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 2.1.0, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --prefix=/apps/gentoo/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/apps/gentoo/usr/share/man --infodir=/apps/gentoo/usr/share/info --datadir=/apps/gentoo/usr/share --sysconfdir=/apps/gentoo/etc --localstatedir=/apps/gentoo/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/apps/gentoo/usr/share/doc/abyss-2.1.0 --htmldir=/apps/gentoo/usr/share/doc/abyss-2.1.0/html --libdir=/apps/gentoo/usr/lib64 --enable-openmp --disable-mpich --with-sqlite --with-mpi --with-boost --with-sparsehash --enable-maxk=192 ## --------- ## ## Platform. ## ## --------- ## hostname = login1 uname -m = x86_64 uname -r = 2.6.32-696.20.1.el6.x86_64 uname -s = Linux uname -v = #1 SMP Fri Jan 26 17:51:45 UTC 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: /apps/gentoo/usr/lib/portage/python2.7/ebuild-helpers/unprivileged PATH: /apps/gentoo/usr/lib/portage/python2.7/ebuild-helpers PATH: /apps/gentoo/usr/local/sbin PATH: /apps/gentoo/usr/local/bin PATH: /apps/gentoo/usr/sbin PATH: /apps/gentoo/usr/bin PATH: /apps/gentoo/sbin PATH: /apps/gentoo/bin PATH: /usr/local/sbin PATH: /usr/local/bin PATH: /usr/sbin PATH: /usr/bin PATH: /sbin PATH: /bin PATH: /apps/gentoo/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0 PATH: /apps/gentoo/usr/lib/llvm/6/bin PATH: /apps/gentoo/usr/lib/llvm/5/bin PATH: /apps/gentoo/usr/lib/llvm/4/bin PATH: /apps/gentoo/usr/local/sbin PATH: /apps/gentoo/usr/local/bin PATH: /apps/gentoo/usr/sbin PATH: /apps/gentoo/usr/bin PATH: /apps/gentoo/sbin PATH: /apps/gentoo/bin PATH: /apps/gentoo/opt/bin PATH: /usr/sbin PATH: /sbin PATH: /usr/bin PATH: /bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2873: checking for a BSD-compatible install configure:2941: result: /apps/gentoo/usr/bin/install -c configure:2952: checking whether build environment is sane configure:3007: result: yes configure:3158: checking for a thread-safe mkdir -p configure:3197: result: /apps/gentoo/bin/mkdir -p configure:3204: checking for gawk configure:3220: found /apps/gentoo/usr/bin/gawk configure:3231: result: gawk configure:3242: checking whether make sets $(MAKE) configure:3264: result: yes configure:3293: checking whether make supports nested variables configure:3310: result: yes configure:3445: checking for gawk configure:3472: result: gawk configure:3491: checking for x86_64-pc-linux-gnu-gcc configure:3507: found /apps/gentoo/usr/bin/x86_64-pc-linux-gnu-gcc configure:3518: result: x86_64-pc-linux-gnu-gcc configure:3787: checking for C compiler version configure:3796: x86_64-pc-linux-gnu-gcc --version >&5 x86_64-pc-linux-gnu-gcc (Gentoo 5.4.0-r4 p1.8, pie-0.6.5) 5.4.0 Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:3807: $? = 0 configure:3796: x86_64-pc-linux-gnu-gcc -v >&5 Using built-in specs. COLLECT_GCC=/apps/gentoo/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0/x86_64-pc-linux-gnu-gcc COLLECT_LTO_WRAPPER=/apps/gentoo/usr/libexec/gcc/x86_64-pc-linux-gnu/5.4.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /apps/gentoo/var/tmp/portage/sys-devel/gcc-5.4.0-r4/work/gcc-5.4.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/apps/gentoo/usr --bindir=/apps/gentoo/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0 --includedir=/apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include --datadir=/apps/gentoo/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0 --mandir=/apps/gentoo/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/man --infodir=/apps/gentoo/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/info --with-gxx-include-dir=/apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/python --enable-languages=c,c++,objc,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 5.4.0-r4 p1.8, pie-0.6.5' --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --disable-multilib --with-multilib-list=m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --disable-libmpx --enable-vtable-verify --enable-libvtv --enable-lto --without-isl --enable-libsanitizer --with-sysroot=/apps/gentoo Thread model: posix gcc version 5.4.0 (Gentoo 5.4.0-r4 p1.8, pie-0.6.5) configure:3807: $? = 0 configure:3796: x86_64-pc-linux-gnu-gcc -V >&5 x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-V' x86_64-pc-linux-gnu-gcc: fatal error: no input files compilation terminated. configure:3807: $? = 1 configure:3796: x86_64-pc-linux-gnu-gcc -qversion >&5 x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-qversion' x86_64-pc-linux-gnu-gcc: fatal error: no input files compilation terminated. configure:3807: $? = 1 configure:3827: checking whether the C compiler works configure:3849: x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:3853: $? = 0 configure:3901: result: yes configure:3904: checking for C compiler default output file name configure:3906: result: a.out configure:3912: checking for suffix of executables configure:3919: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:3923: $? = 0 configure:3945: result: configure:3967: checking whether we are cross compiling configure:3975: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:3979: $? = 0 configure:3986: ./conftest configure:3990: $? = 0 configure:4005: