This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by ABySS configure 2.1.5, which was generated by GNU Autoconf 2.63. Invocation command line was $ ./configure --prefix=/home/psgendb/BIRCHDEV/lib-linux-x86_64/abyss CPPFLAGS=-I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src ## --------- ## ## Platform. ## ## --------- ## hostname = venus uname -m = x86_64 uname -r = 2.6.32-754.10.1.el6.x86_64 uname -s = Linux uname -v = #1 SMP Thu Nov 29 15:44:01 EST 2018 /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: /opt/rh/python27/root/usr/bin PATH: /opt/rh/python27/root/usr/bin 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:2059: checking for a BSD-compatible install configure:2127: result: /usr/bin/install -c configure:2138: checking whether build environment is sane configure:2198: result: yes configure:2339: checking for a thread-safe mkdir -p configure:2378: result: /bin/mkdir -p configure:2391: checking for gawk configure:2407: found /bin/gawk configure:2418: result: gawk configure:2429: checking whether make sets $(MAKE) configure:2451: result: yes configure:2542: checking for gawk configure:2569: result: gawk configure:2628: checking for gcc configure:2644: found /usr/bin/gcc configure:2655: result: gcc configure:2887: checking for C compiler version configure:2895: gcc --version >&5 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23) 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:2899: $? = 0 configure:2906: 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 4.4.7-23) (GCC) configure:2910: $? = 0 configure:2917: gcc -V >&5 gcc: '-V' option must have argument configure:2921: $? = 1 configure:2944: checking for C compiler default output file name configure:2966: gcc -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:2970: $? = 0 configure:3008: result: a.out configure:3027: checking whether the C compiler works configure:3037: ./a.out configure:3041: $? = 0 configure:3060: result: yes configure:3067: checking whether we are cross compiling configure:3069: result: no configure:3072: checking for suffix of executables configure:3079: gcc -o conftest -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:3083: $? = 0 configure:3109: result: configure:3115: checking for suffix of object files configure:3141: gcc -c -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:3145: $? = 0 configure:3170: result: o configure:3174: checking whether we are using the GNU C compiler configure:3203: gcc -c -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:3210: $? = 0 configure:3227: result: yes configure:3236: checking whether gcc accepts -g configure:3266: gcc -c -g -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:3273: $? = 0 configure:3374: result: yes configure:3391: checking for gcc option to accept ISO C89 configure:3465: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:3472: $? = 0 configure:3495: result: none needed configure:3524: checking for style of include used by make configure:3552: result: GNU configure:3577: checking dependency style of gcc configure:3687: result: gcc3 configure:3707: checking how to run the C preprocessor configure:3747: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c configure:3754: $? = 0 configure:3785: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c conftest.c:10:28: error: ac_nonexistent.h: No such file or directory configure:3792: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | /* end confdefs.h. */ | #include configure:3825: result: gcc -E configure:3854: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c configure:3861: $? = 0 configure:3892: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c conftest.c:10:28: error: ac_nonexistent.h: No such file or directory configure:3899: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | /* end confdefs.h. */ | #include configure:3996: checking for g++ configure:4012: found /usr/bin/g++ configure:4023: result: g++ configure:4050: checking for C++ compiler version configure:4058: g++ --version >&5 g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23) 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:4062: $? = 0 configure:4069: 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 4.4.7-23) (GCC) configure:4073: $? = 0 configure:4080: g++ -V >&5 g++: '-V' option must have argument configure:4084: $? = 1 configure:4087: checking whether we are using the GNU C++ compiler configure:4116: g++ -c -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.cpp >&5 configure:4123: $? = 0 configure:4140: result: yes configure:4149: checking whether g++ accepts -g configure:4179: g++ -c -g -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.cpp >&5 configure:4186: $? = 0 configure:4287: result: yes configure:4312: checking dependency style of g++ configure:4422: result: gcc3 configure:4451: checking for a BSD-compatible install configure:4519: result: /usr/bin/install -c configure:4573: checking for ranlib configure:4589: found /usr/bin/ranlib configure:4600: result: ranlib configure:4665: checking for ghc configure:4695: result: no configure:4724: checking for pandoc configure:4740: found /usr/bin/pandoc configure:4751: result: yes configure:4771: checking for grep that handles long lines and -e configure:4831: result: /bin/grep configure:4836: checking for egrep configure:4900: result: /bin/grep -E configure:4905: checking for ANSI C header files configure:4935: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:4942: $? = 0 configure:5041: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5045: $? = 0 configure:5051: ./conftest configure:5055: $? = 0 configure:5073: result: yes configure:5097: checking for sys/types.h configure:5118: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5125: $? = 0 configure:5142: result: yes configure:5097: checking for sys/stat.h configure:5118: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5125: $? = 0 configure:5142: result: yes configure:5097: checking for stdlib.h configure:5118: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5125: $? = 0 configure:5142: result: yes configure:5097: checking for string.h configure:5118: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5125: $? = 0 configure:5142: result: yes configure:5097: