This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by gbtools configure 0.2-dirty, which was generated by GNU Autoconf 2.65. Invocation command line was $ ./configure --disable-option-checking --prefix=/usr/local --cache-file=/dev/null --srcdir=. ## --------- ## ## Platform. ## ## --------- ## hostname = mars uname -m = x86_64 uname -r = 2.6.32-642.el6.x86_64 uname -s = Linux uname -v = #1 SMP Wed Apr 13 00:51:26 EDT 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: /home/psgendb/BIRCHDEV/local/script PATH: /home/psgendb/BIRCHDEV/local/bin-linux-x86_64 PATH: /usr/lib64/qt-3.3/bin PATH: /usr/local/bin PATH: /bin PATH: /usr/bin PATH: /opt/thinlinc/bin PATH: /usr/local/bin PATH: /usr/bin/X11 PATH: /usr/dt/bin PATH: /usr/openwin/bin PATH: /sbin PATH: /usr/sbin PATH: /usr/local/sbin PATH: /var/cfengine/bin PATH: /home/psgendb/BIRCHDEV/script PATH: /home/psgendb/BIRCHDEV/bin-linux-x86_64 PATH: /home/psgendb/BIRCHDEV/local/pkg/EMBOSS/linux-x86_64/bin PATH: /home/psgendb/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2263: checking for a BSD-compatible install configure:2331: result: /usr/bin/install -c configure:2342: checking whether build environment is sane configure:2392: result: yes configure:2533: checking for a thread-safe mkdir -p configure:2572: result: /bin/mkdir -p configure:2585: checking for gawk configure:2601: found /bin/gawk configure:2612: result: gawk configure:2623: checking whether make sets $(MAKE) configure:2645: result: yes configure:2807: checking for g++ configure:2823: found /usr/bin/g++ configure:2834: result: g++ configure:2861: checking for C++ compiler version configure:2870: g++ --version >&5 g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17) Copyright (C) 2010 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:2881: $? = 0 configure:2870: g++ -v >&5 Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux Thread model: posix gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC) configure:2881: $? = 0 configure:2870: g++ -V >&5 g++: '-V' option must have argument configure:2881: $? = 1 configure:2870: g++ -qversion >&5 g++: unrecognized option '-qversion' g++: no input files configure:2881: $? = 1 configure:2901: checking whether the C++ compiler works configure:2923: g++ conftest.cpp >&5 configure:2927: $? = 0 configure:2976: result: yes configure:2979: checking for C++ compiler default output file name configure:2981: result: a.out configure:2987: checking for suffix of executables configure:2994: g++ -o conftest conftest.cpp >&5 configure:2998: $? = 0 configure:3020: result: configure:3042: checking whether we are cross compiling configure:3050: g++ -o conftest conftest.cpp >&5 configure:3054: $? = 0 configure:3061: ./conftest configure:3065: $? = 0 configure:3080: result: no configure:3085: checking for suffix of object files configure:3107: g++ -c conftest.cpp >&5 configure:3111: $? = 0 configure:3132: result: o configure:3136: checking whether we are using the GNU C++ compiler configure:3155: g++ -c conftest.cpp >&5 configure:3155: $? = 0 configure:3164: result: yes configure:3173: checking whether g++ accepts -g configure:3193: g++ -c -g conftest.cpp >&5 configure:3193: $? = 0 configure:3234: result: yes configure:3268: checking for style of include used by make configure:3296: result: GNU configure:3321: checking dependency style of g++ configure:3431: result: gcc3 configure:3494: checking for gcc configure:3510: found /usr/bin/gcc configure:3521: result: gcc configure:3750: checking for C compiler version configure:3759: 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:3770: $? = 0 configure:3759: 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:3770: $? = 0 configure:3759: gcc -V >&5 gcc: '-V' option must have argument configure:3770: $? = 1 configure:3759: gcc -qversion >&5 gcc: unrecognized option '-qversion' gcc: no input files configure:3770: $? = 1 configure:3774: checking whether we are using the GNU C compiler configure:3793: gcc -c conftest.c >&5 configure:3793: $? = 0 configure:3802: result: yes configure:3811: checking whether gcc accepts -g configure:3831: gcc -c -g conftest.c >&5 configure:3831: $? = 0 configure:3872: result: yes configure:3889: checking for gcc option to accept ISO C89 configure:3953: gcc -c -g -O2 conftest.c >&5 configure:3953: $? = 0 