Hey Ubuntu's,

I'm a new user and I'm having problems installing a bioinformatics package named FSA (Fast Statistical Alignment) developed in Berkeley. The instalation was done with mummer and exonerate bioinformatics packages, but these 2 packages seem well installed.

The config log says:


configure: failed program was:

I /* confdefs.h. */


Any help is welcome, many thanks in advance.


The full config.log is bellow:

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by FSA configure 1.14.1, which was
generated by GNU Autoconf 2.63. Invocation command line was

$ ./configure --with-mummer --with-exonerate

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

hostname = ubuntu
uname -m = x86_64
uname -r = 2.6.27-11-generic
uname -s = Linux
uname -v = #1 SMP Thu Jan 29 19:28:32 UTC 2009

/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: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games


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

configure:1925: checking for gawk
configure:1941: found /usr/bin/gawk
configure:1952: result: gawk
configure:2021: checking for g++
configure:2037: found /usr/bin/g++
configure:2048: result: g++
configure:2075: checking for C++ compiler version
configure:2083: g++ --version >&5
g++ (Ubuntu 4.3.2-1ubuntu12) 4.3.2
Copyright (C) 2008 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:2087: $? = 0
configure:2094: g++ -v >&5
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.3.2-1ubuntu12' --with-bugurl=file:///usr/share/doc/gcc-4.3/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.3 --program-suffix=-4.3 --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-mpfr --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.3.2 (Ubuntu 4.3.2-1ubuntu12)
configure:2098: $? = 0
configure:2105: g++ -V >&5
g++: '-V' option must have argument
configure:2109: $? = 1
configure:2132: checking for C++ compiler default output file name
configure:2154: g++ conftest.cpp >&5
configure:2158: $? = 0
configure:2196: result: a.out
configure:2215: checking whether the C++ compiler works
configure:2225: ./a.out
configure:2229: $? = 0
configure:2248: result: yes
configure:2255: checking whether we are cross compiling
configure:2257: result: no
configure:2260: checking for suffix of executables
configure:2267: g++ -o conftest conftest.cpp >&5
configure:2271: $? = 0
configure:2297: result:
configure:2303: checking for suffix of object files
configure:2329: g++ -c conftest.cpp >&5
configure:2333: $? = 0
configure:2358: result: o
configure:2362: checking whether we are using the GNU C++ compiler
configure:2391: g++ -c conftest.cpp >&5
configure:2398: $? = 0
configure:2415: result: yes
configure:2424: checking whether g++ accepts -g
configure:2454: g++ -c -g conftest.cpp >&5
configure:2461: $? = 0
configure:2562: result: yes
configure:2633: checking for gcc
configure:2649: found /usr/bin/gcc
configure:2660: result: gcc
configure:2892: checking for C compiler version
configure:2900: gcc --version >&5
gcc (Ubuntu 4.3.2-1ubuntu12) 4.3.2
Copyright (C) 2008 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:2904: $? = 0
configure:2911: gcc -v >&5
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.3.2-1ubuntu12' --with-bugurl=file:///usr/share/doc/gcc-4.3/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.3 --program-suffix=-4.3 --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-mpfr --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.3.2 (Ubuntu 4.3.2-1ubuntu12)
configure:2915: $? = 0
configure:2922: gcc -V >&5
gcc: '-V' option must have argument
configure:2926: $? = 1
configure:2929: checking whether we are using the GNU C compiler
configure:2958: gcc -c conftest.c >&5
configure:2965: $? = 0
configure:2982: result: yes
configure:2991: checking whether gcc accepts -g
configure:3021: gcc -c -g conftest.c >&5
configure:3028: $? = 0
configure:3129: result: yes
configure:3146: checking for gcc option to accept ISO C89
configure:3220: gcc -c -g -O2 conftest.c >&5
configure:3227: $? = 0
configure:3250: result: none needed
configure:3268: checking whether make sets $(MAKE)
configure:3290: result: yes
configure:3342: checking for ranlib
configure:3358: found /usr/bin/ranlib
configure:3369: result: ranlib
configure:3405: checking for a BSD-compatible install
configure:3473: result: /usr/bin/install -c
configure:3492: checking how to run the C preprocessor
configure:3532: gcc -E conftest.c
configure:3539: $? = 0
configure:3570: gcc -E conftest.c
conftest.c:8:28: error: ac_nonexistent.h: No such file or directory
configure:3577: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:3610: result: gcc -E
configure:3639: gcc -E conftest.c
configure:3646: $? = 0
configure:3677: gcc -E conftest.c
conftest.c:8:28: error: ac_nonexistent.h: No such file or directory
configure:3684: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:3724: checking for grep that handles long lines and -e
configure:3784: result: /bin/grep
configure:3789: checking for egrep
configure:3853: result: /bin/grep -E
configure:3858: checking for ANSI C header files
configure:3888: gcc -c -g -O2 conftest.c >&5
configure:3895: $? = 0
configure:3994: gcc -o conftest -g -O2 conftest.c >&5
