This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by jbrowse configure 0.1, which was generated by GNU Autoconf 2.68. Invocation command line was $ ./configure ## --------- ## ## Platform. ## ## --------- ## hostname = dgvbrowser.uab.es uname -m = x86_64 uname -r = 3.10.0-327.22.2.el7.x86_64 uname -s = Linux uname -v = #1 SMP Thu Jun 23 17:05:11 UTC 2016 /usr/bin/uname -p = x86_64 /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/jbrowse/perl5/perlbrew/bin PATH: /usr/local/bin PATH: /bin PATH: /usr/bin PATH: /usr/local/sbin PATH: /usr/sbin PATH: /home/jbrowse/.local/bin PATH: /home/jbrowse/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2230: checking for g++ configure:2246: found /bin/g++ configure:2257: result: g++ configure:2284: checking for C++ compiler version configure:2293: g++ --version >&5 g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) Copyright (C) 2015 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:2304: $? = 0 configure:2293: g++ -v >&5 Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper 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-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC) configure:2304: $? = 0 configure:2293: g++ -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:2304: $? = 4 configure:2293: g++ -qversion >&5 g++: error: unrecognized command line option '-qversion' g++: fatal error: no input files compilation terminated. configure:2304: $? = 4 configure:2324: checking whether the C++ compiler works configure:2346: g++ conftest.cpp >&5 configure:2350: $? = 0 configure:2398: result: yes configure:2401: checking for C++ compiler default output file name configure:2403: result: a.out configure:2409: checking for suffix of executables configure:2416: g++ -o conftest conftest.cpp >&5 configure:2420: $? = 0 configure:2442: result: configure:2464: checking whether we are cross compiling configure:2472: g++ -o conftest conftest.cpp >&5 configure:2476: $? = 0 configure:2483: ./conftest configure:2487: $? = 0 configure:2502: result: no configure:2507: checking for suffix of object files configure:2529: g++ -c conftest.cpp >&5 configure:2533: $? = 0 configure:2554: result: o configure:2558: checking whether we are using the GNU C++ compiler configure:2577: g++ -c conftest.cpp >&5 configure:2577: $? = 0 configure:2586: result: yes configure:2595: checking whether g++ accepts -g configure:2615: g++ -c -g conftest.cpp >&5 configure:2615: $? = 0 configure:2656: result: yes configure:2727: checking for gcc configure:2743: found /bin/gcc configure:2754: result: gcc configure:2983: checking for C compiler version configure:2992: gcc --version >&5 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) Copyright (C) 2015 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:3003: $? = 0 configure:2992: gcc -v >&5 Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper 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-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC) configure:3003: $? = 0 configure:2992: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:3003: $? = 4 configure:2992: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:3003: $? = 4 configure:3007: checking whether we are using the GNU C compiler configure:3026: gcc -c conftest.c >&5 configure:3026: $? = 0 configure:3035: result: yes configure:3044: checking whether gcc accepts -g configure:3064: gcc -c -g conftest.c >&5 configure:3064: $? = 0 configure:3105: result: yes configure:3122: checking for gcc option to accept ISO C89 configure:3186: gcc -c -g -O2 conftest.c >&5 configure:3186: $? = 0 configure:3199: result: none needed configure:3219: checking whether ln -s works configure:3223: result: yes configure:3241: checking for library containing png_create_write_struct configure:3272: gcc -o conftest -g -O2 conftest.c >&5 /tmp/ccYQv0og.o: In function `main': /home/jbrowse/JBROWSE/popfly/src/wig2png/conftest.c:21: undefined reference to `png_create_write_struct' collect2: error: ld returned 1 exit status configure:3272: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | /* 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 png_create_write_struct (); | int | main () | { | return png_create_write_struct (); | ; | return 0; | } configure:3272: gcc -o conftest -g -O2 conftest.c -lpng >&5 configure:3272: $? = 0 configure:3289: result: -lpng configure:3306: checking how to run the C preprocessor configure:3337: gcc -E conftest.c