configure:3966: result: none needed configure:3988: checking dependency style of gcc configure:4098: result: gcc3 configure:4118: checking how to run the C preprocessor configure:4149: gcc -E conftest.c configure:4149: $? = 0 configure:4163: gcc -E conftest.c conftest.c:12:28: error: ac_nonexistent.h: No such file or directory configure:4163: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | /* end confdefs.h. */ | #include configure:4188: result: gcc -E configure:4208: gcc -E conftest.c configure:4208: $? = 0 configure:4222: gcc -E conftest.c conftest.c:12:28: error: ac_nonexistent.h: No such file or directory configure:4222: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | /* end confdefs.h. */ | #include configure:4251: checking whether ln -s works configure:4255: result: yes configure:4262: checking whether make sets $(MAKE) configure:4284: result: yes configure:4336: checking for ranlib configure:4352: found /usr/bin/ranlib configure:4363: result: ranlib configure:4391: checking for grep that handles long lines and -e configure:4449: result: /bin/grep configure:4454: checking for egrep configure:4516: result: /bin/grep -E configure:4521: checking for ANSI C header files configure:4541: gcc -c -g -O2 conftest.c >&5 configure:4541: $? = 0 configure:4614: gcc -o conftest -g -O2 conftest.c >&5 configure:4614: $? = 0 configure:4614: ./conftest configure:4614: $? = 0 configure:4625: result: yes configure:4638: checking for sys/types.h configure:4638: gcc -c -g -O2 conftest.c >&5 configure:4638: $? = 0 configure:4638: result: yes configure:4638: checking for sys/stat.h configure:4638: gcc -c -g -O2 conftest.c >&5 configure:4638: $? = 0 configure:4638: result: yes configure:4638: checking for stdlib.h configure:4638: gcc -c -g -O2 conftest.c >&5 configure:4638: $? = 0 configure:4638: result: yes configure:4638: checking for string.h configure:4638: gcc -c -g -O2 conftest.c >&5 configure:4638: $? = 0 configure:4638: result: yes configure:4638: checking for memory.h configure:4638: gcc -c -g -O2 conftest.c >&5 configure:4638: $? = 0 configure:4638: result: yes configure:4638: checking for strings.h configure:4638: gcc -c -g -O2 conftest.c >&5 configure:4638: $? = 0 configure:4638: result: yes configure:4638: checking for inttypes.h configure:4638: gcc -c -g -O2 conftest.c >&5 configure:4638: $? = 0 configure:4638: result: yes configure:4638: checking for stdint.h configure:4638: gcc -c -g -O2 conftest.c >&5 configure:4638: $? = 0 configure:4638: result: yes configure:4638: checking for unistd.h configure:4638: gcc -c -g -O2 conftest.c >&5 configure:4638: $? = 0 configure:4638: result: yes configure:4654: checking arpa/inet.h usability configure:4654: gcc -c -g -O2 conftest.c >&5 configure:4654: $? = 0 configure:4654: result: yes configure:4654: checking arpa/inet.h presence configure:4654: gcc -E conftest.c configure:4654: $? = 0 configure:4654: result: yes configure:4654: checking for arpa/inet.h configure:4654: result: yes configure:4654: checking netdb.h usability configure:4654: gcc -c -g -O2 conftest.c >&5 configure:4654: $? = 0 configure:4654: result: yes configure:4654: checking netdb.h presence configure:4654: gcc -E conftest.c configure:4654: $? = 0 configure:4654: result: yes configure:4654: checking for netdb.h configure:4654: result: yes configure:4654: checking netinet/in.h usability configure:4654: gcc -c -g -O2 conftest.c >&5 configure:4654: $? = 0 configure:4654: result: yes configure:4654: checking netinet/in.h presence configure:4654: gcc -E conftest.c configure:4654: $? = 0 configure:4654: result: yes configure:4654: checking for netinet/in.h configure:4654: result: yes configure:4654: checking for stdlib.h configure:4654: result: yes configure:4654: checking for string.h configure:4654: result: yes configure:4654: checking sys/socket.h usability configure:4654: gcc -c -g -O2 conftest.c >&5 configure:4654: $? = 0 configure:4654: result: yes configure:4654: checking sys/socket.h presence configure:4654: gcc -E conftest.c configure:4654: $? = 0 configure:4654: result: yes configure:4654: checking for sys/socket.h configure:4654: result: yes configure:4654: checking for unistd.h configure:4654: result: yes configure:4654: checking gtk.h usability configure:4654: gcc -c -g -O2 conftest.c >&5 conftest.c:62:17: error: gtk.h: No