This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by HMMER configure 3.1b2, which was generated by GNU Autoconf 2.68. Invocation command line was $ ./configure ## --------- ## ## Platform. ## ## --------- ## hostname = sunflower.rnet.missouri.edu uname -m = x86_64 uname -r = 2.6.32-431.23.3.el6.x86_64 uname -s = Linux uname -v = #1 SMP Wed Jul 16 06:12:23 EDT 2014 /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: /usr/lib64/qt-3.3/bin PATH: /usr/local/bin PATH: /bin PATH: /usr/bin PATH: /usr/local/sbin PATH: /usr/sbin PATH: /sbin PATH: /home/jh7x3/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2268: Configuring HMMER for your system. configure:2411: checking build system type configure:2425: result: x86_64-unknown-linux-gnu configure:2445: checking host system type configure:2458: result: x86_64-unknown-linux-gnu configure:2489: Full HMMER source distribution - using full configuration configure:2681: checking for gcc configure:2697: found /usr/bin/gcc configure:2708: result: gcc configure:2937: checking for C compiler version configure:2946: gcc --version >&5 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) 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:2957: $? = 0 configure:2946: 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 4.4.7-4) (GCC) configure:2957: $? = 0 configure:2946: gcc -V >&5 gcc: '-V' option must have argument configure:2957: $? = 1 configure:2946: gcc -qversion >&5 gcc: unrecognized option '-qversion' gcc: no input files configure:2957: $? = 1 configure:2977: checking whether the C compiler works configure:2999: gcc conftest.c >&5 configure:3003: $? = 0 configure:3051: result: yes configure:3054: checking for C compiler default output file name configure:3056: result: a.out configure:3062: checking for suffix of executables configure:3069: gcc -o conftest conftest.c >&5 configure:3073: $? = 0 configure:3095: result: configure:3117: checking whether we are cross compiling configure:3125: gcc -o conftest conftest.c >&5 configure:3129: $? = 0 configure:3136: ./conftest configure:3140: $? = 0 configure:3155: result: no configure:3160: checking for suffix of object files configure:3182: gcc -c conftest.c >&5 configure:3186: $? = 0 configure:3207: result: o configure:3211: checking whether we are using the GNU C compiler configure:3230: gcc -c conftest.c >&5 configure:3230: $? = 0 configure:3239: result: yes configure:3248: checking whether gcc accepts -g configure:3268: gcc -c -g conftest.c >&5 configure:3268: $? = 0 configure:3309: result: yes configure:3326: checking for gcc option to accept ISO C89 configure:3390: gcc -c -g -O2 conftest.c >&5 configure:3390: $? = 0 configure:3403: result: none needed configure:3425: checking for C compiler vendor configure:3449: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:26: error: 'thisisanerror' undeclared (first use in this function) conftest.c:26: error: (Each undeclared identifier is reported only once conftest.c:26: error: for each function it appears in.) configure:3449: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | | int | main () | { | | #if !(defined(__ICC) || defined(__ECC) || defined(__INTEL_COMPILER)) | thisisanerror; | #endif | | ; | return 0; | } configure:3449: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:26: error: 'thisisanerror' undeclared (first use in this function) conftest.c:26: error: (Each undeclared identifier is reported only once conftest.c:26: error: for each function it appears in.) configure:3449: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | | int | main () | { | | #if !(defined(__xlc__) || defined(__xlC__) || defined(__IBMC__) || defined(__IBMCPP__)) | thisisanerror; | #endif | | ; | return 0; | } configure:3449: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:26: error: 'thisisanerror' undeclared (first use in this function) conftest.c:26: error: (Each undeclared identifier is reported only once conftest.c:26: error: for each function it appears in.) configure:3449: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | | int | main () | { | | #if !