configure:3998: $? = 0
configure:4004: ./conftest
configure:4008: $? = 0
configure:4026: result: yes
configure:4050: checking for sys/types.h
configure:4071: gcc -c -g -O2 conftest.c >&5
configure:4078: $? = 0
configure:4095: result: yes
configure:4050: checking for sys/stat.h
configure:4071: gcc -c -g -O2 conftest.c >&5
configure:4078: $? = 0
configure:4095: result: yes
configure:4050: checking for stdlib.h
configure:4071: gcc -c -g -O2 conftest.c >&5
configure:4078: $? = 0
configure:4095: result: yes
configure:4050: checking for string.h
configure:4071: gcc -c -g -O2 conftest.c >&5
configure:4078: $? = 0
configure:4095: result: yes
configure:4050: checking for memory.h
configure:4071: gcc -c -g -O2 conftest.c >&5
configure:4078: $? = 0
configure:4095: result: yes
configure:4050: checking for strings.h
configure:4071: gcc -c -g -O2 conftest.c >&5
configure:4078: $? = 0
configure:4095: result: yes
configure:4050: checking for inttypes.h
configure:4071: gcc -c -g -O2 conftest.c >&5
configure:4078: $? = 0
configure:4095: result: yes
configure:4050: checking for stdint.h
configure:4071: gcc -c -g -O2 conftest.c >&5
configure:4078: $? = 0
configure:4095: result: yes
configure:4050: checking for unistd.h
configure:4071: gcc -c -g -O2 conftest.c >&5
configure:4078: $? = 0
configure:4095: result: yes
configure:4116: checking for stdlib.h
configure:4123: result: yes
configure:4116: checking for string.h
configure:4123: result: yes
configure:4116: checking for unistd.h
configure:4123: result: yes
configure:4264: checking for stdbool.h that conforms to C99
configure:4359: gcc -c -g -O2 conftest.c >&5
configure:4366: $? = 0
configure:4381: result: yes
configure:4383: checking for _Bool
configure:4411: gcc -c -g -O2 conftest.c >&5
configure:4418: $? = 0
configure:4445: gcc -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:57: error: expected expression before ')' token
configure:4452: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_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 ((_Bool)))
| return 0;
| ;
| return 0;
| }
configure:4475: result: yes
configure:4494: checking for inline
configure:4520: gcc -c -g -O2 conftest.c >&5
configure:4527: $? = 0
configure:4545: result: inline
configure:4564: checking for pid_t
configure:4592: gcc -c -g -O2 conftest.c >&5
configure:4599: $? = 0
configure:4626: gcc -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:59: error: expected expression before ')' token
configure:4633: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_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 ((pid_t)))
| return 0;
| ;
| return 0;
| }
configure:4656: result: yes
configure:4668: checking for size_t
configure:4696: gcc -c -g -O2 conftest.c >&5
configure:4703: $? = 0
configure:4730: gcc -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:59: error: expected expression before ')' token
configure:4737: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_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:4760: result: yes
configure:4773: checking for unsigned long long int
configure:4804: gcc -o conftest -g -O2 conftest.c >&5
configure:4811: $? = 0
configure:4831: result: yes
configure:4843: checking for uintmax_t
configure:4871: gcc -c -g -O2 conftest.c >&5
configure:4878: $? = 0
configure:4905: gcc -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:60: error: expected expression before ')' token
configure:4912: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 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 ((uintmax_t)))
| return 0;
| ;
| return 0;
| }
configure:4935: result: yes
configure:4955: checking for ptrdiff_t
configure:4983: gcc -c -g -O2 conftest.c >&5
configure:4990: $? = 0
configure:5017: gcc -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:61: error: expected expression before ')' token
configure:5024: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 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 ((ptrdiff_t)))
| return 0;
| ;
| return 0;
| }
configure:5047: result: yes
configure:5062: checking whether the compiler supports __gnu_cxx::hash_map
configure:5096: g++ -c conftest.cpp >&5
In file included from /usr/include/c++/4.3/ext/hash_map:64,
from conftest.cpp:26:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
configure:5103: $? = 0
configure:5125: result: yes
configure:5135: checking whether the compiler implements namespaces
configure:5168: g++ -c conftest.cpp >&5
configure:5175: $? = 0
configure:5197: result: yes
configure:5207: checking whether the compiler has ext/hash_map
configure:5244: g++ -c conftest.cpp >&5
In file included from /usr/include/c++/4.3/ext/hash_map:64,
from conftest.cpp:28:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
conftest.cpp: In function 'int main()':
conftest.cpp:35: error: 'hash_map' was not declared in this scope
conftest.cpp:35: error: expected primary-expression before 'int'
conftest.cpp:35: error: expected `;' before 'int'
configure:5251: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| /* end confdefs.h. */
| #include <ext/hash_map>
| #ifdef HAVE_NAMESPACES
| using namespace std;
| #endif
| int
| main ()
| {
| hash_map<int, int> t; return 0;
| ;
| return 0;
| }
