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| This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by ViennaRNA configure 1.8.5, which was
generated by GNU Autoconf 2.63. Invocation command line was
$ ./configure
## --------- ##
## Platform. ##
## --------- ##
hostname = michelr
uname -m = x86_64
uname -r = 3.2.0-38-generic
uname -s = Linux
uname -v = #60-Ubuntu SMP Wed Feb 13 13:22:43 UTC 2013
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = unknown
/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/michel/bin/apache-maven-2.2.1/bin
PATH: /home/michel/bin/eclipse
PATH: /home/michel/bin/jdk1.6.0_34/bin
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games
PATH: /home/michel/bin/apache-ant-1.8.0//bin
PATH: /usr/bin/gcc
## ----------- ##
## Core tests. ##
## ----------- ##
configure:1922: checking for a BSD-compatible install
configure:1990: result: /usr/bin/install -c
configure:2001: checking whether build environment is sane
configure:2061: result: yes
configure:2202: checking for a thread-safe mkdir -p
configure:2241: result: /bin/mkdir -p
configure:2254: checking for gawk
configure:2284: result: no
configure:2254: checking for mawk
configure:2270: found /usr/bin/mawk
configure:2281: result: mawk
configure:2292: checking whether make sets $(MAKE)
configure:2314: result: yes
configure:2397: checking if malloc debugging is wanted
configure:2417: result: no
configure:2468: checking build system type
configure:2486: result: x86_64-unknown-linux-gnu
configure:2508: checking host system type
configure:2523: result: x86_64-unknown-linux-gnu
configure:2594: checking for gcc
configure:2610: found /usr/bin/gcc
configure:2621: result: gcc
configure:2853: checking for C compiler version
configure:2861: gcc --version >&5
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 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:2865: $? = 0
configure:2872: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
configure:2876: $? = 0
configure:2883: gcc -V >&5
gcc: error: unrecognized option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2887: $? = 4
configure:2910: checking for C compiler default output file name
configure:2932: gcc conftest.c >&5
configure:2936: $? = 0
configure:2974: result: a.out
configure:2993: checking whether the C compiler works
configure:3003: ./a.out
configure:3007: $? = 0
configure:3026: result: yes
configure:3033: checking whether we are cross compiling
configure:3035: result: no
configure:3038: checking for suffix of executables
configure:3045: gcc -o conftest conftest.c >&5
configure:3049: $? = 0
configure:3075: result:
configure:3081: checking for suffix of object files
configure:3107: gcc -c conftest.c >&5
configure:3111: $? = 0
configure:3136: result: o
configure:3140: checking whether we are using the GNU C compiler
configure:3169: gcc -c conftest.c >&5
configure:3176: $? = 0
configure:3193: result: yes
configure:3202: checking whether gcc accepts -g
configure:3232: gcc -c -g conftest.c >&5
configure:3239: $? = 0
configure:3340: result: yes
configure:3357: checking for gcc option to accept ISO C89
configure:3431: gcc -c -g -O2 conftest.c >&5
configure:3438: $? = 0
configure:3461: result: none needed
configure:3490: checking for style of include used by make
configure:3518: result: GNU
configure:3543: checking dependency style of gcc
configure:3653: result: gcc3
configure:3671: checking whether gcc accepts -fpic
configure:3697: gcc -c -fpic conftest.c >&5
configure:3704: $? = 0
configure:3719: result: yes
configure:3754: checking for a BSD-compatible install
configure:3822: result: /usr/bin/install -c
configure:3876: checking for ranlib
configure:3892: found /usr/bin/ranlib
configure:3903: result: ranlib
configure:3926: checking whether gcc and cc understand -c and -o together
configure:3961: gcc -c conftest.c -o conftest2.o >&5
configure:3965: $? = 0
configure:3971: gcc -c conftest.c -o conftest2.o >&5
configure:3975: $? = 0
configure:3986: cc -c conftest.c >&5
configure:3990: $? = 0
configure:3998: cc -c conftest.c -o conftest2.o >&5
configure:4002: $? = 0
configure:4008: cc -c conftest.c -o conftest2.o >&5
configure:4012: $? = 0
configure:4030: result: yes
configure:4060: checking for perl
configure:4078: found /usr/bin/perl
configure:4090: result: /usr/bin/perl
configure:4184: checking how to run the C preprocessor
configure:4224: gcc -E conftest.c
configure:4231: $? = 0
configure:4262: gcc -E conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:4269: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "ViennaRNA"
| #define PACKAGE_TARNAME "ViennaRNA"