(defined(__PATHCC__) || defined(__PATHSCALE__)) | thisisanerror; | #endif | | ; | return 0; | } configure:3449: gcc -c -g -O2 conftest.c >&5 configure:3449: $? = 0 configure:3456: result: gnu configure:3665: checking for the pthreads library -lpthreads configure:3698: gcc -o conftest -g -O2 conftest.c -lpthreads >&5 /usr/bin/ld: cannot find -lpthreads collect2: ld returned 1 exit status configure:3698: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | #include | int | main () | { | pthread_t th; pthread_join(th, 0); | pthread_attr_init(0); pthread_cleanup_push(0, 0); | pthread_create(0,0,0,0); pthread_cleanup_pop(0); | ; | return 0; | } configure:3707: result: no configure:3610: checking whether pthreads work without any flags configure:3698: gcc -o conftest -g -O2 conftest.c >&5 /tmp/cc06hz3k.o: In function `main': /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:24: undefined reference to `pthread_join' /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:25: undefined reference to `__pthread_register_cancel' /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:26: undefined reference to `pthread_create' /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:26: undefined reference to `__pthread_unregister_cancel' collect2: ld returned 1 exit status configure:3698: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | #include | int | main () | { | pthread_t th; pthread_join(th, 0); | pthread_attr_init(0); pthread_cleanup_push(0, 0); | pthread_create(0,0,0,0); pthread_cleanup_pop(0); | ; | return 0; | } configure:3707: result: no configure:3615: checking whether pthreads work with -Kthread configure:3698: gcc -o conftest -g -O2 -Kthread conftest.c >&5 gcc: unrecognized option '-Kthread' /tmp/ccUr2S4F.o: In function `main': /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:24: undefined reference to `pthread_join' /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:25: undefined reference to `__pthread_register_cancel' /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:26: undefined reference to `pthread_create' /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:26: undefined reference to `__pthread_unregister_cancel' collect2: ld returned 1 exit status configure:3698: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | #include | int | main () | { | pthread_t th; pthread_join(th, 0); | pthread_attr_init(0); pthread_cleanup_push(0, 0); | pthread_create(0,0,0,0); pthread_cleanup_pop(0); | ; | return 0; | } configure:3707: result: no configure:3615: checking whether pthreads work with -kthread configure:3698: gcc -o conftest -g -O2 -kthread conftest.c >&5 gcc: unrecognized option '-kthread' /tmp/ccwLUexP.o: In function `main': /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:24: undefined reference to `pthread_join' /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:25: undefined reference to `__pthread_register_cancel' /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:26: undefined reference to `pthread_create' /home/casp13/DNCON2/hmmer-3.1b2-linux-intel-x86_64/conftest.c:26: undefined reference to `__pthread_unregister_cancel' collect2: ld returned 1 exit status configure:3698: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | #include | int | main () | { | pthread_t th; pthread_join(th, 0); | pthread_attr_init(0); pthread_cleanup_push(0, 0); | pthread_create(0,0,0,0); pthread_cleanup_pop(0); | ; | return 0; | } configure:3707: result: no configure:3665: checking for the pthreads library -llthread configure:3698: gcc -o conftest -g -O2 conftest.c -llthread >&5 /usr/bin/ld: cannot find -llthread collect2: ld returned 1 exit status configure:3698: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | #include | int | main () | { | pthread_t th; pthread_join(th, 0); | pthread_attr_init(0); pthread_cleanup_push(0, 0); | pthread_create(0,0,0,0); pthread_cleanup_pop(0); | ; | return 0; | } configure:3707: result: no configure:3615: checking whether pthreads work with -pthread configure:3698: gcc -o conftest -g -O2 -pthread conftest.c >&5 configure:3698: $? = 0 configure:3707: result: yes configure:3727: checking for joinable