checking for memory.h configure:5118: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5125: $? = 0 configure:5142: result: yes configure:5097: checking for strings.h configure:5118: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5125: $? = 0 configure:5142: result: yes configure:5097: checking for inttypes.h configure:5118: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5125: $? = 0 configure:5142: result: yes configure:5097: checking for stdint.h configure:5118: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5125: $? = 0 configure:5142: result: yes configure:5097: checking for unistd.h configure:5118: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5125: $? = 0 configure:5142: result: yes configure:5180: checking dlfcn.h usability configure:5197: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5204: $? = 0 configure:5218: result: yes configure:5222: checking dlfcn.h presence configure:5237: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c configure:5244: $? = 0 configure:5258: result: yes configure:5291: checking for dlfcn.h configure:5300: result: yes configure:5180: checking fcntl.h usability configure:5197: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5204: $? = 0 configure:5218: result: yes configure:5222: checking fcntl.h presence configure:5237: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c configure:5244: $? = 0 configure:5258: result: yes configure:5291: checking for fcntl.h configure:5300: result: yes configure:5180: checking float.h usability configure:5197: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5204: $? = 0 configure:5218: result: yes configure:5222: checking float.h presence configure:5237: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c configure:5244: $? = 0 configure:5258: result: yes configure:5291: checking for float.h configure:5300: result: yes configure:5180: checking limits.h usability configure:5197: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5204: $? = 0 configure:5218: result: yes configure:5222: checking limits.h presence configure:5237: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c configure:5244: $? = 0 configure:5258: result: yes configure:5291: checking for limits.h configure:5300: result: yes configure:5180: checking stddef.h usability configure:5197: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5204: $? = 0 configure:5218: result: yes configure:5222: checking stddef.h presence configure:5237: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c configure:5244: $? = 0 configure:5258: result: yes configure:5291: checking for stddef.h configure:5300: result: yes configure:5169: checking for stdint.h configure:5176: result: yes configure:5169: checking for stdlib.h configure:5176: result: yes configure:5180: checking sys/param.h usability configure:5197: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5204: $? = 0 configure:5218: result: yes configure:5222: checking sys/param.h presence configure:5237: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c configure:5244: $? = 0 configure:5258: result: yes configure:5291: checking for sys/param.h configure:5300: result: yes configure:5315: checking for stdbool.h that conforms to C99 configure:5410: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5417: $? = 0 configure:5432: result: yes configure:5434: checking for _Bool configure:5462: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5469: $? = 0 configure:5496: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c: In function 'main': conftest.c:64: error: expected expression before ')' token configure:5503: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_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:5526: result: yes configure:5545: checking for ANSI C header files configure:5713: result: yes configure:5726: checking whether byte ordering is bigendian configure:5751: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c:32: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'a' configure:5758: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | /* end confdefs.h. */ | #ifndef __APPLE_CC__ | not a universal capable compiler | #endif | typedef int dummy; | configure:5808: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:5815: $? = 0 configure:5847: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c: In function 'main': conftest.c:38: error: 'not' undeclared (first use in this function) conftest.c:38: error: (Each undeclared identifier is reported only once conftest.c:38: error: for each function it appears in.) conftest.c:38: error: expected ';' before 'big' configure:5854: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | /* end confdefs.h. */ | #include | #include | | int | main () | { | #if BYTE_ORDER != BIG_ENDIAN | not big endian | #endif | | ; | return 0; | } configure:6106: result: no configure:6131: checking for an ANSI C-conforming const configure:6206: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:6213: $? = 0 configure:6228: result: yes configure:6238: checking for inline configure:6264: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:6271: $? = 0 configure:6289: result: inline configure:6308: checking for ptrdiff_t configure:6336: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:6343: $? = 0 configure:6370: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c: In function 'main': conftest.c:67: error: expected expression before ')' token configure:6377: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 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 ((ptrdiff_t))) | return 0; | ; | return 0; | } configure:6400: result: yes configure:6411: checking for mode_t configure:6439: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:6446: $? = 0 configure:6473: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c: In function 'main': conftest.c:68: error: expected expression before ')' token configure:6480: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #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 | int | main () | { | if (sizeof ((mode_t))) | return 0; | ; | return 0; | } configure:6503: result: yes configure:6515: checking for pid_t configure:6543: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:6550: $? = 0 