cross compiling
configure:2890: result: no
configure:2893: checking for suffix of executables
configure:2900: gcc -o conftest    conftest.c  >&5
configure:2904: $? = 0
configure:2930: result: 
configure:2936: checking for suffix of object files
configure:2962: gcc -c   conftest.c >&5
configure:2966: $? = 0
configure:2991: result: o
configure:2995: checking whether we are using the GNU C compiler
configure:3024: gcc -c   conftest.c >&5
configure:3031: $? = 0
configure:3048: result: yes
configure:3057: checking whether gcc accepts -g
configure:3087: gcc -c -g  conftest.c >&5
configure:3094: $? = 0
configure:3195: result: yes
configure:3212: checking for gcc option to accept ISO C89
configure:3286: gcc  -c -g -O2  conftest.c >&5
configure:3293: $? = 0
configure:3316: result: none needed
configure:3345: checking for style of include used by make
configure:3373: result: GNU
configure:3398: checking dependency style of gcc
configure:3508: result: gcc3
configure:3538: checking build system type
configure:3556: result: x86_64-unknown-linux-gnu
configure:3578: checking host system type
configure:3593: result: x86_64-unknown-linux-gnu
configure:3623: checking for strdup
configure:3679: gcc -o conftest -g -O2   conftest.c  >&5
conftest.c:33: warning: conflicting types for built-in function 'strdup'
configure:3686: $? = 0
configure:3708: result: yes
configure:3623: checking for memset
configure:3679: gcc -o conftest -g -O2   conftest.c  >&5
conftest.c:34: warning: conflicting types for built-in function 'memset'
configure:3686: $? = 0
configure:3708: result: yes
configure:3623: checking for strchr
configure:3679: gcc -o conftest -g -O2   conftest.c  >&5
conftest.c:35: warning: conflicting types for built-in function 'strchr'
configure:3686: $? = 0
configure:3708: result: yes
configure:3743: checking for gcc option to support OpenMP
configure:3763: gcc -o conftest -g -O2   conftest.c  >&5
conftest.c:3: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'me'
In file included from conftest.c:5:
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:68: error: expected ')' before '*' token
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:69: error: expected ')' before '*' token
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:70: error: expected ')' before '*' token
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:71: error: expected ')' before '*' token
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:72: error: expected ')' before '*' token
configure:3770: $? = 1
configure: failed program was:
| 
| #ifndef _OPENMP
|  choke me
| #endif
| #include <omp.h>
| int main () { return omp_get_num_threads (); }
| 
configure:3802: gcc -o conftest -g -O2 -fopenmp   conftest.c  >&5
configure:3809: $? = 0
configure:3839: result: -fopenmp
configure:3851: checking for ViennaRNA package
configure:3894: result:  headers in "../H" and library... "../lib"
configure:3904: checking how to run the C preprocessor
configure:3944: gcc -E  -I../H conftest.c
configure:3951: $? = 0
configure:3982: gcc -E  -I../H conftest.c
conftest.c:13:28: error: ac_nonexistent.h: No such file or directory
configure:3989: $? = 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 "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:4022: result: gcc -E
configure:4051: gcc -E  -I../H conftest.c
configure:4058: $? = 0
configure:4089: gcc -E  -I../H conftest.c
conftest.c:13:28: error: ac_nonexistent.h: No such file or directory
configure:4096: $? = 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 "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:4136: checking for grep that handles long lines and -e
configure:4196: result: /bin/grep
configure:4201: checking for egrep
configure:4265: result: /bin/grep -E
configure:4270: checking for ANSI C header files
configure:4300: gcc -c -g -O2  -I../H conftest.c >&5
configure:4307: $? = 0
configure:4406: gcc -o conftest -g -O2  -I../H -L../lib  conftest.c  >&5
configure:4410: $? = 0
configure:4416: ./conftest
configure:4420: $? = 0
configure:4438: result: yes
configure:4462: checking for sys/types.h
configure:4483: gcc -c -g -O2  -I../H conftest.c >&5
configure:4490: $? = 0
configure:4507: result: yes
configure:4462: checking for sys/stat.h
configure:4483: gcc -c -g -O2  -I../H conftest.c >&5
configure:4490: $? = 0
configure:4507: result: yes
configure:4462: checking for stdlib.h
configure:4483: gcc -c -g -O2  -I../H conftest.c >&5
configure:4490: $? = 0
configure:4507: result: yes
configure:4462: checking for string.h
configure:4483: gcc -c -g -O2  -I../H conftest.c >&5
configure:4490: $? = 0
configure:4507: result: yes
configure:4462: checking for memory.h
configure:4483: gcc -c -g -O2  -I../H conftest.c >&5
configure:4490: $? = 0
configure:4507: result: yes
configure:4462: checking for strings.h
configure:4483: gcc -c -g -O2  -I../H conftest.c >&5
configure:4490: $? = 0
configure:4507: result: yes
configure:4462: checking for inttypes.h
configure:4483: gcc -c -g -O2  -I../H conftest.c >&5
configure:4490: $? = 0
configure:4507: result: yes
configure:4462: checking for stdint.h
configure:4483: gcc -c -g -O2  -I../H conftest.c >&5
configure:4490: $? = 0
configure:4507: result: yes
configure:4462: checking for unistd.h
configure:4483: gcc -c -g -O2  -I../H conftest.c >&5
configure:4490: $? = 0
configure:4507: result: yes
configure:4530: checking for stdlib.h
configure:4537: result: yes
configure:4530: checking for string.h
configure:4537: result: yes
configure:4530: checking for strings.h
configure:4537: result: yes
configure:4530: checking for unistd.h
configure:4537: result: yes
configure:4541: checking fold.h usability
configure:4558: gcc -c -g -O2  -I../H conftest.c >&5
configure:4565: $? = 0
configure:4579: result: yes
configure:4583: checking fold.h presence
configure:4598: gcc -E  -I../H conftest.c
configure:4605: $? = 0
configure:4619: result: yes
configure:4652: checking for fold.h
configure:4661: result: yes
configure:4678: checking for exp in -lm
configure:4713: gcc -o conftest -g -O2  -I../H -L../lib  conftest.c -lm   >&5
conftest.c:35: warning: conflicting types for built-in function 'exp'
configure:4720: $? = 0
configure:4741: result: yes
configure:4757: checking for stdlib.h
configure:4764: result: yes
configure:4903: checking for GNU libc compatible malloc
configure:4937: gcc -o conftest -g -O2  -I../H -L../lib  conftest.c -lm  >&5
configure:4941: $? = 0
configure:4947: ./conftest
configure:4951: $? = 0
configure:4968: result: yes
configure:5001: checking for stdlib.h
configure:5008: result: yes
configure:5147: checking for GNU libc compatible realloc
configure:5181: gcc -o conftest -g -O2  -I../H -L../lib  conftest.c -lm  >&5
configure:5185: $? = 0
configure:5191: ./conftest
configure:5195: $? = 0
configure:5212: result: yes
configure:5243: checking for an ANSI C-conforming const
configure:5318: gcc -c -g -O2  -I../H conftest.c >&5
configure:5325: $? = 0
configure:5340: result: yes
configure:5478: creating ./config.status