pthread attribute configure:3740: gcc -o conftest -g -O2 -pthread conftest.c >&5 configure:3740: $? = 0 configure:3772: result: PTHREAD_CREATE_JOINABLE configure:3779: checking if more special flags are required for pthreads configure:3789: result: no configure:3801: checking for cc_r configure:3829: result: gcc configure:3995: checking for gcc configure:4022: result: gcc configure:4251: checking for C compiler version configure:4260: gcc --version >&5 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) 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:4271: $? = 0 configure:4260: 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 4.4.7-4) (GCC) configure:4271: $? = 0 configure:4260: gcc -V >&5 gcc: '-V' option must have argument configure:4271: $? = 1 configure:4260: gcc -qversion >&5 gcc: unrecognized option '-qversion' gcc: no input files configure:4271: $? = 1 configure:4275: checking whether we are using the GNU C compiler configure:4303: result: yes configure:4312: checking whether gcc accepts -g configure:4373: result: yes configure:4390: checking for gcc option to accept ISO C89 configure:4467: result: none needed configure:4501: checking for a BSD-compatible install configure:4569: result: /usr/bin/install -c configure:4778: checking how to run the C preprocessor configure:4809: gcc -E conftest.c configure:4809: $? = 0 configure:4823: gcc -E conftest.c conftest.c:22:28: error: ac_nonexistent.h: No such file or directory configure:4823: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | #define HMMER_THREADS 1 | #define HAVE_PTHREAD 1 | /* end confdefs.h. */ | #include configure:4848: result: gcc -E configure:4868: gcc -E conftest.c configure:4868: $? = 0 configure:4882: gcc -E conftest.c conftest.c:22:28: error: ac_nonexistent.h: No such file or directory configure:4882: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | #define HMMER_THREADS 1 | #define HAVE_PTHREAD 1 | /* end confdefs.h. */ | #include configure:4911: checking for C compiler vendor configure:4942: result: gnu configure:4951: checking for gcc option to accept ISO C99 configure:5100: gcc -c -g -O2 conftest.c >&5 conftest.c:72: error: expected ';', ',' or ')' before 'text' conftest.c: In function 'main': conftest.c:126: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'newvar' conftest.c:126: error: 'newvar' undeclared (first use in this function) conftest.c:126: error: (Each undeclared identifier is reported only once conftest.c:126: error: for each function it appears in.) conftest.c:136: error: 'for' loop initial declarations are only allowed in C99 mode conftest.c:136: note: use option -std=c99 or -std=gnu99 to compile your code configure:5100: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | #define HMMER_THREADS 1 | #define HAVE_PTHREAD 1 | /* end confdefs.h. */ | #include | #include | #include | #include | #include | | // Check varargs macros. These examples are taken from C99 6.10.3.5. | #define debug(...) fprintf (stderr, __VA_ARGS__) | #define showlist(...) puts (#__VA_ARGS__) | #define report(test,...) ((test) ? puts (#test) : printf (__VA_ARGS__)) | static void | test_varargs_macros (void) | { | int x = 1234; | int y = 5678; | debug ("Flag"); | debug ("X = %d\n", x); | showlist (The first, second, and third items.); | report (x>y, "x is %d but y is %d", x, y); | } | | // Check long long types. | #define BIG64 18446744073709551615ull | #define BIG32 4294967295ul | #define BIG_OK (BIG64 / BIG32 == 4294967297ull && BIG64 % BIG32 == 0) | #if !BIG_OK | your preprocessor is broken; | #endif | #if BIG_OK | #else | your preprocessor is broken; | #endif | static long long int bignum = -9223372036854775807LL; | static unsigned long long int ubignum = BIG64; | | struct incomplete_array | { | int datasize; | double data[]; | }; | | struct named_init { | int number; | const wchar_t *name; | double average; | }; | | typedef const char *ccp; | | static inline int | test_restrict (ccp restrict text) | { | // See if C++-style comments work. | // Iterate through items via the restricted pointer. | // Also check for declarations in for loops. | for (unsigned int i = 0; *(text+i) != '\0'; ++i) | continue; | return 0; | } | | // Check varargs and va_copy. | static void | test_varargs (const char *format, ...) | { | va_list args; | va_start (args, format); | va_list args_copy; | va_copy (args_copy, args); | | const char *str; | int number; | float fnumber; | | while (*format) | { | switch (*format++) | { | case 's': // string | str = va_arg (args_copy, const char *); | break; | case 'd': // int | number = va_arg (args_copy, int); | break; | case 'f': // float | fnumber = va_arg (args_copy, double); | break; | default: | break; | } | } | va_end (args_copy); | va_end (args); | } | | int | main () | { | | // Check bool. | _Bool success = false; | | // Check restrict. | if (test_restrict ("String literal") == 0) | success = true; | char *restrict newvar = "Another string"; | | // Check varargs. | test_varargs ("s, d' f .", "string", 65, 34.234); | test_varargs_macros (); | | // Check flexible array members. | struct incomplete_array *ia = | malloc (sizeof (struct incomplete_array) + (sizeof (double) * 10)); | ia->datasize = 10; | for (int i = 0; i < ia->datasize; ++i) | ia->data[i] = i * 1.234; | | // Check named initializers. | struct named_init ni = { | .number = 34, | .name = L"Test wide string", | .average = 543.34343, | }; | | ni.number = 58; | | int dynamic_array[ni.number]; | dynamic_array[ni.number - 1] = 543; | | // work around unused variable warnings | return (!success || bignum == 0LL || ubignum == 0uLL || newvar[0] == 'x' | || dynamic_array[ni.number - 1] != 543); | | ; | return 0; | } configure:5100: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:5100: $? = 0 configure:5120: result: -std=gnu99 configure:5222: checking for gcc -std=gnu99 option to accept ISO Standard C configure:5236: result: -std=gnu99 configure:5284: checking for ranlib configure:5300: found /usr/bin/ranlib configure:5311: result: ranlib configure:5335: checking for ar configure:5354: found /usr/bin/ar configure:5367: result: /usr/bin/ar configure:5376: checking whether you have a GNU make configure:5387: result: yes, you do; and we assume you will use it! configure:5404: checking for a sed that does not truncate output configure:5468: result: /bin/sed configure:5741: checking whether C compiler accepts -fstrict-aliasing configure:5760: gcc -std=gnu99 -c -fstrict-aliasing conftest.c >&5 configure:5760: $? = 0 configure:5770: result: yes configure:5796: checking for gcc architecture flag configure:5798: result: configure:5820: checking for x86 cpuid 0 output configure:5849: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing conftest.c >&5 configure:5849: $? = 0 configure:5849: ./conftest configure:5849: $? = 0 configure:5859: result: d:756e6547:6c65746e:49656e69 configure:5875: checking for x86 cpuid 1 output configure:5904: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing conftest.c >&5 configure:5904: $? = 0 configure:5904: ./conftest configure:5904: $? = 0 configure:5914: result: 306e4:4200800:7fbee3ff:bfebfbff configure:6138: checking whether C compiler accepts -march=core2 configure:6157: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:6157: $? = 0 configure:6166: result: yes configure:6183: checking for gcc architecture flag configure:6185: result: -march=core2 configure:6207: checking whether C compiler accepts -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 configure:6222: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:6222: $? = 0 configure:6230: result: yes configure:6275: checking for gcc -std=gnu99 option to produce PIC configure:6361: result: -fPIC configure:6370: checking whether C compiler accepts -msse2 configure:6389: gcc -std=gnu99 -c -msse2 conftest.c >&5 configure:6389: $? = 0 configure:6399: result: yes configure:6683: checking compiler support for sse2 cast functions configure:6708: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 -msse2 conftest.c >&5 configure:6708: $? = 0 configure:6714: result: yes configure:6726: checking whether SSE2 is supported configure:6749: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 -msse2 conftest.c >&5 configure:6749: $? = 0 configure:6750: result: yes configure:6815: checking whether _MM_SET_FLUSH_ZERO_MODE is supported configure:6831: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 -msse2 conftest.c >&5 configure:6831: $? = 0 configure:6832: result: yes configure:6847: Activating Intel/AMD SSE optimized DP implementation configure:6884: checking compiler support --start-group configure:6899: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 -Wl,--start-group -Wl,--end-group conftest.c >&5 configure:6899: $? = 0 configure:6900: result: yes configure:6921: checking for gzip configure:6939: found /bin/gzip configure:6952: result: /bin/gzip configure:7032: checking for grep that handles long lines and -e configure:7090: result: /bin/grep configure:7095: checking for egrep configure:7157: result: /bin/grep -E configure:7162: checking for ANSI C header files configure:7182: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7182: $? = 0 configure:7255: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7255: $? = 0 configure:7255: ./conftest configure:7255: $? = 0 configure:7266: result: yes configure:7279: checking for sys/types.h configure:7279: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7279: $? = 0 configure:7279: result: yes configure:7279: checking for sys/stat.h configure:7279: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7279: $? = 0 configure:7279: result: yes configure:7279: checking for stdlib.h configure:7279: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7279: $? = 0 configure:7279: result: yes configure:7279: checking for string.h configure:7279: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7279: $? = 0 configure:7279: result: yes configure:7279: checking for memory.h configure:7279: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7279: $? = 0 configure:7279: result: yes configure:7279: checking for strings.h configure:7279: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7279: $? = 0 configure:7279: result: yes configure:7279: checking for inttypes.h configure:7279: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7279: $? = 0 configure:7279: result: yes configure:7279: checking for stdint.h configure:7279: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7279: $? = 0 configure:7279: result: yes configure:7279: checking for unistd.h configure:7279: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7279: $? = 0 configure:7279: result: yes configure:7301: checking endian.h usability configure:7301: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7301: $? = 0 configure:7301: result: yes configure:7301: checking endian.h presence configure:7301: gcc -E conftest.c configure:7301: $? = 0 configure:7301: result: yes configure:7301: checking for endian.h configure:7301: result: yes configure:7301: checking for inttypes.h configure:7301: result: yes configure:7301: checking for stdint.h configure:7301: result: yes configure:7301: checking for unistd.h configure:7301: result: yes configure:7301: checking for sys/types.h configure:7301: result: yes configure:7301: checking netinet/in.h usability configure:7301: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7301: $? = 0 configure:7301: result: yes configure:7301: checking netinet/in.h presence configure:7301: gcc -E conftest.c configure:7301: $? = 0 configure:7301: result: yes configure:7301: checking for netinet/in.h configure:7301: result: yes configure:7317: checking sys/param.h usability configure:7317: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7317: $? = 0 configure:7317: result: yes configure:7317: checking sys/param.h presence configure:7317: gcc -E conftest.c configure:7317: $? = 0 configure:7317: result: yes configure:7317: checking for sys/param.h configure:7317: result: yes configure:7329: checking for sys/sysctl.h configure:7329: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7329: $? = 0 configure:7329: result: yes configure:7370: checking whether byte ordering is bigendian configure:7385: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 