configure:6577: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c: In function 'main': conftest.c:68: error: expected expression before ')' token configure:6584: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #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 | int | main () | { | if (sizeof ((pid_t))) | return 0; | ; | return 0; | } configure:6607: result: yes configure:6619: checking for size_t configure:6647: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:6654: $? = 0 configure:6681: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c: In function 'main': conftest.c:68: error: expected expression before ')' token configure:6688: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #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 | int | main () | { | if (sizeof ((size_t))) | return 0; | ; | return 0; | } configure:6711: result: yes configure:6723: checking for ssize_t configure:6751: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:6758: $? = 0 configure:6785: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c: In function 'main': conftest.c:68: error: expected expression before ')' token configure:6792: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #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 | int | main () | { | if (sizeof ((ssize_t))) | return 0; | ; | return 0; | } configure:6815: result: yes configure:6828: checking for int64_t configure:6859: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:6866: $? = 0 configure:6895: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c: In function 'main': conftest.c:69: warning: integer overflow in expression conftest.c:69: error: size of array 'test_array' is negative configure:6902: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #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 | int | main () | { | static int test_array [1 - 2 * !((int64_t) ((((int64_t) 1 << (64 - 2)) - 1) * 2 + 1) | < (int64_t) ((((int64_t) 1 << (64 - 2)) - 1) * 2 + 2))]; | test_array [0] = 0 | | ; | return 0; | } configure:6931: result: yes configure:6944: checking for uint8_t configure:6975: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:6982: $? = 0 configure:7003: result: yes configure:7021: checking for uint16_t configure:7052: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7059: $? = 0 configure:7080: result: yes configure:7094: checking for uint32_t configure:7125: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7132: $? = 0 configure:7153: result: yes configure:7171: checking for uint64_t configure:7202: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7209: $? = 0 configure:7230: result: yes configure:7256: checking for std::hash configure:7290: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:42: error: 'hash' is not a member of 'std' conftest.cpp:42: error: expected primary-expression before 'int' conftest.cpp:42: error: expected ')' before 'int' conftest.cpp:43: error: expected ')' before ';' token configure:7297: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | /* end confdefs.h. */ | | #ifdef __FUJITSU | #include | #else | #include | #endif | | int | main () | { | if (sizeof (std::hash)) | return 0; | ; | return 0; | } configure:7360: result: no configure:7370: checking for std::tr1::hash configure:7399: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.cpp >&5 configure:7406: $? = 0 configure:7434: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:37: error: expected primary-expression before ')' token configure:7441: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | /* end confdefs.h. */ | #include | | int | main () | { | if (sizeof ((std::tr1::hash))) | return 0; | ; | return 0; | } configure:7464: result: yes configure:7474: checking for std::tr1::tuple configure:7503: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.cpp >&5 configure:7510: $? = 0 configure:7538: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:38: error: expected primary-expression before ')' token configure:7545: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | /* end confdefs.h. */ | #include | | int | main () | { | if (sizeof ((std::tr1::tuple))) | return 0; | ; | return 0; | } configure:7568: result: yes configure:7616: checking for dup2 configure:7672: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7679: $? = 0 configure:7701: result: yes configure:7616: checking for gethostname configure:7672: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7679: $? = 0 configure:7701: result: yes configure:7616: checking for getopt_long configure:7672: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7679: $? = 0 configure:7701: result: yes configure:7616: checking for getpagesize configure:7672: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7679: $? = 0 configure:7701: result: yes configure:7616: checking for memset configure:7672: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c:62: warning: conflicting types for built-in function 'memset' configure:7679: $? = 0 configure:7701: result: yes configure:7616: checking for strdup configure:7672: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c:63: warning: conflicting types for built-in function 'strdup' configure:7679: $? = 0 configure:7701: result: yes configure:7616: checking for strerror configure:7672: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7679: $? = 0 configure:7701: result: yes configure:7616: checking for strtoul configure:7672: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7679: $? = 0 configure:7701: result: yes configure:7729: checking vfork.h usability configure:7746: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c:76:19: error: vfork.h: No such file or directory configure:7753: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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:7767: result: no configure:7771: checking vfork.h presence configure:7786: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c conftest.c:43:19: error: vfork.h: No such file or directory configure:7793: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 1 | /* end confdefs.h. */ | #include configure:7807: result: no configure:7840: checking for vfork.h configure:7849: result: no configure:7869: checking for fork