such file or directory configure:4654: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | #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_ARPA_INET_H 1 | #define HAVE_NETDB_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_SYS_SOCKET_H 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #include | #ifdef HAVE_SYS_TYPES_H | # include | #endif | #ifdef HAVE_SYS_STAT_H | # include | #endif | #ifdef STDC_HEADERS | # include | # include | #else | # ifdef HAVE_STDLIB_H | # include | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include | # endif | # include | #endif | #ifdef HAVE_STRINGS_H | # include | #endif | #ifdef HAVE_INTTYPES_H | # include | #endif | #ifdef HAVE_STDINT_H | # include | #endif | #ifdef HAVE_UNISTD_H | # include | #endif | #include configure:4654: result: no configure:4654: checking gtk.h presence configure:4654: gcc -E conftest.c conftest.c:29:17: error: gtk.h: No such file or directory configure:4654: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | #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_ARPA_INET_H 1 | #define HAVE_NETDB_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_SYS_SOCKET_H 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #include configure:4654: result: no configure:4654: checking for gtk.h configure:4654: result: no configure:4667: checking for pid_t configure:4667: gcc -c -g -O2 conftest.c >&5 configure:4667: $? = 0 configure:4667: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:65: error: expected expression before ')' token configure:4667: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | #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_ARPA_INET_H 1 | #define HAVE_NETDB_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_SYS_SOCKET_H 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #include | #ifdef HAVE_SYS_TYPES_H | # include | #endif | #ifdef HAVE_SYS_STAT_H | # include | #endif | #ifdef STDC_HEADERS | # include | # include | #else | # ifdef HAVE_STDLIB_H | # include | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include | # endif | # include | #endif | #ifdef HAVE_STRINGS_H | # include | #endif | #ifdef HAVE_INTTYPES_H | # include | #endif | #ifdef HAVE_STDINT_H | # include | #endif | #ifdef HAVE_UNISTD_H | # include | #endif | int | main () | { | if (sizeof ((pid_t))) | return 0; | ; | return 0; | } configure:4667: result: yes configure:4678: checking for size_t configure:4678: gcc -c -g -O2 conftest.c >&5 configure:4678: $? = 0 configure:4678: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:65: error: expected expression before ')' token configure:4678: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | #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_ARPA_INET_H 1 | #define HAVE_NETDB_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_SYS_SOCKET_H 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #include | #ifdef HAVE_SYS_TYPES_H | # include | #endif | #ifdef HAVE_SYS_STAT_H | # include | #endif | #ifdef STDC_HEADERS | # include | # include | #else | # ifdef HAVE_STDLIB_H | # include | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include | # endif | # include | #endif | #ifdef HAVE_STRINGS_H | # include | #endif | #ifdef HAVE_INTTYPES_H | # include | #endif | #ifdef HAVE_STDINT_H | # include | #endif | #ifdef HAVE_UNISTD_H | # include | #endif | int | main () | { | if (sizeof ((size_t))) | return 0; | ; | return 0; | } configure:4678: result: yes configure:4693: checking vfork.h usability configure:4693: gcc -c -g -O2 conftest.c >&5 conftest.c:62:19: error: vfork.h: No such file or directory configure:4693: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | #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_ARPA_INET_H 1 | #define HAVE_NETDB_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_SYS_SOCKET_H 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #include | #ifdef HAVE_SYS_TYPES_H | # include | #endif | #ifdef HAVE_SYS_STAT_H | # include | #endif | #ifdef STDC_HEADERS | # include | # include | #else | # ifdef HAVE_STDLIB_H | # include | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include | # endif | # include | #endif | #ifdef HAVE_STRINGS_H | # include | #endif | #ifdef HAVE_INTTYPES_H | # include | #endif | #ifdef HAVE_STDINT_H | # include | #endif | #ifdef HAVE_UNISTD_H | # include | #endif | #include configure:4693: result: no configure:4693: checking vfork.h presence configure:4693: gcc -E conftest.c conftest.c:29:19: error: vfork.h: No such file or directory configure:4693: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | #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_ARPA_INET_H 1 | #define HAVE_NETDB_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_SYS_SOCKET_H 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #include configure:4693: result: no configure:4693: checking for vfork.h configure:4693: result: no configure:4706: checking for fork configure:4706: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:52: warning: conflicting types for built-in function 'fork' configure:4706: $? = 0 configure:4706: result: yes configure:4706: checking for vfork configure:4706: gcc -o conftest -g -O2 conftest.c >&5 configure:4706: $? = 0 configure:4706: result: yes configure:4717: checking for working fork configure:4739: gcc -o conftest -g -O2 conftest.c >&5 configure:4739: $? = 0 configure:4739: ./conftest configure:4739: $? = 0 configure:4749: result: yes configure:4770: checking for working vfork configure:4880: result: yes configure:4907: checking for stdlib.h configure:4907: result: yes configure:4917: checking for GNU libc compatible malloc configure:4941: gcc -o conftest -g -O2 conftest.c >&5 configure:4941: $? = 0 configure:4941: ./conftest configure:4941: $? = 0 configure:4951: result: yes configure:4975: checking for dup2 configure:4975: gcc -o conftest -g -O2 conftest.c >&5 configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for floor configure:4975: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:59: warning: conflicting types for built-in function 'floor' /tmp/ccryawxY.o: In function `main': /home/psgendb/BIRCHDEV/install/seqtools/seqtools-4.37.0/gbtools/conftest.c:70: undefined reference to `floor' collect2: ld returned 1 exit status configure:4975: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | #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_ARPA_INET_H 1 | #define HAVE_NETDB_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_SYS_SOCKET_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_FORK 1 | #define HAVE_VFORK 1 | #define HAVE_WORKING_VFORK 1 | #define HAVE_WORKING_FORK 1 | #define HAVE_STDLIB_H 1 | #define HAVE_MALLOC 1 | #define HAVE_DUP2 1 | /* end confdefs.h. */ | /* Define floor to an innocuous variant, in case declares floor. | For example, HP-UX 11i declares gettimeofday. */ | #define floor innocuous_floor | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char floor (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #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:4975: result: no configure:4975: checking for gethostbyname configure:4975: gcc -o conftest -g -O2 conftest.c >&5 configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for memset configure:4975: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:60: warning: conflicting types for built-in function 'memset' configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for socket configure:4975: gcc -o conftest -g -O2 conftest.c >&5 configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for sqrt configure:4975: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:62: warning: conflicting types for built-in function 'sqrt' /tmp/ccs6MZoo.o: In function `main': /home/psgendb/BIRCHDEV/install/seqtools/seqtools-4.37.0/gbtools/conftest.c:73: undefined reference to `sqrt' collect2: ld returned 1 exit status configure:4975: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gbtools" | #define PACKAGE_TARNAME "gbtools" | #define PACKAGE_VERSION "0.2-dirty" | #define PACKAGE_STRING "gbtools 0.2-dirty" | #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "gbtools" | #define VERSION "0.2-dirty" | #define GBTOOLS_VERSION PACKAGE_VERSION | #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_ARPA_INET_H 1 | #define HAVE_NETDB_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_SYS_SOCKET_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_FORK 1 | #define HAVE_VFORK 1 | #define HAVE_WORKING_VFORK 1 | #define HAVE_WORKING_FORK 1 | #define HAVE_STDLIB_H 1 | #define HAVE_MALLOC 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTBYNAME 1 | #define HAVE_MEMSET 