| #define PACKAGE_VERSION "1.8.5"
| #define PACKAGE_STRING "ViennaRNA 1.8.5"
| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at"
| #define PACKAGE "ViennaRNA"
| #define VERSION "1.8.5"
| #define UNUSED __attribute__ ((unused))
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4302: result: gcc -E
configure:4331: gcc -E conftest.c
configure:4338: $? = 0
configure:4369: gcc -E conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:4376: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "ViennaRNA"
| #define PACKAGE_TARNAME "ViennaRNA"
| #define PACKAGE_VERSION "1.8.5"
| #define PACKAGE_STRING "ViennaRNA 1.8.5"
| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at"
| #define PACKAGE "ViennaRNA"
| #define VERSION "1.8.5"
| #define UNUSED __attribute__ ((unused))
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4416: checking for grep that handles long lines and -e
configure:4476: result: /bin/grep
configure:4481: checking for egrep
configure:4545: result: /bin/grep -E
configure:4550: checking for ANSI C header files
configure:4580: gcc -c -g -O2 conftest.c >&5
configure:4587: $? = 0
configure:4686: gcc -o conftest -g -O2 conftest.c >&5
configure:4690: $? = 0
configure:4696: ./conftest
configure:4700: $? = 0
configure:4718: result: yes
configure:4742: checking for sys/types.h
configure:4763: gcc -c -g -O2 conftest.c >&5
configure:4770: $? = 0
configure:4787: result: yes
configure:4742: checking for sys/stat.h
configure:4763: gcc -c -g -O2 conftest.c >&5
configure:4770: $? = 0
configure:4787: result: yes
configure:4742: checking for stdlib.h
configure:4763: gcc -c -g -O2 conftest.c >&5
configure:4770: $? = 0
configure:4787: result: yes
configure:4742: checking for string.h
configure:4763: gcc -c -g -O2 conftest.c >&5
configure:4770: $? = 0
configure:4787: result: yes
configure:4742: checking for memory.h
configure:4763: gcc -c -g -O2 conftest.c >&5
configure:4770: $? = 0
configure:4787: result: yes
configure:4742: checking for strings.h
configure:4763: gcc -c -g -O2 conftest.c >&5
configure:4770: $? = 0
configure:4787: result: yes
configure:4742: checking for inttypes.h
configure:4763: gcc -c -g -O2 conftest.c >&5
configure:4770: $? = 0
configure:4787: result: yes
configure:4742: checking for stdint.h
configure:4763: gcc -c -g -O2 conftest.c >&5
configure:4770: $? = 0
configure:4787: result: yes
configure:4742: checking for unistd.h
configure:4763: gcc -c -g -O2 conftest.c >&5
configure:4770: $? = 0
configure:4787: result: yes
configure:4819: checking malloc.h usability
configure:4836: gcc -c -g -O2 conftest.c >&5
configure:4843: $? = 0
configure:4857: result: yes
configure:4861: checking malloc.h presence
configure:4876: gcc -E conftest.c
configure:4883: $? = 0
configure:4897: result: yes
configure:4930: checking for malloc.h
configure:4939: result: yes
configure:4808: checking for strings.h
configure:4815: result: yes
configure:4808: checking for unistd.h
configure:4815: result: yes
configure:4955: checking for an ANSI C-conforming const
configure:5030: gcc -c -g -O2 conftest.c >&5
configure:5037: $? = 0
configure:5052: result: yes
configure:5062: checking for size_t
configure:5090: gcc -c -g -O2 conftest.c >&5
configure:5097: $? = 0
configure:5124: gcc -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:60:21: error: expected expression before ')' token
configure:5131: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "ViennaRNA"
| #define PACKAGE_TARNAME "ViennaRNA"
| #define PACKAGE_VERSION "1.8.5"
| #define PACKAGE_STRING "ViennaRNA 1.8.5"
| #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at"
| #define PACKAGE "ViennaRNA"
| #define VERSION "1.8.5"
| #define UNUSED __attribute__ ((unused))
| #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_MALLOC_H 1
| #define HAVE_STRINGS_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:5154: result: yes
configure:5166: checking for inline
configure:5192: gcc -c -g -O2 conftest.c >&5
configure:5199: $? = 0
configure:5217: result: inline
configure:5244: checking for strdup
configure:5300: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:47:6: warning: conflicting types for built-in function 'strdup' [enabled by default]
configure:5307: $? = 0
configure:5329: result: yes
configure:5244: checking for strstr
configure:5300: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:48:6: warning: conflicting types for built-in function 'strstr' [enabled by default]
configure:5307: $? = 0
configure:5329: result: yes
configure:5244: checking for strchr
configure:5300: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:49:6: warning: conflicting types for built-in function 'strchr' [enabled by default]