configure:7925: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c:66: warning: conflicting types for built-in function 'fork' configure:7932: $? = 0 configure:7954: result: yes configure:7869: checking for vfork configure:7925: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:7932: $? = 0 configure:7954: result: yes configure:7967: checking for working fork configure:7999: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:8003: $? = 0 configure:8009: ./conftest configure:8013: $? = 0 configure:8030: result: yes configure:8051: checking for working vfork configure:8192: result: yes configure:8228: checking for stdlib.h configure:8235: result: yes configure:8374: checking for GNU libc compatible malloc configure:8408: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:8412: $? = 0 configure:8418: ./conftest configure:8422: $? = 0 configure:8439: result: yes configure:8467: checking for working memcmp configure:8520: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:8524: $? = 0 configure:8530: ./conftest configure:8534: $? = 0 configure:8551: result: yes configure:8565: checking for stdlib.h configure:8572: result: yes configure:8711: checking for GNU libc compatible realloc configure:8745: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:8749: $? = 0 configure:8755: ./conftest configure:8759: $? = 0 configure:8776: result: yes configure:8815: checking for vprintf configure:8871: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 conftest.c:74: warning: conflicting types for built-in function 'vprintf' configure:8878: $? = 0 configure:8900: result: yes configure:8909: checking for _doprnt configure:8965: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 /tmp/ccTvNtZ9.o: In function `main': /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:86: undefined reference to `_doprnt' collect2: ld returned 1 exit status configure:8972: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | /* end confdefs.h. */ | /* Define _doprnt to an innocuous variant, in case declares _doprnt. | For example, HP-UX 11i declares gettimeofday. */ | #define _doprnt innocuous__doprnt | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char _doprnt (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #endif | | #undef _doprnt | | /* 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 _doprnt (); | /* 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__doprnt || defined __stub____doprnt | choke me | #endif | | int | main () | { | return _doprnt (); | ; | return 0; | } configure:8992: result: no configure:9008: checking whether HOST_NAME_MAX is declared configure:9038: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src conftest.c >&5 configure:9045: $? = 0 configure:9060: result: yes configure:9198: checking build system type configure:9216: result: x86_64-unknown-linux-gnu configure:9238: checking host system type configure:9253: result: x86_64-unknown-linux-gnu configure:9418: checking if compiler needs -Werror to reject unknown flags configure:9444: gcc -c -g -O2 -Werror -Wunknown-warning-option -Wsizeof-array-argument -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c >&5 cc1: error: unrecognized command line option "-Wunknown-warning-option" cc1: error: unrecognized command line option "-Wsizeof-array-argument" configure:9451: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | /* end confdefs.h. */ | int foo(void); | int | main () | { | foo() | ; | return 0; | } configure:9463: result: no configure:9530: checking for the pthreads library -lpthreads configure:9578: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c -lpthreads >&5 /usr/bin/ld: cannot find -lpthreads collect2: ld returned 1 exit status configure:9585: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | /* end confdefs.h. */ | #include | static void routine(void *a) { a = 0; } | static void *start_routine(void *a) { return a; } | int | main () | { | pthread_t th; pthread_attr_t attr; | pthread_create(&th, 0, start_routine, 0); | pthread_join(th, 0); | pthread_attr_init(&attr); | pthread_cleanup_push(routine, 0); | pthread_cleanup_pop(0) /* ; */ | ; | return 0; | } configure:9608: result: no configure:9475: checking whether pthreads work without any flags configure:9578: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c >&5 /tmp/ccpYojxH.o: In function `main': /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:62: undefined reference to `pthread_create' /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:63: undefined reference to `pthread_join' /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:65: undefined reference to `__pthread_register_cancel' /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:66: undefined reference to `__pthread_unregister_cancel' collect2: ld returned 1 exit status configure:9585: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | /* end confdefs.h. */ | #include | static void routine(void *a) { a = 0; } | static void *start_routine(void *a) { return a; } | int | main () | { | pthread_t th; pthread_attr_t attr; | pthread_create(&th, 0, start_routine, 0); | pthread_join(th, 0); | pthread_attr_init(&attr); | pthread_cleanup_push(routine, 0); | pthread_cleanup_pop(0) /* ; */ | ; | return 0; | } configure:9608: result: no configure:9480: checking whether pthreads work with -Kthread configure:9578: gcc -o conftest -g -O2 -Kthread -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c >&5 gcc: unrecognized option '-Kthread' /tmp/cc8n4F9F.o: In function `main': /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:62: undefined reference to `pthread_create' /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:63: undefined reference to `pthread_join' /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:65: undefined reference to `__pthread_register_cancel' /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:66: undefined reference to `__pthread_unregister_cancel' collect2: ld returned 1 exit status configure:9585: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | /* end confdefs.h. */ | #include | static void routine(void *a) { a = 0; } | static void *start_routine(void *a) { return a; } | int | main () | { | pthread_t th; pthread_attr_t attr; | pthread_create(&th, 0, start_routine, 0); | pthread_join(th, 