configure:5273: result: no
configure:5284: checking whether the compiler supports std::hash_map
configure:5318: g++ -c conftest.cpp >&5
In file included from /usr/include/c++/4.3/backward/hash_map:64,
from conftest.cpp:28:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
conftest.cpp:29: error: 'std::hash_map' has not been declared
configure:5325: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| /* end confdefs.h. */
| #include <hash_map>
| using std::hash_map;
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:5347: result: no
configure:5375: checking vfork.h usability
configure:5392: gcc -c -g -O2 conftest.c >&5
conftest.c:61:19: error: vfork.h: No such file or directory
configure:5399: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| /* 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 <vfork.h>
configure:5413: result: no
configure:5417: checking vfork.h presence
configure:5432: gcc -E conftest.c
conftest.c:28:19: error: vfork.h: No such file or directory
configure:5439: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| /* end confdefs.h. */
| #include <vfork.h>
configure:5453: result: no
configure:5486: checking for vfork.h
configure:5495: result: no
configure:5515: checking for fork
configure:5571: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:51: warning: conflicting types for built-in function 'fork'
configure:5578: $? = 0
configure:5600: result: yes
configure:5515: checking for vfork
configure:5571: gcc -o conftest -g -O2 conftest.c >&5
configure:5578: $? = 0
configure:5600: result: yes
configure:5613: checking for working fork
configure:5645: gcc -o conftest -g -O2 conftest.c >&5
configure:5649: $? = 0
configure:5655: ./conftest
configure:5659: $? = 0
configure:5676: result: yes
configure:5697: checking for working vfork
configure:5838: result: yes
configure:5881: checking for floor
configure:5937: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:55: warning: conflicting types for built-in function 'floor'
/tmp/ccI1575X.o: In function `main':
/home/pj/FSA/fsa-1.14.1/conftest.c:66: undefined reference to `floor'
collect2: ld returned 1 exit status
configure:5944: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| /* end confdefs.h. */
| /* Define floor to an innocuous variant, in case <limits.h> declares floor.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define floor innocuous_floor
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char floor (); 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 floor
|
| /* 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 floor ();
| /* 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_floor || defined __stub___floor
| choke me
| #endif
|
| int
| main ()
| {
| return floor ();
| ;
| return 0;
| }
configure:5966: result: no
configure:5881: checking for memmove
configure:5937: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:55: warning: conflicting types for built-in function 'memmove'
configure:5944: $? = 0
configure:5966: result: yes
configure:5881: checking for pow
configure:5937: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:56: warning: conflicting types for built-in function 'pow'
/tmp/ccwDC2Hc.o: In function `main':
/home/pj/FSA/fsa-1.14.1/conftest.c:67: undefined reference to `pow'
collect2: ld returned 1 exit status
configure:5944: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_MEMMOVE 1
| /* end confdefs.h. */
| /* Define pow to an innocuous variant, in case <limits.h> declares pow.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define pow innocuous_pow
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char pow (); 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 pow
|
| /* 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 pow ();
| /* 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_pow || defined __stub___pow
| choke me
| #endif
|
| int
| main ()
| {
| return pow ();
| ;
| return 0;
| }
configure:5966: result: no
configure:5881: checking for regcomp
configure:5937: gcc -o conftest -g -O2 conftest.c >&5
configure:5944: $? = 0
configure:5966: result: yes
configure:5881: checking for sqrt
configure:5937: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:57: warning: conflicting types for built-in function 'sqrt'
/tmp/ccWYsw2q.o: In function `main':
/home/pj/FSA/fsa-1.14.1/conftest.c:68: undefined reference to `sqrt'
collect2: ld returned 1 exit status
configure:5944: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_MEMMOVE 1
| #define HAVE_REGCOMP 1
| /* end confdefs.h. */
| /* Define sqrt to an innocuous variant, in case <limits.h> declares sqrt.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define sqrt innocuous_sqrt
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char sqrt (); 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 sqrt
|
| /* 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 sqrt ();
| /* 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_sqrt || defined __stub___sqrt
| choke me
| #endif
|
| int
| main ()
| {
| return sqrt ();
| ;
| return 0;
| }
configure:5966: result: no
configure:5881: checking for strchr
configure:5937: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:57: warning: conflicting types for built-in function 'strchr'