result: no configure:4010: checking for suffix of object files configure:4032: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:4036: $? = 0 configure:4057: result: o configure:4061: checking whether we are using the GNU C compiler configure:4080: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:4080: $? = 0 configure:4089: result: yes configure:4098: checking whether x86_64-pc-linux-gnu-gcc accepts -g configure:4118: x86_64-pc-linux-gnu-gcc -c -g conftest.c >&5 configure:4118: $? = 0 configure:4159: result: yes configure:4176: checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89 configure:4239: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:4239: $? = 0 configure:4252: result: none needed configure:4277: checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together configure:4299: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o configure:4302: $? = 0 configure:4299: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o configure:4302: $? = 0 configure:4314: result: yes configure:4334: checking whether make supports the include directive configure:4349: make -f confmf.GNU && cat confinc.out this is the am__doit target configure:4352: $? = 0 configure:4371: result: yes (GNU style) configure:4396: checking dependency style of x86_64-pc-linux-gnu-gcc configure:4507: result: none configure:4527: checking how to run the C preprocessor configure:4558: x86_64-pc-linux-gnu-gcc -E conftest.c configure:4558: $? = 0 configure:4572: x86_64-pc-linux-gnu-gcc -E conftest.c conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory compilation terminated. configure:4572: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | /* end confdefs.h. */ | #include configure:4597: result: x86_64-pc-linux-gnu-gcc -E configure:4617: x86_64-pc-linux-gnu-gcc -E conftest.c configure:4617: $? = 0 configure:4631: x86_64-pc-linux-gnu-gcc -E conftest.c conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory compilation terminated. configure:4631: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | /* end confdefs.h. */ | #include configure:4673: checking for x86_64-pc-linux-gnu-g++ configure:4689: found /apps/gentoo/usr/bin/x86_64-pc-linux-gnu-g++ configure:4700: result: x86_64-pc-linux-gnu-g++ configure:4771: checking for C++ compiler version configure:4780: x86_64-pc-linux-gnu-g++ --version >&5 x86_64-pc-linux-gnu-g++ (Gentoo 5.4.0-r4 p1.8, pie-0.6.5) 5.4.0 Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:4791: $? = 0 configure:4780: x86_64-pc-linux-gnu-g++ -v >&5 Using built-in specs. COLLECT_GCC=/apps/gentoo/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0/x86_64-pc-linux-gnu-g++ COLLECT_LTO_WRAPPER=/apps/gentoo/usr/libexec/gcc/x86_64-pc-linux-gnu/5.4.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /apps/gentoo/var/tmp/portage/sys-devel/gcc-5.4.0-r4/work/gcc-5.4.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/apps/gentoo/usr --bindir=/apps/gentoo/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0 --includedir=/apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include --datadir=/apps/gentoo/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0 --mandir=/apps/gentoo/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/man --infodir=/apps/gentoo/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/info --with-gxx-include-dir=/apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/python --enable-languages=c,c++,objc,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 5.4.0-r4 p1.8, pie-0.6.5' --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --disable-multilib --with-multilib-list=m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --disable-libmpx --enable-vtable-verify --enable-libvtv --enable-lto --without-isl --enable-libsanitizer --with-sysroot=/apps/gentoo Thread model: posix gcc version 5.4.0 (Gentoo 5.4.0-r4 p1.8, pie-0.6.5) configure:4791: $? = 0 configure:4780: x86_64-pc-linux-gnu-g++ -V >&5 x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-V' x86_64-pc-linux-gnu-g++: fatal error: no input files compilation terminated. configure:4791: $? = 1 configure:4780: x86_64-pc-linux-gnu-g++ -qversion >&5 x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-qversion' x86_64-pc-linux-gnu-g++: fatal error: no input files compilation terminated. configure:4791: $? = 1 configure:4795: checking whether we are using the GNU C++ compiler configure:4814: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.cpp >&5 configure:4814: $? = 0 configure:4823: result: yes configure:4832: checking whether x86_64-pc-linux-gnu-g++ accepts -g configure:4852: x86_64-pc-linux-gnu-g++ -c -g conftest.cpp >&5 configure:4852: $? = 0 configure:4893: result: yes configure:4918: checking dependency style of x86_64-pc-linux-gnu-g++ configure:5029: result: none configure:5048: checking for x86_64-pc-linux-gnu-ranlib configure:5064: found /apps/gentoo/usr/bin/x86_64-pc-linux-gnu-ranlib configure:5075: result: x86_64-pc-linux-gnu-ranlib configure:5140: checking for x86_64-pc-linux-gnu-ghc configure:5170: result: no configure:5180: checking for ghc configure:5210: result: no configure:5239: checking for pandoc configure:5269: result: no configure:5286: checking for grep that handles long lines and -e