0); | pthread_attr_init(&attr); | pthread_cleanup_push(routine, 0); | pthread_cleanup_pop(0) /* ; */ | ; | return 0; | } configure:9608: result: no configure:9480: checking whether pthreads work with -kthread configure:9578: gcc -o conftest -g -O2 -kthread -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c >&5 gcc: unrecognized option '-kthread' /tmp/ccujEuuP.o: In function `main': /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:62: undefined reference to `pthread_create' /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:63: undefined reference to `pthread_join' /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:65: undefined reference to `__pthread_register_cancel' /home/psgendb/BIRCHDEV/install/abyss-master/conftest.c:66: undefined reference to `__pthread_unregister_cancel' collect2: ld returned 1 exit status configure:9585: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | /* end confdefs.h. */ | #include | static void routine(void *a) { a = 0; } | static void *start_routine(void *a) { return a; } | int | main () | { | pthread_t th; pthread_attr_t attr; | pthread_create(&th, 0, start_routine, 0); | pthread_join(th, 0); | pthread_attr_init(&attr); | pthread_cleanup_push(routine, 0); | pthread_cleanup_pop(0) /* ; */ | ; | return 0; | } configure:9608: result: no configure:9530: checking for the pthreads library -llthread configure:9578: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c -llthread >&5 /usr/bin/ld: cannot find -llthread collect2: ld returned 1 exit status configure:9585: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | /* end confdefs.h. */ | #include | static void routine(void *a) { a = 0; } | static void *start_routine(void *a) { return a; } | int | main () | { | pthread_t th; pthread_attr_t attr; | pthread_create(&th, 0, start_routine, 0); | pthread_join(th, 0); | pthread_attr_init(&attr); | pthread_cleanup_push(routine, 0); | pthread_cleanup_pop(0) /* ; */ | ; | return 0; | } configure:9608: result: no configure:9480: checking whether pthreads work with -pthread configure:9578: gcc -o conftest -g -O2 -pthread -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c >&5 configure:9585: $? = 0 configure:9608: result: yes configure:9627: checking for joinable pthread attribute configure:9652: gcc -o conftest -g -O2 -pthread -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c >&5 configure:9659: $? = 0 configure:9679: result: PTHREAD_CREATE_JOINABLE configure:9689: checking if more special flags are required for pthreads configure:9704: result: no configure:9710: checking for PTHREAD_PRIO_INHERIT configure:9737: gcc -o conftest -g -O2 -pthread -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c >&5 conftest.c: In function 'main': conftest.c:59: error: 'PTHREAD_PRIO_INHERIT' undeclared (first use in this function) conftest.c:59: error: (Each undeclared identifier is reported only once conftest.c:59: error: for each function it appears in.) configure:9744: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | /* end confdefs.h. */ | #include | int | main () | { | int i = PTHREAD_PRIO_INHERIT; | ; | return 0; | } configure:9765: result: no configure:9900: checking mpi.h usability configure:9917: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c >&5 conftest.c:90:17: error: mpi.h: No such file or directory configure:9924: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 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:9938: result: no configure:9942: checking mpi.h presence configure:9957: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c conftest.c:57:17: error: mpi.h: No such file or directory configure:9964: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | /* end confdefs.h. */ | #include configure:9978: result: no configure:10011: checking for mpi.h configure:10020: result: no configure:10646: checking for MPI_Init in -lmpi configure:10681: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c -lmpi >&5 /usr/bin/ld: cannot find -lmpi collect2: ld returned 1 exit status configure:10688: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | /* 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 MPI_Init (); | int | main () | { | return MPI_Init (); | ; | return 0; | } configure:10709: result: no configure:10735: checking for sqrt in -lm configure:10770: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c -lm >&5 conftest.c:64: warning: conflicting types for built-in function 'sqrt' configure:10777: $? = 0 configure:10798: result: yes configure:10814: checking for pow configure:10870: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c -lm >&5 conftest.c:81: warning: conflicting types for built-in function 'pow' configure:10877: $? = 0 configure:10899: result: yes configure:10814: checking for sqrt configure:10870: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c -lm >&5 conftest.c:82: warning: conflicting types for built-in function 'sqrt' configure:10877: $? = 0 configure:10899: result: yes configure:10911: checking for ceilf configure:10967: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c -lm >&5 conftest.c:83: warning: conflicting types for built-in function 'ceilf' configure:10974: $? = 0 configure:10994: result: yes configure:11009: checking for dlsym in -ldl configure:11044: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c -ldl -lm >&5 configure:11051: $? = 0 configure:11072: result: yes configure:11107: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.c >&5 conftest.c:61:20: warning: extra tokens at end of #include directive configure:11114: $? = 0 configure:11149: checking how to run the C++ preprocessor configure:11185: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11192: $? = 0 configure:11223: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp conftest.cpp:62:28: error: ac_nonexistent.h: No such file or directory configure:11230: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_LIBM 1 | #define HAVE_POW 1 | #define HAVE_SQRT 1 | #define HAVE_LIBDL 1 | #define HAVE_POPCNT 1 | /* end confdefs.h. */ | #include configure:11263: result: g++ -E configure:11292: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11299: $? = 0 configure:11330: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp conftest.cpp:62:28: error: ac_nonexistent.h: No such file or directory configure:11337: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_LIBM 1 | #define HAVE_POW 1 | #define HAVE_SQRT 1 | #define HAVE_LIBDL 1 | #define HAVE_POPCNT 1 | /* end confdefs.h. */ | #include configure:11411: checking functional usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 configure:11435: $? = 0 configure:11449: result: yes configure:11453: checking functional presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11475: $? = 0 configure:11489: result: yes configure:11522: checking for functional configure:11531: result: yes configure:11411: checking tr1/functional usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 configure:11435: $? = 0 configure:11449: result: yes configure:11453: checking tr1/functional presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11475: $? = 0 configure:11489: result: yes configure:11522: checking for tr1/functional configure:11531: result: yes configure:11411: checking boost/functional/hash.hpp usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 configure:11435: $? = 0 configure:11449: result: yes configure:11453: checking boost/functional/hash.hpp presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11475: $? = 0 configure:11489: result: yes configure:11522: checking for boost/functional/hash.hpp configure:11531: result: yes configure:11411: checking boost/property_map/property_map.hpp usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 configure:11435: $? = 0 configure:11449: result: yes configure:11453: checking boost/property_map/property_map.hpp presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11475: $? = 0 configure:11489: result: yes configure:11522: checking for boost/property_map/property_map.hpp configure:11531: result: yes configure:11411: checking google/sparse_hash_map usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 configure:11435: $? = 0 configure:11449: result: yes configure:11453: checking google/sparse_hash_map presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11475: $? = 0 configure:11489: result: yes configure:11522: checking for google/sparse_hash_map configure:11531: result: yes configure:11411: checking unordered_map usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/unordered_map:35, from conftest.cpp:100: /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/c++0x_warning.h:31:2: error: #error This file requires compiler and library support for the upcoming ISO C++ standard, C++0x. This support is currently experimental, and must be enabled with the -std=c++0x or -std=gnu++0x compiler options. configure:11435: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_LIBM 1 | #define HAVE_POW 1 | #define HAVE_SQRT 1 | #define HAVE_LIBDL 1 | #define HAVE_POPCNT 1 | #define HAVE_FUNCTIONAL 1 | #define HAVE_TR1_FUNCTIONAL 1 | #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | #define HAVE_GOOGLE_SPARSE_HASH_MAP 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:11449: result: no configure:11453: checking unordered_map presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/unordered_map:35, from conftest.cpp:67: /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/c++0x_warning.h:31:2: error: #error This file requires compiler and library support for the upcoming ISO C++ standard, C++0x. This support is currently experimental, and must be enabled with the -std=c++0x or -std=gnu++0x compiler options. configure:11475: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_LIBM 1 | #define HAVE_POW 1 | #define HAVE_SQRT 1 | #define HAVE_LIBDL 1 | #define HAVE_POPCNT 1 | #define HAVE_FUNCTIONAL 1 | #define HAVE_TR1_FUNCTIONAL 1 | #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 | /* end confdefs.h. */ | #include configure:11489: result: no configure:11522: checking for unordered_map configure:11531: result: no configure:11411: checking tr1/unordered_map usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 configure:11435: $? = 0 configure:11449: result: yes configure:11453: checking tr1/unordered_map presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11475: $? = 0 configure:11489: result: yes configure:11522: checking for tr1/unordered_map configure:11531: result: yes configure:11411: checking unordered_set usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/unordered_set:35, from conftest.cpp:101: /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/c++0x_warning.h:31:2: error: #error This file requires compiler and library support for the upcoming ISO C++ standard, C++0x. This support is currently experimental, and must be enabled with the -std=c++0x or -std=gnu++0x compiler options. configure:11435: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_LIBM 1 | #define HAVE_POW 1 | #define HAVE_SQRT 1 | #define HAVE_LIBDL 1 | #define HAVE_POPCNT 1 | #define HAVE_FUNCTIONAL 1 | #define HAVE_TR1_FUNCTIONAL 1 | #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 | #define HAVE_TR1_UNORDERED_MAP 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:11449: result: no configure:11453: checking unordered_set presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/unordered_set:35, from conftest.cpp:68: /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/c++0x_warning.h:31:2: error: #error This file requires compiler and library support for the upcoming ISO C++ standard, C++0x. This support is currently experimental, and must be enabled with the -std=c++0x or -std=gnu++0x compiler options. configure:11475: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.5" | #define PACKAGE_STRING "ABySS 2.1.5" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE "abyss" | #define VERSION "2.1.5" | #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_DLFCN_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define STDC_HEADERS 1 | #define HAVE_PTRDIFF_T 1 | #define HAVE_STD_TR1_HASH 1 | #define HAVE_STD_TR1_TUPLE 1 | #define BOOST_HAS_TR1_TUPLE 1 | #define HAVE_DUP2 1 | #define HAVE_GETHOSTNAME 1 | #define HAVE_GETOPT_LONG 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MEMSET 1 | #define HAVE_STRDUP 1 | #define HAVE_STRERROR 1 | #define HAVE_STRTOUL 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_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_VPRINTF 