1 | #define HAVE_SOCKET 1 | /* end confdefs.h. */ | /* Define sqrt to an innocuous variant, in case declares sqrt. | For example, HP-UX 11i declares gettimeofday. */ | #define sqrt innocuous_sqrt | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char sqrt (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #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:4975: result: no configure:4975: checking for strcasecmp configure:4975: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:62: warning: conflicting types for built-in function 'strcasecmp' configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for strchr configure:4975: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:63: warning: conflicting types for built-in function 'strchr' configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for strcspn configure:4975: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:64: warning: conflicting types for built-in function 'strcspn' configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for strerror configure:4975: gcc -o conftest -g -O2 conftest.c >&5 configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for strncasecmp configure:4975: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:66: warning: conflicting types for built-in function 'strncasecmp' configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for strrchr configure:4975: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:67: warning: conflicting types for built-in function 'strrchr' configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for strstr configure:4975: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:68: warning: conflicting types for built-in function 'strstr' configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for strtol configure:4975: gcc -o conftest -g -O2 conftest.c >&5 configure:4975: $? = 0 configure:4975: result: yes configure:4975: checking for uname configure:4975: gcc -o conftest -g -O2 conftest.c >&5 configure:4975: $? = 0 configure:4975: result: yes configure:5036: checking for pkg-config configure:5054: found /usr/bin/pkg-config configure:5066: result: /usr/bin/pkg-config configure:5091: checking pkg-config is at least version 0.9.0 configure:5094: result: yes configure:5105: checking for DEPS configure:5113: $PKG_CONFIG --exists --print-errors "glib-2.0 gtk+-2.0 >= 2.10" configure:5116: $? = 0 configure:5131: $PKG_CONFIG --exists --print-errors "glib-2.0 gtk+-2.0 >= 2.10" configure:5134: $? = 0 configure:5189: result: yes configure:5202: checking curl/curl.h usability configure:5202: gcc -c -g -O2 conftest.c >&5 configure:5202: $? = 0 configure:5202: result: yes configure:5202: checking curl/curl.h presence configure:5202: gcc -E conftest.c configure:5202: $? = 0 configure:5202: result: yes configure:5202: checking for curl/curl.h configure:5202: result: yes configure:5227: checking execinfo.h usability configure:5227: gcc -c -g -O2 conftest.c >&5 configure:5227: $? = 0 configure:5227: result: yes configure:5227: checking execinfo.h presence configure:5227: gcc -E conftest.c configure:5227: $? = 0 configure:5227: result: yes configure:5227: checking for execinfo.h configure:5227: result: yes configure:5365: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by gbtools config.status 0.2-dirty, which was generated by GNU Autoconf 2.65. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on mars config.status:898: creating Makefile config.status:898: creating src/Makefile config.status:898: creating src/include/Makefile config.status:898: creating src/gbtoolsUtils/Makefile config.status:898: creating src/gbtoolsGUI/Makefile config.status:898: creating config.h config.status:1118: executing depfiles commands ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_c_compiler_gnu=yes ac_cv_cxx_compiler_gnu=yes ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_CXXFLAGS_set= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_DEPS_CFLAGS_set= ac_cv_env_DEPS_CFLAGS_value= ac_cv_env_DEPS_LIBS_set= ac_cv_env_DEPS_LIBS_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_PKG_CONFIG_set= ac_cv_env_PKG_CONFIG_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_dup2=yes ac_cv_func_floor=no ac_cv_func_fork=yes ac_cv_func_fork_works=yes ac_cv_func_gethostbyname=yes ac_cv_func_malloc_0_nonnull=yes