configure:5944: $? = 0
configure:5966: result: yes
configure:5881: checking for strcspn
configure:5937: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:58: warning: conflicting types for built-in function 'strcspn'
configure:5944: $? = 0
configure:5966: result: yes
configure:5881: checking for strspn
configure:5937: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:59: warning: conflicting types for built-in function 'strspn'
configure:5944: $? = 0
configure:5966: result: yes
configure:5881: checking for strstr
configure:5937: gcc -o conftest -g -O2 conftest.c >&5
conftest.c:60: warning: conflicting types for built-in function 'strstr'
configure:5944: $? = 0
configure:5966: result: yes
configure:5982: checking for condor_compile
configure:6012: result: no
configure:6151: checking for mummer
configure:6169: found /usr/bin/mummer
configure:6182: result: /usr/bin/mummer
configure:6239: checking for exonerate
configure:6257: found /usr/bin/exonerate
configure:6270: result: /usr/bin/exonerate
configure:6326: checking for PQconnectdb in -lpq
configure:6361: gcc -o conftest -g -O2 conftest.c -lpq >&5
/usr/bin/ld: cannot find -lpq
collect2: ld returned 1 exit status
configure:6368: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_MEMMOVE 1
| #define HAVE_REGCOMP 1
| #define HAVE_STRCHR 1
| #define HAVE_STRCSPN 1
| #define HAVE_STRSPN 1
| #define HAVE_STRSTR 1
| #define MUMMER_EXEC "/usr/bin/mummer"
| #define EXONERATE_EXEC "/usr/bin/exonerate"
| /* end confdefs.h. */
|
| /* 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 PQconnectdb ();
| int
| main ()
| {
| return PQconnectdb ();
| ;
| return 0;
| }
configure:6389: result: no
configure:6694: checking for struct sysinfo.totalram
configure:6723: gcc -c -g -O2 conftest.c >&5
configure:6730: $? = 0
configure:6789: result: yes
configure:6800: checking whether sysctl is declared
configure:6830: gcc -c -g -O2 conftest.c >&5
configure:6837: $? = 0
configure:6852: result: yes
configure:6868: checking whether CTL_HW is declared
configure:6898: gcc -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:48: error: 'CTL_HW' undeclared (first use in this function)
conftest.c:48: error: (Each undeclared identifier is reported only once
conftest.c:48: error: for each function it appears in.)
configure:6905: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_MEMMOVE 1
| #define HAVE_REGCOMP 1
| #define HAVE_STRCHR 1
| #define HAVE_STRCSPN 1
| #define HAVE_STRSPN 1
| #define HAVE_STRSTR 1
| #define MUMMER_EXEC "/usr/bin/mummer"
| #define EXONERATE_EXEC "/usr/bin/exonerate"
| #define HAVE_STRUCT_SYSINFO_TOTALRAM 1
| #define HAVE_DECL_SYSCTL 1
| /* end confdefs.h. */
| #include <sys/sysctl.h>
|
| int
| main ()
| {
| #ifndef CTL_HW
| (void) CTL_HW;
| #endif
|
| ;
| return 0;
| }
configure:6920: result: no
configure:6936: checking whether HW_PHYSMEM is declared
configure:6966: gcc -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:49: error: 'HW_PHYSMEM' undeclared (first use in this function)
conftest.c:49: error: (Each undeclared identifier is reported only once
conftest.c:49: error: for each function it appears in.)
configure:6973: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "FSA"
| #define PACKAGE_TARNAME "fsa"
| #define PACKAGE_VERSION "1.14.1"
| #define PACKAGE_STRING "FSA 1.14.1"
| #define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
| #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_UNISTD_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_UNSIGNED_LONG_LONG_INT 1
| #define HAVE_UINTMAX_T 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_GNUCXX_HASHMAP /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_FORK 1
| #define HAVE_VFORK 1
| #define HAVE_WORKING_VFORK 1
| #define HAVE_WORKING_FORK 1
| #define HAVE_MEMMOVE 1
| #define HAVE_REGCOMP 1
| #define HAVE_STRCHR 1
| #define HAVE_STRCSPN 1
| #define HAVE_STRSPN 1
| #define HAVE_STRSTR 1
| #define MUMMER_EXEC "/usr/bin/mummer"
| #define EXONERATE_EXEC "/usr/bin/exonerate"
| #define HAVE_STRUCT_SYSINFO_TOTALRAM 1
| #define HAVE_DECL_SYSCTL 1
| #define HAVE_DECL_CTL_HW 0
| /* end confdefs.h. */
| #include <sys/sysctl.h>
|
| int
| main ()
| {
| #ifndef HW_PHYSMEM
| (void) HW_PHYSMEM;
| #endif
|
| ;
| return 0;
| }
configure:6988: result: no
configure:7010: checking for javac
configure:7038: result: no
configure:7057: checking whether build environment is sane
configure:7100: result: yes
configure:7125: checking for a thread-safe mkdir -p
configure:7164: result: /bin/mkdir -p
configure:7194: checking for style of include used by make
configure:7222: result: GNU
configure:7405: checking how to create a ustar tar archive
configure:7418: tar --version
tar (GNU tar) 1.20
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
configure:7421: $? = 0
configure:7461: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir" >conftest.tar
configure:7464: $? = 0
configure:7468: tar -xf - <conftest.tar
configure:7471: $? = 0
configure:7484: result: gnutar
configure:7492: checking dependency style of gcc
configure:7583: result: gcc3
configure:7600: checking dependency style of g++
configure:7691: result: gcc3
configure:7855: creating ./config.status