1 | #define FMBITS 64 | #define MAX_KMER 128 | #define MAX_HASHES 32 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_LIBM 1 | #define HAVE_POW 1 | #define HAVE_SQRT 1 | #define HAVE_LIBDL 1 | #define HAVE_POPCNT 1 | #define HAVE_FUNCTIONAL 1 | #define HAVE_TR1_FUNCTIONAL 1 | #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 | #define HAVE_TR1_UNORDERED_MAP 1 | /* end confdefs.h. */ | #include configure:11489: result: no configure:11522: checking for unordered_set configure:11531: result: no configure:11411: checking tr1/unordered_set usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 configure:11435: $? = 0 configure:11449: result: yes configure:11453: checking tr1/unordered_set presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11475: $? = 0 configure:11489: result: yes configure:11522: checking for tr1/unordered_set configure:11531: result: yes configure:11411: checking boost/unordered_set.hpp usability configure:11428: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 configure:11435: $? = 0 configure:11449: result: yes configure:11453: checking boost/unordered_set.hpp presence configure:11468: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11475: $? = 0 configure:11489: result: yes configure:11522: checking for boost/unordered_set.hpp configure:11531: result: yes configure:11587: checking sqlite3.h usability configure:11604: g++ -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp >&5 configure:11611: $? = 0 configure:11625: result: yes configure:11629: checking sqlite3.h presence configure:11644: g++ -E -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp configure:11651: $? = 0 configure:11665: result: yes configure:11698: checking for sqlite3.h configure:11707: result: yes configure:11723: checking for main in -lsqlite3 configure:11752: g++ -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp -lsqlite3 -ldl -lm >&5 configure:11759: $? = 0 configure:11780: result: yes configure:11820: checking for gcc option to support OpenMP configure:11840: g++ -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp -ldl -lm >&5 conftest.cpp:3: error: 'choke' does not name a type In file included from conftest.cpp:5: /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:38: error: expected constructor, destructor, or type conversion before ';' token /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:76: error: variable or field 'omp_init_lock' declared void /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:76: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:76: error: expected primary-expression before ')' token /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:77: error: variable or field 'omp_destroy_lock' declared void /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:77: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:77: error: expected primary-expression before ')' token /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:78: error: variable or field 'omp_set_lock' declared void /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:78: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:78: error: expected primary-expression before ')' token /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:79: error: variable or field 'omp_unset_lock' declared void /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:79: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:79: error: expected primary-expression before ')' token /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:80: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:80: error: expected primary-expression before ')' token /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:80: error: expected ',' or ';' before 'throw' configure:11847: $? = 1 configure: failed program was: | | #ifndef _OPENMP | choke me | #endif | #include | int main () { return omp_get_num_threads (); } | configure:11879: g++ -o conftest -g -O2 -fopenmp -I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0 conftest.cpp -ldl -lm >&5 configure:11886: $? = 0 configure:11916: result: -fopenmp configure:12166: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by ABySS config.status 2.1.5, which was generated by GNU Autoconf 2.63. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on venus config.status:905: creating Makefile config.status:905: creating ABYSS/Makefile config.status:905: creating Align/Makefile config.status:905: creating Assembly/Makefile config.status:905: creating Common/Makefile config.status:905: creating DataLayer/Makefile config.status:905: creating FMIndex/Makefile config.status:905: creating Graph/Makefile config.status:905: creating Parallel/Makefile config.status:905: creating bin/Makefile config.status:905: creating doc/Makefile config.status:905: creating dialign/Makefile config.status:905: creating kmerprint/Makefile config.status:905: creating AdjList/Makefile config.status:905: creating Konnector/Makefile config.status:905: creating DAssembler/Makefile config.status:905: creating DistanceEst/Makefile config.status:905: creating Layout/Makefile config.status:905: creating Map/Makefile config.status:905: creating Misc/Makefile config.status:905: creating Overlap/Makefile config.status:905: creating PopBubbles/Makefile config.status:905: creating Scaffold/Makefile config.status:905: creating SimpleGraph/Makefile config.status:905: creating MergePaths/Makefile config.status:905: creating KAligner/Makefile config.status:905: creating PairedDBG/Makefile config.status:905: creating ParseAligns/Makefile config.status:905: creating PathOverlap/Makefile config.status:905: creating Consensus/Makefile config.status:905: creating FilterGraph/Makefile config.status:905: creating GapFiller/Makefile config.status:905: creating Sealer/Makefile config.status:905: creating lib/gtest-1.7.0/Makefile config.status:905: creating Unittest/Makefile config.status:905: creating LogKmerCount/Makefile config.status:905: creating Bloom/Makefile config.status:905: creating BloomDBG/Makefile config.status:905: creating DataBase/Makefile config.status:905: creating lib/bloomfilter/Makefile config.status:905: creating lib/nthash/Makefile config.status:905: creating config.h config.status:1179: executing