ac_cv_func_memset=yes ac_cv_func_socket=yes ac_cv_func_sqrt=no ac_cv_func_strcasecmp=yes ac_cv_func_strchr=yes ac_cv_func_strcspn=yes ac_cv_func_strerror=yes ac_cv_func_strncasecmp=yes ac_cv_func_strrchr=yes ac_cv_func_strstr=yes ac_cv_func_strtol=yes ac_cv_func_uname=yes ac_cv_func_vfork=yes ac_cv_func_vfork_works=yes ac_cv_header_arpa_inet_h=yes ac_cv_header_curl_curl_h=yes ac_cv_header_execinfo_h=yes ac_cv_header_gtk_h=no ac_cv_header_inttypes_h=yes ac_cv_header_memory_h=yes ac_cv_header_netdb_h=yes ac_cv_header_netinet_in_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_socket_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_objext=o ac_cv_path_EGREP='/bin/grep -E' ac_cv_path_GREP=/bin/grep ac_cv_path_ac_pt_PKG_CONFIG=/usr/bin/pkg-config 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_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_pid_t=yes ac_cv_type_size_t=yes am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 pkg_cv_DEPS_CFLAGS='-pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 ' pkg_cv_DEPS_LIBS='-pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 ' ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /home/psgendb/BIRCHDEV/install/seqtools/seqtools-4.37.0/gbtools/config/missing --run aclocal-1.11' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='${SHELL} /home/psgendb/BIRCHDEV/install/seqtools/seqtools-4.37.0/gbtools/config/missing --run tar' AUTOCONF='${SHELL} /home/psgendb/BIRCHDEV/install/seqtools/seqtools-4.37.0/gbtools/config/missing --run autoconf' AUTOHEADER='${SHELL} /home/psgendb/BIRCHDEV/install/seqtools/seqtools-4.37.0/gbtools/config/missing --run autoheader' AUTOMAKE='${SHELL} /home/psgendb/BIRCHDEV/install/seqtools/seqtools-4.37.0/gbtools/config/missing --run automake-1.11' AWK='gawk' CC='gcc' CCDEPMODE='depmode=gcc3' CFLAGS='-g -O2' CPP='gcc -E' CPPFLAGS='' CXX='g++' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-g -O2' CYGPATH_W='echo' DEFS='-DHAVE_CONFIG_H' DEPDIR='.deps' DEPS_CFLAGS='-pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 ' DEPS_LIBS='-pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 ' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' GREP='/bin/grep' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS='' LIBOBJS='' LIBS='' LN_S='ln -s' LTLIBOBJS='' MAKEINFO='${SHELL} /home/psgendb/BIRCHDEV/install/seqtools/seqtools-4.37.0/gbtools/config/missing --run makeinfo' MKDIR_P='/bin/mkdir -p' OBJEXT='o' PACKAGE='gbtools' PACKAGE_BUGREPORT='annosoft@sanger.ac.uk' PACKAGE_NAME='gbtools' PACKAGE_STRING='gbtools 0.2-dirty' PACKAGE_TARNAME='gbtools' PACKAGE_URL='' PACKAGE_VERSION='0.2-dirty' PATH_SEPARATOR=':' PKG_CONFIG='/usr/bin/pkg-config' RANLIB='ranlib' SET_MAKE='' SHELL='/bin/sh' STRIP='' USE_LIBCURL_FALSE='#' USE_LIBCURL_TRUE='' VERSION='0.2-dirty' ac_ct_CC='gcc' ac_ct_CXX='g++' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='#' am__fastdepCC_FALSE='#' am__fastdepCC_TRUE='' am__fastdepCXX_FALSE='#' am__fastdepCXX_TRUE='' am__include='include' am__isrc='' am__leading_dot='.' am__quote='' am__tar='${AMTAR} chof - "$$tardir"' am__untar='${AMTAR} xf -' bindir='${exec_prefix}/bin' build_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/psgendb/BIRCHDEV/install/seqtools/seqtools-4.37.0/gbtools/config/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 "gbtools" #define PACKAGE_TARNAME "gbtools" #define PACKAGE_VERSION "0.2-dirty" #define PACKAGE_STRING "gbtools 0.2-dirty" #define PACKAGE_BUGREPORT "annosoft@sanger.ac.uk" #define PACKAGE_URL "" #define PACKAGE "gbtools" #define VERSION "0.2-dirty" #define GBTOOLS_VERSION PACKAGE_VERSION #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_ARPA_INET_H 1 #define HAVE_NETDB_H 1 #define HAVE_NETINET_IN_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_SYS_SOCKET_H 1 #define HAVE_UNISTD_H 1 #define HAVE_FORK 1 #define HAVE_VFORK 1 #define HAVE_WORKING_VFORK 1 #define HAVE_WORKING_FORK 1 #define HAVE_STDLIB_H 1 #define HAVE_MALLOC 1 #define HAVE_DUP2 1 #define HAVE_GETHOSTBYNAME 1 #define HAVE_MEMSET 1 #define HAVE_SOCKET 1 #define HAVE_STRCASECMP 1 #define HAVE_STRCHR 1 #define HAVE_STRCSPN 1 #define HAVE_STRERROR 1 #define HAVE_STRNCASECMP 1 #define HAVE_STRRCHR 1 #define HAVE_STRSTR 1 #define HAVE_STRTOL 1 #define HAVE_UNAME 1 #define HAVE_CURL_CURL_H 1 #define HAVE_EXECINFO_H 1 configure: exit 0