conftest.c:46: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'a' configure:7385: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | #define HMMER_THREADS 1 | #define HAVE_PTHREAD 1 | #define HAVE_SSE2_CAST 1 | #define HAVE_FLUSH_ZERO_MODE 1 | #define HAVE_SSE2 1 | #define p7_IMPL_SSE 1 | #define HAVE_GZIP 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_ENDIAN_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_SYS_SYSCTL_H 1 | /* end confdefs.h. */ | #ifndef __APPLE_CC__ | not a universal capable compiler | #endif | typedef int dummy; | configure:7430: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7430: $? = 0 configure:7448: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 conftest.c: In function 'main': conftest.c:52: error: 'not' undeclared (first use in this function) conftest.c:52: error: (Each undeclared identifier is reported only once conftest.c:52: error: for each function it appears in.) conftest.c:52: error: expected ';' before 'big' configure:7448: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | #define HMMER_THREADS 1 | #define HAVE_PTHREAD 1 | #define HAVE_SSE2_CAST 1 | #define HAVE_FLUSH_ZERO_MODE 1 | #define HAVE_SSE2 1 | #define p7_IMPL_SSE 1 | #define HAVE_GZIP 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_ENDIAN_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_SYS_SYSCTL_H 1 | /* end confdefs.h. */ | #include | #include | | int | main () | { | #if BYTE_ORDER != BIG_ENDIAN | not big endian | #endif | | ; | return 0; | } configure:7576: result: no configure:7594: checking for uint8_t configure:7594: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7594: $? = 0 configure:7594: result: yes configure:7608: checking for uint16_t configure:7608: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7608: $? = 0 configure:7608: result: yes configure:7620: checking for uint32_t configure:7620: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7620: $? = 0 configure:7620: result: yes configure:7634: checking for uint64_t configure:7634: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7634: $? = 0 configure:7634: result: yes configure:7648: checking for off_t configure:7648: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7648: $? = 0 configure:7648: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 conftest.c: In function 'main': conftest.c:81: error: expected expression before ')' token configure:7648: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.1b2" | #define PACKAGE_STRING "HMMER 3.1b2" | #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" | #define PACKAGE_URL "" | #define HMMER_DATE "February 2015" | #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." | #define HMMER_VERSION "3.1b2" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "February 2015" | #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." | #define EASEL_VERSION "h3.1b2" | #define eslLIBRARY 1 | #define eslDEBUGLEVEL 0 | #define HMMER_THREADS 1 | #define HAVE_PTHREAD 1 | #define HAVE_SSE2_CAST 1 | #define HAVE_FLUSH_ZERO_MODE 1 | #define HAVE_SSE2 1 | #define p7_IMPL_SSE 1 | #define HAVE_GZIP 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_ENDIAN_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_NETINET_IN_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_SYS_SYSCTL_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 ((off_t))) | return 0; | ; | return 0; | } configure:7648: result: yes configure:7664: checking for mkstemp configure:7664: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7664: $? = 0 configure:7664: result: yes configure:7675: checking for popen configure:7675: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7675: $? = 0 configure:7675: result: yes configure:7686: checking for strcasecmp configure:7686: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 conftest.c:70: warning: conflicting types for built-in function 'strcasecmp' configure:7686: $? = 0 configure:7686: result: yes configure:7697: checking for times configure:7697: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7697: $? = 0 configure:7697: result: yes configure:7708: checking for getpid configure:7708: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7708: $? = 0 configure:7708: result: yes configure:7719: checking for sysctl configure:7719: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7719: $? = 0 configure:7719: result: yes configure:7730: checking for sysconf configure:7730: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7730: $? = 0 configure:7730: result: yes configure:7741: checking for getcwd configure:7741: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7741: $? = 0 configure:7741: result: yes configure:7752: checking for stat configure:7752: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7752: $? = 0 configure:7752: result: yes configure:7763: checking for fstat configure:7763: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7763: $? = 0 configure:7763: result: yes configure:7775: checking for ntohs configure:7775: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7775: $? = 0 configure:7775: result: yes configure:7832: checking for ntohl configure:7832: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7832: $? = 0 configure:7832: result: yes configure:7889: checking for htons configure:7889: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7889: $? = 0 configure:7889: result: yes configure:7946: checking for htonl configure:7946: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:7946: $? = 0 configure:7946: result: yes configure:8001: checking for _LARGEFILE_SOURCE value needed for large files configure:8020: gcc -std=gnu99 -o conftest -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:8020: $? = 0 configure:8048: result: no configure:8080: checking for special C compiler options needed for large files configure:8125: result: no configure:8131: checking for _FILE_OFFSET_BITS value needed for large files configure:8156: gcc -std=gnu99 -c -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 conftest.c >&5 configure:8156: $? = 0 configure:8188: result: no configure:8447: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by HMMER config.status 3.1b2, which was generated by GNU Autoconf 2.68. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on sunflower.rnet.missouri.edu config.status:915: creating documentation/Makefile config.status:915: creating documentation/man/Makefile config.status:915: creating src/Makefile config.status:915: creating testsuite/Makefile config.status:915: creating profmark/Makefile config.status:915: creating src/impl_sse/Makefile config.status:915: creating easel/miniapps/Makefile config.status:915: creating easel/testsuite/Makefile config.status:915: creating easel/Makefile config.status:915: creating libdivsufsort/Makefile config.status:915: creating Makefile config.status:915: creating src/p7_config.h config.status:915: creating easel/esl_config.h config.status:915: creating libdivsufsort/divsufsort.h config.status:1116: linking src/impl_sse to src/impl ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-unknown-linux-gnu ac_cv_c_bigendian=no ac_cv_c_compiler_gnu=yes ac_cv_c_uint16_t=yes ac_cv_c_uint32_t=yes ac_cv_c_uint64_t=yes ac_cv_c_uint8_t=yes ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_MPICC_set= ac_cv_env_MPICC_value= ac_cv_env_PIC_FLAGS_set= ac_cv_env_PIC_FLAGS_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_fstat=yes ac_cv_func_getcwd=yes ac_cv_func_getpid=yes ac_cv_func_htonl=yes ac_cv_func_htons=yes ac_cv_func_mkstemp=yes ac_cv_func_ntohl=yes ac_cv_func_ntohs=yes ac_cv_func_popen=yes ac_cv_func_stat=yes ac_cv_func_strcasecmp=yes ac_cv_func_sysconf=yes ac_cv_func_sysctl=yes ac_cv_func_times=yes ac_cv_header_endian_h=yes ac_cv_header_inttypes_h=yes ac_cv_header_memory_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_param_h=yes ac_cv_header_sys_stat_h=yes ac_cv_header_sys_sysctl_h=yes ac_cv_header_sys_types_h=yes ac_cv_header_unistd_h=yes ac_cv_host=x86_64-unknown-linux-gnu ac_cv_objext=o ac_cv_path_AR=/usr/bin/ar ac_cv_path_EGREP='/bin/grep -E' ac_cv_path_GREP=/bin/grep ac_cv_path_HAVE_GZIP=/bin/gzip ac_cv_path_SED=/bin/sed ac_cv_path_install='/usr/bin/install -c' ac_cv_prog_CPP='gcc -E' ac_cv_prog_PTHREAD_CC=gcc ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_cc_c89= ac_cv_prog_cc_c99=-std=gnu99 