configure:3337: $? = 0 configure:3351: gcc -E conftest.c conftest.c:10:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:3351: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | /* end confdefs.h. */ | #include configure:3376: result: gcc -E configure:3396: gcc -E conftest.c configure:3396: $? = 0 configure:3410: gcc -E conftest.c conftest.c:10:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:3410: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | /* end confdefs.h. */ | #include configure:3439: checking for grep that handles long lines and -e configure:3497: result: /bin/grep configure:3502: checking for egrep configure:3564: result: /bin/grep -E configure:3569: checking for ANSI C header files configure:3589: gcc -c -g -O2 conftest.c >&5 configure:3589: $? = 0 configure:3662: gcc -o conftest -g -O2 conftest.c -lpng >&5 configure:3662: $? = 0 configure:3662: ./conftest configure:3662: $? = 0 configure:3673: result: yes configure:3681: checking for sys/wait.h that is POSIX.1 compatible configure:3707: gcc -c -g -O2 conftest.c >&5 configure:3707: $? = 0 configure:3714: result: yes configure:3727: checking for sys/types.h configure:3727: gcc -c -g -O2 conftest.c >&5 configure:3727: $? = 0 configure:3727: result: yes configure:3727: checking for sys/stat.h configure:3727: gcc -c -g -O2 conftest.c >&5 configure:3727: $? = 0 configure:3727: result: yes configure:3727: checking for stdlib.h configure:3727: gcc -c -g -O2 conftest.c >&5 configure:3727: $? = 0 configure:3727: result: yes configure:3727: checking for string.h configure:3727: gcc -c -g -O2 conftest.c >&5 configure:3727: $? = 0 configure:3727: result: yes configure:3727: checking for memory.h configure:3727: gcc -c -g -O2 conftest.c >&5 configure:3727: $? = 0 configure:3727: result: yes configure:3727: checking for strings.h configure:3727: gcc -c -g -O2 conftest.c >&5 configure:3727: $? = 0 configure:3727: result: yes configure:3727: checking for inttypes.h configure:3727: gcc -c -g -O2 conftest.c >&5 configure:3727: $? = 0 configure:3727: result: yes configure:3727: checking for stdint.h configure:3727: gcc -c -g -O2 conftest.c >&5 configure:3727: $? = 0 configure:3727: result: yes configure:3727: checking for unistd.h configure:3727: gcc -c -g -O2 conftest.c >&5 configure:3727: $? = 0 configure:3727: result: yes configure:3742: checking float.h usability configure:3742: gcc -c -g -O2 conftest.c >&5 configure:3742: $? = 0 configure:3742: result: yes configure:3742: checking float.h presence configure:3742: gcc -E conftest.c configure:3742: $? = 0 configure:3742: result: yes configure:3742: checking for float.h configure:3742: result: yes configure:3742: checking for stdlib.h configure:3742: result: yes configure:3742: checking for string.h configure:3742: result: yes configure:3742: checking for unistd.h configure:3742: result: yes configure:3742: checking png.h usability configure:3742: gcc -c -g -O2 conftest.c >&5 configure:3742: $? = 0 configure:3742: result: yes configure:3742: checking png.h presence configure:3742: gcc -E conftest.c configure:3742: $? = 0 configure:3742: result: yes configure:3742: checking for png.h configure:3742: result: yes configure:3754: checking for stdbool.h that conforms to C99 configure:3821: gcc -c -g -O2 conftest.c >&5 configure:3821: $? = 0 configure:3828: result: yes configure:3830: checking for _Bool configure:3830: gcc -c -g -O2 conftest.c >&5 configure:3830: $? = 0 configure:3830: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:62:20: error: expected expression before ')' token if (sizeof ((_Bool))) ^ configure:3830: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | #define STDC_HEADERS 1 | #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_PNG_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 ((_Bool))) | return 0; | ; | return 0; | } configure:3830: result: yes configure:3846: checking for an ANSI C-conforming const configure:3911: gcc -c -g -O2 conftest.c >&5 configure:3911: $? = 0 configure:3918: result: yes configure:3926: checking for inline configure:3942: gcc -c -g -O2 conftest.c >&5 configure:3942: $? = 0 configure:3950: result: inline configure:3968: checking for pid_t configure:3968: gcc -c -g -O2 conftest.c >&5 configure:3968: $? = 0 configure:3968: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:64:20: error: expected expression before ')' token if (sizeof ((pid_t))) ^ configure:3968: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | #define STDC_HEADERS 1 | #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_PNG_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_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:3968: result: yes configure:3979: checking for C/C++ restrict keyword configure:4004: gcc -c -g -O2 conftest.c >&5 configure:4004: $? = 0 configure:4012: result: __restrict configure:4025: checking for size_t configure:4025: gcc -c -g -O2 conftest.c >&5 configure:4025: $? = 0 configure:4025: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:65:21: error: expected expression before ')' token if (sizeof ((size_t))) ^ configure:4025: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | #define STDC_HEADERS 1 | #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_PNG_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define restrict __restrict | /* 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:4025: result: yes configure:4036: checking whether struct tm is in sys/time.h or time.h configure:4056: gcc -c -g -O2 conftest.c >&5 configure:4056: $? = 0 configure:4063: result: time.h configure:4071: checking for ptrdiff_t configure:4071: gcc -c -g -O2 conftest.c >&5 configure:4071: $? = 0 configure:4071: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:65:24: error: expected expression before ')' token if (sizeof ((ptrdiff_t))) ^ configure:4071: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | #define STDC_HEADERS 1 | #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_PNG_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define restrict __restrict | /* 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 ((ptrdiff_t))) | return 0; | ; | return 0; | } configure:4071: result: yes configure:4085: checking vfork.h usability configure:4085: gcc -c -g -O2 conftest.c >&5 conftest.c:63:19: fatal error: vfork.h: No such file or directory #include ^ compilation terminated. configure:4085: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | #define STDC_HEADERS 1 | #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_PNG_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define restrict __restrict | #define HAVE_PTRDIFF_T 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:4085: result: no configure:4085: checking vfork.h presence configure:4085: gcc -E conftest.c conftest.c:30:19: fatal error: vfork.h: No such file or directory #include ^ compilation terminated. configure:4085: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | #define STDC_HEADERS 1 | #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_PNG_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define restrict __restrict | #define HAVE_PTRDIFF_T 1 | /* end confdefs.h. */ | #include configure:4085: result: no configure:4085: checking for vfork.h configure:4085: result: no configure:4098: checking for fork configure:4098: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:53:6: warning: conflicting types for built-in function 'fork' [enabled by default] char fork (); ^ configure:4098: $? = 0 configure:4098: result: yes configure:4098: checking for vfork configure:4098: gcc -o conftest -g -O2 conftest.c -lpng >&5 configure:4098: $? = 0 configure:4098: result: yes configure:4108: checking for working fork configure:4130: gcc -o conftest -g -O2 conftest.c -lpng >&5 configure:4130: $? = 0 configure:4130: ./conftest configure:4130: $? = 0 configure:4140: result: yes configure:4161: checking for working vfork configure:4271: result: yes configure:4296: checking whether lstat correctly handles trailing slash configure:4322: gcc -o conftest -g -O2 conftest.c -lpng >&5 configure:4322: $? = 0 configure:4322: ./conftest configure:4322: $? = 0 configure:4339: result: yes configure:4358: checking whether lstat accepts an empty string configure:4378: gcc -o conftest -g -O2 conftest.c -lpng >&5 configure:4378: $? = 0 configure:4378: ./conftest configure:4378: $? = 0 configure:4388: result: no configure:4404: checking whether lstat correctly handles trailing slash configure:4447: result: yes configure:4468: checking for stdlib.h configure:4468: result: yes configure:4478: checking for GNU libc compatible malloc configure:4502: gcc -o conftest -g -O2 conftest.c -lpng >&5 configure:4502: $? = 0 configure:4502: ./conftest configure:4502: $? = 0 configure:4512: result: yes configure:4535: checking for strftime configure:4535: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:61:6: warning: conflicting types for built-in function 'strftime' [enabled by default] char strftime (); ^ configure:4535: $? = 0 configure:4535: result: yes configure:4591: checking for dup2 configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 configure:4591: $? = 0 configure:4591: result: yes configure:4591: checking for floor configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:63:6: warning: conflicting types for built-in function 'floor' [enabled by default] char floor (); ^ /bin/ld: /tmp/cc0KF6E7.o: undefined reference to symbol 'floor@@GLIBC_2.2.5' /bin/ld: note: 'floor@@GLIBC_2.2.5' is defined in DSO /lib64/libm.so.6 so try adding it to the linker command line /lib64/libm.so.6: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status configure:4591: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | #define STDC_HEADERS 1 | #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_PNG_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define restrict __restrict | #define HAVE_PTRDIFF_T 1 | #define HAVE_FORK 1 | #define HAVE_VFORK 1 | #define HAVE_WORKING_VFORK 1 | #define HAVE_WORKING_FORK 1 | #define LSTAT_FOLLOWS_SLASHED_SYMLINK 1 | #define LSTAT_FOLLOWS_SLASHED_SYMLINK 1 | #define HAVE_STDLIB_H 1 | #define HAVE_MALLOC 1 | #define HAVE_STRFTIME 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:4591: result: no configure:4591: checking for memmove configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:63:6: warning: conflicting types for built-in function 'memmove' [enabled by default] char memmove (); ^ configure:4591: $? = 0 configure:4591: result: yes configure:4591: checking for pow configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:64:6: warning: conflicting types for built-in function 'pow' [enabled by default] char pow (); ^ /bin/ld: /tmp/ccr6OSpl.o: undefined reference to symbol 'pow@@GLIBC_2.2.5' /bin/ld: note: 'pow@@GLIBC_2.2.5' is defined in DSO /lib64/libm.so.6 so try adding it to the linker command line /lib64/libm.so.6: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status configure:4591: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | #define STDC_HEADERS 1 | #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_PNG_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define restrict __restrict | #define HAVE_PTRDIFF_T 1 | #define HAVE_FORK 1 | #define HAVE_VFORK 1 | #define HAVE_WORKING_VFORK 1 | #define HAVE_WORKING_FORK 1 | #define LSTAT_FOLLOWS_SLASHED_SYMLINK 1 | #define LSTAT_FOLLOWS_SLASHED_SYMLINK 1 | #define HAVE_STDLIB_H 1 | #define HAVE_MALLOC 1 | #define HAVE_STRFTIME 1 | #define HAVE_DUP2 1 | #define HAVE_MEMMOVE 1 | /* end confdefs.h. */ | /* Define pow to an innocuous variant, in case declares pow. | For example, HP-UX 11i declares gettimeofday. */ | #define pow innocuous_pow | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char pow (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #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:4591: result: no configure:4591: checking for regcomp configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 configure:4591: $? = 0 configure:4591: result: yes configure:4591: checking for sqrt configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:65:6: warning: conflicting types for built-in function 'sqrt' [enabled by default] char sqrt (); ^ /bin/ld: /tmp/ccSaVxmk.o: undefined reference to symbol 'sqrt@@GLIBC_2.2.5' /bin/ld: note: 'sqrt@@GLIBC_2.2.5' is defined in DSO /lib64/libm.so.6 so try adding it to the linker command line /lib64/libm.so.6: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status configure:4591: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jbrowse" | #define PACKAGE_TARNAME "jbrowse" | #define PACKAGE_VERSION "0.1" | #define PACKAGE_STRING "jbrowse 0.1" | #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" | #define PACKAGE_URL "" | #define CPLUSPLUS_COMPILER "g++" | #define STDC_HEADERS 1 | #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_PNG_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define restrict __restrict | #define HAVE_PTRDIFF_T 1 | #define HAVE_FORK 1 | #define HAVE_VFORK 1 | #define HAVE_WORKING_VFORK 1 | #define HAVE_WORKING_FORK 1 | #define LSTAT_FOLLOWS_SLASHED_SYMLINK 1 | #define LSTAT_FOLLOWS_SLASHED_SYMLINK 1 | #define HAVE_STDLIB_H 1 | #define HAVE_MALLOC 1 | #define HAVE_STRFTIME 1 | #define HAVE_DUP2 1 | #define HAVE_MEMMOVE 1 | #define HAVE_REGCOMP 