configure:5344: result: /apps/gentoo/bin/grep configure:5349: checking for egrep configure:5411: result: /apps/gentoo/bin/grep -E configure:5416: checking for ANSI C header files configure:5436: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5436: $? = 0 configure:5509: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:5509: $? = 0 configure:5509: ./conftest configure:5509: $? = 0 configure:5520: result: yes configure:5533: checking for sys/types.h configure:5533: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5533: $? = 0 configure:5533: result: yes configure:5533: checking for sys/stat.h configure:5533: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5533: $? = 0 configure:5533: result: yes configure:5533: checking for stdlib.h configure:5533: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5533: $? = 0 configure:5533: result: yes configure:5533: checking for string.h configure:5533: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5533: $? = 0 configure:5533: result: yes configure:5533: checking for memory.h configure:5533: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5533: $? = 0 configure:5533: result: yes configure:5533: checking for strings.h configure:5533: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5533: $? = 0 configure:5533: result: yes configure:5533: checking for inttypes.h configure:5533: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5533: $? = 0 configure:5533: result: yes configure:5533: checking for stdint.h configure:5533: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5533: $? = 0 configure:5533: result: yes configure:5533: checking for unistd.h configure:5533: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5533: $? = 0 configure:5533: result: yes configure:5549: checking dlfcn.h usability configure:5549: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking dlfcn.h presence configure:5549: x86_64-pc-linux-gnu-gcc -E conftest.c configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking for dlfcn.h configure:5549: result: yes configure:5549: checking fcntl.h usability configure:5549: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking fcntl.h presence configure:5549: x86_64-pc-linux-gnu-gcc -E conftest.c configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking for fcntl.h configure:5549: result: yes configure:5549: checking float.h usability configure:5549: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking float.h presence configure:5549: x86_64-pc-linux-gnu-gcc -E conftest.c configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking for float.h configure:5549: result: yes configure:5549: checking limits.h usability configure:5549: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking limits.h presence configure:5549: x86_64-pc-linux-gnu-gcc -E conftest.c configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking for limits.h configure:5549: result: yes configure:5549: checking stddef.h usability configure:5549: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking stddef.h presence configure:5549: x86_64-pc-linux-gnu-gcc -E conftest.c configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking for stddef.h configure:5549: result: yes configure:5549: checking for stdint.h configure:5549: result: yes configure:5549: checking for stdlib.h configure:5549: result: yes configure:5549: checking sys/param.h usability configure:5549: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking sys/param.h presence configure:5549: x86_64-pc-linux-gnu-gcc -E conftest.c configure:5549: $? = 0 configure:5549: result: yes configure:5549: checking for sys/param.h configure:5549: result: yes configure:5559: checking for stdbool.h that conforms to C99 configure:5626: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5626: $? = 0 configure:5633: result: yes configure:5635: checking for _Bool configure:5635: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5635: $? = 0 configure:5635: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c: In function 'main': conftest.c:65:20: error: expected expression before ')' token if (sizeof ((_Bool))) ^ configure:5635: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:5635: result: yes configure:5652: checking for ANSI C header files configure:5756: result: yes configure:5766: checking whether byte ordering is bigendian configure:5781: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c:33:9: error: unknown type name 'not' not a universal capable compiler ^ conftest.c:33:15: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'universal' not a universal capable compiler ^ conftest.c:33:15: error: unknown type name 'universal' configure:5781: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:5826: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:5826: $? = 0 configure:5844: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c: In function 'main': conftest.c:39:4: error: unknown type name 'not' not big endian ^ conftest.c:39:12: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'endian' not big endian ^ configure:5844: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:5972: result: no configure:5990: checking for an ANSI C-conforming const