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

This file was extended by FSA config.status 1.14.1, which was
generated by GNU Autoconf 2.63. Invocation command line was

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

on ubuntu

config.status:828: creating Makefile
config.status:828: creating src/main/Makefile
config.status:828: creating src/manager/Makefile
config.status:828: creating src/fsa/Makefile
config.status:828: creating src/annealing/Makefile
config.status:828: creating src/util/Makefile
config.status:828: creating src/seq/Makefile
config.status:828: creating display/Makefile
config.status:828: creating display/mad/manifest.mf
config.status:828: creating perl/Makefile
config.status:828: creating examples/Makefile
config.status:828: creating doc/Makefile
config.status:828: creating doc/version.tex
config.status:828: creating html/Makefile
config.status:828: creating tests/Makefile
config.status:828: creating config.h
config.status:1102: executing depfiles commands

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_c_compiler_gnu=yes
ac_cv_c_inline=inline
ac_cv_cxx_compiler_gnu=yes
ac_cv_cxx_gnucxx_hashmap=yes
ac_cv_cxx_have_ext_hash_map=no
ac_cv_cxx_namespaces=yes
ac_cv_cxx_stlport_hashmap=no
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_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_MAD_MAIN_CLASS_set=
ac_cv_env_MAD_MAIN_CLASS_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_floor=no
ac_cv_func_fork=yes
ac_cv_func_fork_works=yes
ac_cv_func_memmove=yes
ac_cv_func_pow=no
ac_cv_func_regcomp=yes
ac_cv_func_sqrt=no
ac_cv_func_strchr=yes
ac_cv_func_strcspn=yes
ac_cv_func_strspn=yes
ac_cv_func_strstr=yes
ac_cv_func_vfork=yes
ac_cv_func_vfork_works=yes
ac_cv_have_decl_CTL_HW=no
ac_cv_have_decl_HW_PHYSMEM=no
ac_cv_have_decl_sysctl=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdbool_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_header_vfork_h=no
ac_cv_lib_pq_PQconnectdb=no
ac_cv_member_struct_sysinfo_totalram=yes
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_EXONERATE_EXEC=/usr/bin/exonerate
ac_cv_path_GREP=/bin/grep
ac_cv_path_MUMMER_EXEC=/usr/bin/mummer
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_HAVE_JAVAC=no
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_ac_ct_RANLIB=ranlib
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_type__Bool=yes
ac_cv_type_pid_t=yes
ac_cv_type_ptrdiff_t=yes
ac_cv_type_size_t=yes
ac_cv_type_uintmax_t=yes
ac_cv_type_unsigned_long_long_int=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
am_cv_prog_tar_ustar=gnutar