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

This file was extended by kinfold config.status 1.3, which was
generated by GNU Autoconf 2.63.  Invocation command line was

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

on xhost09.bcgsc.ca

config.status:795: creating Example/Makefile
config.status:795: creating Makefile
config.status:795: creating config.h
config.status:1017: config.h is unchanged
config.status:1069: 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

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

ACLOCAL='${SHELL} /projects/remc_bigdata/miR/ViennaRNA-2.0.0/Kinfold/missing --run aclocal-1.11'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /projects/remc_bigdata/miR/ViennaRNA-2.0.0/Kinfold/missing --run tar'
AUTOCONF='${SHELL} /projects/remc_bigdata/miR/ViennaRNA-2.0.0/Kinfold/missing --run autoconf'
AUTOHEADER='${SHELL} /projects/remc_bigdata/miR/ViennaRNA-2.0.0/Kinfold/missing --run autoheader'
AUTOMAKE='${SHELL} /projects/remc_bigdata/miR/ViennaRNA-2.0.0/Kinfold/missing --run automake-1.11'
AWK='gawk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=' -I../H'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
ISODATE='2011-05-22'
LDFLAGS='-L../lib '
LIBOBJS=''
LIBS='-lRNA -lm '
LTLIBOBJS=''
MAKEINFO='${SHELL} /projects/remc_bigdata/miR/ViennaRNA-2.0.0/Kinfold/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_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__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} /projects/remc_bigdata/miR/ViennaRNA-2.0.0/Kinfold/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='/projects/remc_bigdata/miR/vRNA-2.0.0'
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 "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 "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