depfiles commands ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-unknown-linux-gnu ac_cv_c_bigendian=no ac_cv_c_compiler_gnu=yes ac_cv_c_const=yes ac_cv_c_inline=inline ac_cv_c_int64_t=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_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=set ac_cv_env_CPPFLAGS_value=-I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_CXXCPP_set= ac_cv_env_CXXCPP_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__doprnt=no ac_cv_func_ceilf=yes ac_cv_func_dup2=yes ac_cv_func_fork=yes ac_cv_func_fork_works=yes ac_cv_func_gethostname=yes ac_cv_func_getopt_long=yes ac_cv_func_getpagesize=yes ac_cv_func_malloc_0_nonnull=yes ac_cv_func_memcmp_working=yes ac_cv_func_memset=yes ac_cv_func_pow=yes ac_cv_func_realloc_0_nonnull=yes ac_cv_func_setvbuf_reversed=no ac_cv_func_sqrt=yes ac_cv_func_strdup=yes ac_cv_func_strerror=yes ac_cv_func_strtoul=yes ac_cv_func_vfork=yes ac_cv_func_vfork_works=yes ac_cv_func_vprintf=yes ac_cv_have_decl_HOST_NAME_MAX=yes ac_cv_header_boost_functional_hash_hpp=yes ac_cv_header_boost_property_map_property_map_hpp=yes ac_cv_header_boost_unordered_set_hpp=yes ac_cv_header_dlfcn_h=yes ac_cv_header_fcntl_h=yes ac_cv_header_float_h=yes ac_cv_header_functional=yes ac_cv_header_google_sparse_hash_map=yes ac_cv_header_inttypes_h=yes ac_cv_header_limits_h=yes ac_cv_header_memory_h=yes ac_cv_header_mpi_h=no ac_cv_header_sqlite3_h=yes ac_cv_header_stdbool_h=yes ac_cv_header_stdc=yes ac_cv_header_stddef_h=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_types_h=yes ac_cv_header_tr1_functional=yes ac_cv_header_tr1_unordered_map=yes ac_cv_header_tr1_unordered_set=yes ac_cv_header_unistd_h=yes ac_cv_header_unordered_map=no ac_cv_header_unordered_set=no ac_cv_header_vfork_h=no ac_cv_host=x86_64-unknown-linux-gnu ac_cv_lib_dl_dlsym=yes ac_cv_lib_m_sqrt=yes ac_cv_lib_mpi_MPI_Init=no ac_cv_lib_sqlite3_main=yes ac_cv_objext=o ac_cv_path_EGREP='/bin/grep -E' ac_cv_path_GREP=/bin/grep 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_CXXCPP='g++ -E' ac_cv_prog_PANDOC=yes 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_cxx_openmp=-fopenmp ac_cv_prog_make_make_set=yes ac_cv_type__Bool=yes ac_cv_type_mode_t=yes ac_cv_type_pid_t=yes ac_cv_type_ptrdiff_t=yes ac_cv_type_size_t=yes ac_cv_type_ssize_t=yes ac_cv_type_std__hash_int_=no ac_cv_type_std__tr1__hash_int_=yes ac_cv_type_std__tr1__tuple_int_=yes am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 ax_cv_PTHREAD_PRIO_INHERIT=no ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-master/missing --run aclocal-1.11' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-master/missing --run tar' AM_CXXFLAGS='-Wall -Wextra' AUTOCONF='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-master/missing --run autoconf' AUTOHEADER='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-master/missing --run autoheader' AUTOMAKE='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-master/missing --run automake-1.11' AWK='gawk' CC='gcc' CCDEPMODE='depmode=gcc3' CFLAGS='-g -O2' CPP='gcc -E' CPPFLAGS='-I/home/psgendb/BIRCHDEV/install/abyss-master -I/home/psgendb/BIRCHDEV/install/abyss-master/sparsehash/src -isystem/home/psgendb/BIRCHDEV/install/abyss-master/boost_1_56_0' CXX='g++' CXXCPP='g++ -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-g -O2' CYGPATH_W='echo' DEFS='-DHAVE_CONFIG_H' DEPDIR='.deps' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' GHC='' GREP='/bin/grep' HAVE_GHC_FALSE='' HAVE_GHC_TRUE='#' HAVE_LIBMPI_FALSE='' HAVE_LIBMPI_TRUE='#' HAVE_PANDOC_FALSE='#' HAVE_PANDOC_TRUE='' HAVE_PTHREAD_FALSE='#' HAVE_PTHREAD_TRUE='' HAVE_SQLITE3_FALSE='#' HAVE_SQLITE3_TRUE='' HAVE_TR1_TUPLE_FALSE='#' HAVE_TR1_TUPLE_TRUE='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS=' ' LIBOBJS='' LIBS='-ldl -lm ' LTLIBOBJS='' MAKEINFO='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-master/missing --run makeinfo' MKDIR_P='/bin/mkdir -p' MPI_LIBS='' OBJEXT='o' OPENMP_CXXFLAGS='-fopenmp' PACKAGE='abyss' PACKAGE_BUGREPORT='abyss-users@bcgsc.ca' PACKAGE_NAME='ABySS' PACKAGE_STRING='ABySS 2.1.5' PACKAGE_TARNAME='abyss' PACKAGE_VERSION='2.1.5' PAIRED_DBG_FALSE='#' PAIRED_DBG_TRUE='' PANDOC='yes' PATH_SEPARATOR=':' PTHREAD_CC='gcc' PTHREAD_CFLAGS='-pthread' PTHREAD_LIBS='' RANLIB='ranlib' SET_MAKE='' SHELL='/bin/sh' SQLITE_LIBS='-lsqlite3 -ldl -lm ' STRIP='' VERSION='2.1.5' 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='${AMTAR} xf -' ax_pthread_config='' bindir='${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='${datarootdir}/info' install_sh='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-master/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='/home/psgendb/BIRCHDEV/lib-linux-x86_64/abyss' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## #define PACKAGE_NAME "ABySS" #define PACKAGE_TARNAME "abyss" #define PACKAGE_VERSION "2.1.5" #define PACKAGE_STRING "ABySS 2.1.5" #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" #define PACKAGE "abyss" #define VERSION "2.1.5" #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_DLFCN_H 1 #define HAVE_FCNTL_H 1 #define HAVE_FLOAT_H 1 #define HAVE_LIMITS_H 1 #define HAVE_STDDEF_H 1 #define HAVE_STDINT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_SYS_PARAM_H 1 #define HAVE__BOOL 1 #define HAVE_STDBOOL_H 1 #define STDC_HEADERS 1 #define HAVE_PTRDIFF_T 1 #define HAVE_STD_TR1_HASH 1 #define HAVE_STD_TR1_TUPLE 1 #define BOOST_HAS_TR1_TUPLE 1 #define HAVE_DUP2 1 #define HAVE_GETHOSTNAME 1 #define HAVE_GETOPT_LONG 1 #define HAVE_GETPAGESIZE 1 #define HAVE_MEMSET 1 #define HAVE_STRDUP 1 #define HAVE_STRERROR 1 #define HAVE_STRTOUL 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_STDLIB_H 1 #define HAVE_REALLOC 1 #define HAVE_VPRINTF 1 #define FMBITS 64 #define MAX_KMER 128 #define MAX_HASHES 32 #define MPICH_SKIP_MPICXX 1 #define OMPI_SKIP_MPICXX 1 #define HAVE_LIBM 1 #define HAVE_POW 1 #define HAVE_SQRT 1 #define HAVE_LIBDL 1 #define HAVE_POPCNT 1 #define HAVE_FUNCTIONAL 1 #define HAVE_TR1_FUNCTIONAL 1 #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 #define HAVE_TR1_UNORDERED_MAP 1 #define HAVE_TR1_UNORDERED_SET 1 #define HAVE_BOOST_UNORDERED_SET_HPP 1 #define HAVE_SQLITE3_H 1 #define HAVE_LIBSQLITE3 1 #define _SQL 1 configure: exit 0