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

ACLOCAL='${SHELL} /home/pj/FSA/fsa-1.14.1/build-aux/missing --run aclocal-1.10'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /home/pj/FSA/fsa-1.14.1/build-aux/missing --run tar'
AUTOCONF='${SHELL} /home/pj/FSA/fsa-1.14.1/build-aux/missing --run autoconf'
AUTOHEADER='${SHELL} /home/pj/FSA/fsa-1.14.1/build-aux/missing --run autoheader'
AUTOMAKE='${SHELL} /home/pj/FSA/fsa-1.14.1/build-aux/missing --run automake-1.10'
AWK='gawk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=''
CXX='g++'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS=' -O3 -DNDEBUG -ffast-math'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
EXONERATE_EXEC='/usr/bin/exonerate'
GREP='/bin/grep'
HAVE_CONDOR=''
HAVE_CONDOR_FALSE=''
HAVE_CONDOR_TRUE='#'
HAVE_JAVAC='no'
HAVE_JAVAC_FALSE=''
HAVE_JAVAC_TRUE='#'
HAVE_POSTGRES_FALSE=''
HAVE_POSTGRES_TRUE='#'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
MAD_MAIN_CLASS='mad.MAD'
MAKEINFO='${SHELL} /home/pj/FSA/fsa-1.14.1/build-aux/missing --run makeinfo'
MKDIR_P='/bin/mkdir -p'
MUMMER_EXEC='/usr/bin/mummer'
OBJEXT='o'
PACKAGE='fsa'
PACKAGE_BUGREPORT='fsa@math.berkeley.edu'
PACKAGE_NAME='FSA'
PACKAGE_STRING='FSA 1.14.1'
PACKAGE_TARNAME='fsa'
PACKAGE_VERSION='1.14.1'
PATH_SEPARATOR=':'
RANLIB='ranlib'
SET_MAKE=''
SHELL='/bin/bash'
STRIP=''
VERSION='1.14.1'
ac_ct_CC='gcc'
ac_ct_CXX='g++'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__quote=''
am__tar='tar --format=ustar -chf - "$$tardir"'
am__untar='tar -xf -'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='$(SHELL) /home/pj/FSA/fsa-1.14.1/build-aux/install-sh'
libdir='${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=''
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

#define PACKAGE_NAME "FSA"
#define PACKAGE_TARNAME "fsa"
#define PACKAGE_VERSION "1.14.1"
#define PACKAGE_STRING "FSA 1.14.1"
#define PACKAGE_BUGREPORT "fsa@math.berkeley.edu"
#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_UNISTD_H 1
#define HAVE__BOOL 1
#define HAVE_STDBOOL_H 1
#define HAVE_UNSIGNED_LONG_LONG_INT 1
#define HAVE_UINTMAX_T 1
#define HAVE_PTRDIFF_T 1
#define HAVE_GNUCXX_HASHMAP /**/
#define HAVE_NAMESPACES /**/
#define HAVE_FORK 1
#define HAVE_VFORK 1
#define HAVE_WORKING_VFORK 1
#define HAVE_WORKING_FORK 1
#define HAVE_MEMMOVE 1
#define HAVE_REGCOMP 1
#define HAVE_STRCHR 1
#define HAVE_STRCSPN 1
#define HAVE_STRSPN 1
#define HAVE_STRSTR 1
#define MUMMER_EXEC "/usr/bin/mummer"
#define EXONERATE_EXEC "/usr/bin/exonerate"
#define HAVE_STRUCT_SYSINFO_TOTALRAM 1
#define HAVE_DECL_SYSCTL 1
#define HAVE_DECL_CTL_HW 0
#define HAVE_DECL_HW_PHYSMEM 0
#define PACKAGE "fsa"
#define VERSION "1.14.1"

configure: exit 0