ac_cv_prog_cc_g=yes ac_cv_prog_cc_stdc=-std=gnu99 ac_cv_sys_file_offset_bits=no ac_cv_sys_largefile_CC=no ac_cv_sys_largefile_source=no ac_cv_type_off_t=yes ax_cv_c_compiler_vendor=gnu ax_cv_c_flags__O3__fomit_frame_pointer__fstrict_aliasing__march_core2=yes ax_cv_c_flags__fstrict_aliasing=yes ax_cv_c_flags__msse2=yes ax_cv_check_cflags___march_core2=yes ax_cv_gcc_archflag=-march=core2 ax_cv_gcc_x86_cpuid_0=d:756e6547:6c65746e:49656e69 ax_cv_gcc_x86_cpuid_1=306e4:4200800:7fbee3ff:bfebfbff ## ----------------- ## ## Output variables. ## ## ----------------- ## AR='/usr/bin/ar' CC='gcc -std=gnu99' CFLAGS='-O3 -fomit-frame-pointer -fstrict-aliasing -march=core2' CPP='gcc -E' CPPFLAGS='' DEFS='-DHAVE_CONFIG_H' EASEL_COPYRIGHT='Copyright (C) 2015 Howard Hughes Medical Institute.' EASEL_DATE='February 2015' EASEL_LICENSE='Freely distributed under the Janelia Farm Software License.' EASEL_URL='http://bioeasel.org/' EASEL_VERSION='h3.1b2' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEC_DEPENDENCY='%: %.o' EXEEXT='' GREP='/bin/grep' GROUPHMMERLIBS='-Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group' HAVE_GZIP='/bin/gzip' HMMERIMPLLIB='impl_sse/libhmmerimpl.a' HMMER_COPYRIGHT='Copyright (C) 2015 Howard Hughes Medical Institute.' HMMER_DATE='February 2015' HMMER_ESLDIR='easel' HMMER_LICENSE='Freely distributed under the GNU General Public License (GPLv3).' HMMER_SADIR='libdivsufsort' HMMER_URL='http://hmmer.org/' HMMER_VERSION='3.1b2' IMPL_CHOICE='sse' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' LDFLAGS='' LIBGSL='' LIBOBJS='' LIBS='' LTLIBOBJS='' MPICC='' MPILIBS='' MPI_BENCHMARKS='' MPI_UTESTS='' OBJEXT='o' PACKAGE_BUGREPORT='eddys@janelia.hhmi.org' PACKAGE_NAME='HMMER' PACKAGE_STRING='HMMER 3.1b2' PACKAGE_TARNAME='hmmer' PACKAGE_URL='' PACKAGE_VERSION='3.1b2' PATH_SEPARATOR=':' PIC_FLAGS='-fPIC' PRTDIAG='' PTHREAD_CC='gcc' PTHREAD_CFLAGS='-pthread' PTHREAD_LIBS='' RANLIB='ranlib' SED='/bin/sed' SHELL='/bin/sh' SIMD_CFLAGS='-msse2' ac_ct_CC='gcc' acx_pthread_config='' bindir='${exec_prefix}/bin' build='x86_64-unknown-linux-gnu' build_alias='' build_cpu='x86_64' build_os='linux-gnu' build_vendor='unknown' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='${prefix}' host='x86_64-unknown-linux-gnu' host_alias='' host_cpu='x86_64' host_os='linux-gnu' host_vendor='unknown' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' libdir='${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 "HMMER" #define PACKAGE_TARNAME "hmmer" #define PACKAGE_VERSION "3.1b2" #define PACKAGE_STRING "HMMER 3.1b2" #define PACKAGE_BUGREPORT "eddys@janelia.hhmi.org" #define PACKAGE_URL "" #define HMMER_DATE "February 2015" #define HMMER_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)." #define HMMER_VERSION "3.1b2" #define HMMER_URL "http://hmmer.org/" #define EASEL_DATE "February 2015" #define EASEL_COPYRIGHT "Copyright (C) 2015 Howard Hughes Medical Institute." #define EASEL_LICENSE "Freely distributed under the Janelia Farm Software License." #define EASEL_VERSION "h3.1b2" #define eslLIBRARY 1 #define eslDEBUGLEVEL 0 #define HMMER_THREADS 1 #define HAVE_PTHREAD 1 #define HAVE_SSE2_CAST 1 #define HAVE_FLUSH_ZERO_MODE 1 #define HAVE_SSE2 1 #define p7_IMPL_SSE 1 #define HAVE_GZIP 1 #define STDC_HEADERS 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_SYS_STAT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_MEMORY_H 1 #define HAVE_STRINGS_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_STDINT_H 1 #define HAVE_UNISTD_H 1 #define HAVE_ENDIAN_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_STDINT_H 1 #define HAVE_UNISTD_H 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_NETINET_IN_H 1 #define HAVE_SYS_PARAM_H 1 #define HAVE_SYS_SYSCTL_H 1 #define HAVE_MKSTEMP 1 #define HAVE_POPEN 1 #define HAVE_STRCASECMP 1 #define HAVE_TIMES 1 #define HAVE_GETPID 1 #define HAVE_SYSCTL 1 #define HAVE_SYSCONF 1 #define HAVE_GETCWD 1 #define HAVE_STAT 1 #define HAVE_FSTAT 1 #define HAVE_NTOHS 1 #define HAVE_NTOHL 1 #define HAVE_HTONS 1 #define HAVE_HTONL 1 #define HAVE_FSEEKO 1 configure: exit 0