configure:5307: $? = 0
configure:5329: result: yes
configure:5244: checking for erand48
configure:5300: gcc -o conftest -g -O2 conftest.c >&5
configure:5307: $? = 0
configure:5329: result: yes
configure:5496: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by ViennaRNA config.status 1.8.5, which was
generated by GNU Autoconf 2.63. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on michelr
config.status:825: creating Makefile
config.status:825: creating ViennaRNA.spec
config.status:825: creating Utils/Makefile
config.status:825: creating Progs/Makefile
config.status:825: creating lib/Makefile
config.status:825: creating man/Makefile
config.status:825: creating Cluster/Makefile
config.status:825: creating H/Makefile
config.status:825: creating Perl/Makefile
config.status:825: creating man/RNAheat.1
config.status:825: creating man/RNAsubopt.1
config.status:825: creating man/RNAdistance.1
config.status:825: creating man/RNAinverse.1
config.status:825: creating man/RNAeval.1
config.status:825: creating man/RNAfold.1
config.status:825: creating man/RNApdist.1
config.status:825: creating man/RNAplot.1
config.status:825: creating man/RNALfold.1
config.status:825: creating man/RNAalifold.1
config.status:825: creating man/RNAduplex.1
config.status:825: creating man/RNAcofold.1
config.status:825: creating man/RNAplfold.1
config.status:825: creating man/RNAup.1
config.status:825: creating man/RNApaln.1
config.status:825: creating man/RNAaliduplex.1
config.status:825: creating config.h
config.status:1047: config.h is unchanged
config.status:1099: executing depfiles commands
configure:6922: === configuring in RNAforester (/home/michel/Documents/Predictions/ViennaRNA-1.8.5/RNAforester)
configure:7025: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local' --cache-file=/dev/null --srcdir=.
configure:7030: error: ./configure failed for RNAforester
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_c_inline=inline
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_FPIC_set=
ac_cv_env_FPIC_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_PERLPREFIX_set=
ac_cv_env_PERLPREFIX_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_erand48=yes
ac_cv_func_strchr=yes
ac_cv_func_strdup=yes
ac_cv_func_strstr=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_malloc_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_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_path_PerlCmd=/usr/bin/perl
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=mawk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_cc_c89=
ac_cv_prog_cc_fpic=yes
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_gcc_c_o=yes
ac_cv_prog_make_make_set=yes
ac_cv_type_size_t=yes
am_cv_CC_dependencies_compiler_type=gcc3
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /home/michel/Documents/Predictions/ViennaRNA-1.8.5/missing --run aclocal-1.11'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /home/michel/Documents/Predictions/ViennaRNA-1.8.5/missing --run tar'
AUTOCONF='${SHELL} /home/michel/Documents/Predictions/ViennaRNA-1.8.5/missing --run autoconf'
AUTOHEADER='${SHELL} /home/michel/Documents/Predictions/ViennaRNA-1.8.5/missing --run autoheader'
AUTOMAKE='${SHELL} /home/michel/Documents/Predictions/ViennaRNA-1.8.5/missing --run automake-1.11'
AWK='mawk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=''
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
FPIC='-fpic'
GREP='/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
ISODATE='2013-02-22'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/michel/Documents/Predictions/ViennaRNA-1.8.5/missing --run makeinfo'
MAKE_CLUSTER_FALSE=''
MAKE_CLUSTER_TRUE='#'
MAKE_FORESTER_FALSE='#'
MAKE_FORESTER_TRUE=''
MAKE_KINFOLD_FALSE='#'
MAKE_KINFOLD_TRUE=''
MAKE_PERL_EXT_FALSE='#'
MAKE_PERL_EXT_TRUE=''
MKDIR_P='/bin/mkdir -p'
OBJEXT='o'
PACKAGE='ViennaRNA'
PACKAGE_BUGREPORT='rna@tbi.univie.ac.at'
PACKAGE_NAME='ViennaRNA'
PACKAGE_STRING='ViennaRNA 1.8.5'
PACKAGE_TARNAME='ViennaRNA'
PACKAGE_VERSION='1.8.5'
PATH_SEPARATOR=':'
PERLPREFIX=''
PerlCmd='/usr/bin/perl'
RANLIB='ranlib'
SET_MAKE=''
SHELL='/bin/bash'
STRIP=''
VERSION='1.8.5'
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} /home/michel/Documents/Predictions/ViennaRNA-1.8.5/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='${prefix}/com'
subdirs=' RNAforester Kinfold'
sysconfdir='${prefix}/etc'
target_alias=''
configure: exit 1 |
configure : error: C++ compiler cannot create executables
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