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:4591: result: no configure:4591: checking for strchr configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:65:6: warning: conflicting types for built-in function 'strchr' [enabled by default] char strchr (); ^ configure:4591: $? = 0 configure:4591: result: yes configure:4591: checking for strcspn configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:66:6: warning: conflicting types for built-in function 'strcspn' [enabled by default] char strcspn (); ^ configure:4591: $? = 0 configure:4591: result: yes configure:4591: checking for strrchr configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:67:6: warning: conflicting types for built-in function 'strrchr' [enabled by default] char strrchr (); ^ configure:4591: $? = 0 configure:4591: result: yes configure:4591: checking for strspn configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:68:6: warning: conflicting types for built-in function 'strspn' [enabled by default] char strspn (); ^ configure:4591: $? = 0 configure:4591: result: yes configure:4591: checking for strstr configure:4591: gcc -o conftest -g -O2 conftest.c -lpng >&5 conftest.c:69:6: warning: conflicting types for built-in function 'strstr' [enabled by default] char strstr (); ^ configure:4591: $? = 0 configure:4591: result: yes configure:4718: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by jbrowse config.status 0.1, which was generated by GNU Autoconf 2.68. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on dgvbrowser.uab.es config.status:841: creating Makefile config.status:841: creating src/config.h ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_c_compiler_gnu=yes ac_cv_c_const=yes ac_cv_c_inline=inline ac_cv_c_restrict=__restrict 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_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_func_dup2=yes ac_cv_func_floor=no ac_cv_func_fork=yes ac_cv_func_fork_works=yes ac_cv_func_lstat_dereferences_slashed_symlink=yes ac_cv_func_lstat_empty_string_bug=no ac_cv_func_malloc_0_nonnull=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_strftime=yes ac_cv_func_strrchr=yes ac_cv_func_strspn=yes ac_cv_func_strstr=yes ac_cv_func_vfork=yes ac_cv_func_vfork_works=yes ac_cv_header_float_h=yes ac_cv_header_inttypes_h=yes ac_cv_header_memory_h=yes ac_cv_header_png_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_sys_wait_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_prog_CPP='gcc -E' ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_CXX=g++ ac_cv_prog_cc_c89= ac_cv_prog_cc_g=yes ac_cv_prog_cxx_g=yes ac_cv_search_png_create_write_struct=-lpng ac_cv_struct_tm=time.h ac_cv_type__Bool=yes ac_cv_type_pid_t=yes ac_cv_type_ptrdiff_t=yes ac_cv_type_size_t=yes ## ----------------- ## ## Output variables. ## ## ----------------- ## CC='gcc' CFLAGS='-g -O2' CPP='gcc -E' CPPFLAGS='' CXX='g++' CXXFLAGS='-g -O2' DEFS='-DHAVE_CONFIG_H' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' GREP='/bin/grep' LDFLAGS='' LIBOBJS='' LIBS='-lpng ' LN_S='ln -s' LTLIBOBJS='' OBJEXT='o' PACKAGE_BUGREPORT='jbrowse-bugs@postbox.biowiki.org' PACKAGE_NAME='jbrowse' PACKAGE_STRING='jbrowse 0.1' PACKAGE_TARNAME='jbrowse' PACKAGE_URL='' PACKAGE_VERSION='0.1' PATH_SEPARATOR=':' SHELL='/bin/sh' ac_ct_CC='gcc' ac_ct_CXX='g++' 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' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' oldincludedir='/usr/include' pdfdir='${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 "jbrowse" #define PACKAGE_TARNAME "jbrowse" #define PACKAGE_VERSION "0.1" #define PACKAGE_STRING "jbrowse 0.1" #define PACKAGE_BUGREPORT "jbrowse-bugs@postbox.biowiki.org" #define PACKAGE_URL "" #define CPLUSPLUS_COMPILER "g++" #define STDC_HEADERS 1 #define HAVE_SYS_WAIT_H 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_FLOAT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_UNISTD_H 1 #define HAVE_PNG_H 1 #define HAVE__BOOL 1 #define HAVE_STDBOOL_H 1 #define restrict __restrict #define HAVE_PTRDIFF_T 1 #define HAVE_FORK 1 #define HAVE_VFORK 1 #define HAVE_WORKING_VFORK 1 #define HAVE_WORKING_FORK 1 #define LSTAT_FOLLOWS_SLASHED_SYMLINK 1 #define LSTAT_FOLLOWS_SLASHED_SYMLINK 1 #define HAVE_STDLIB_H 1 #define HAVE_MALLOC 1 #define HAVE_STRFTIME 1 #define HAVE_DUP2 1 #define HAVE_MEMMOVE 1 #define HAVE_REGCOMP 1 #define HAVE_STRCHR 1 #define HAVE_STRCSPN 1 #define HAVE_STRRCHR 1 #define HAVE_STRSPN 1 #define HAVE_STRSTR 1 configure: exit 0