configure:6056: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6056: $? = 0 configure:6063: result: yes configure:6071: checking for inline configure:6087: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6087: $? = 0 configure:6095: result: inline configure:6113: checking for ptrdiff_t configure:6113: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6113: $? = 0 configure:6113: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c: In function 'main': conftest.c:68:24: error: expected expression before ')' token if (sizeof ((ptrdiff_t))) ^ configure:6113: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6113: result: yes configure:6123: checking for mode_t configure:6123: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6123: $? = 0 configure:6123: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c: In function 'main': conftest.c:69:21: error: expected expression before ')' token if (sizeof ((mode_t))) ^ configure:6123: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6123: result: yes configure:6134: checking for pid_t configure:6134: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6134: $? = 0 configure:6134: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c: In function 'main': conftest.c:69:20: error: expected expression before ')' token if (sizeof ((pid_t))) ^ configure:6134: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6134: result: yes configure:6145: checking for size_t configure:6145: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6145: $? = 0 configure:6145: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c: In function 'main': conftest.c:69:21: error: expected expression before ')' token if (sizeof ((size_t))) ^ configure:6145: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6145: result: yes configure:6156: checking for ssize_t configure:6156: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6156: $? = 0 configure:6156: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c: In function 'main': conftest.c:69:22: error: expected expression before ')' token if (sizeof ((ssize_t))) ^ configure:6156: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6156: result: yes configure:6167: checking for int64_t configure:6167: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6167: $? = 0 configure:6167: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c: In function 'main': conftest.c:71:53: warning: integer overflow in expression [-Woverflow] < (int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 2))]; ^ conftest.c:70:12: error: storage size of 'test_array' isn't constant static int test_array [1 - 2 * !((int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 1) ^ configure:6167: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 | enum { N = 64 / 2 - 1 }; | int | main () | { | static int test_array [1 - 2 * !((int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 1) | < (int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 2))]; | test_array [0] = 0; | return test_array [0]; | | ; | return 0; | } configure:6167: result: yes configure:6178: checking for uint8_t configure:6178: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6178: $? = 0 configure:6178: result: yes configure:6192: checking for uint16_t configure:6192: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6192: $? = 0 configure:6192: result: yes configure:6204: checking for uint32_t configure:6204: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6204: $? = 0 configure:6204: result: yes configure:6218: checking for uint64_t configure:6218: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6218: $? = 0 configure:6218: result: yes configure:6242: checking for std::hash configure:6242: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:43:13: error: 'hash' is not a member of 'std' if (sizeof (std::hash)) ^ conftest.cpp:43:23: error: expected primary-expression before 'int' if (sizeof (std::hash)) ^ conftest.cpp:43:23: error: expected ')' before 'int' conftest.cpp:44:11: error: expected ')' before ';' token return 0; ^ configure:6242: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6242: result: no configure:6256: checking for std::tr1::hash configure:6256: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.cpp >&5 configure:6256: $? = 0 configure:6256: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:38:33: error: expected primary-expression before ')' token if (sizeof ((std::tr1::hash))) ^ configure:6256: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6256: result: yes configure:6265: checking for std::tr1::tuple configure:6265: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.cpp >&5 configure:6265: $? = 0 configure:6265: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:39:34: error: expected primary-expression before ')' token if (sizeof ((std::tr1::tuple))) ^ configure:6265: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6265: result: yes configure:6301: checking for dup2 configure:6301: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6301: $? = 0 configure:6301: result: yes configure:6301: checking for gethostname configure:6301: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6301: $? = 0 configure:6301: result: yes configure:6301: checking for getopt_long configure:6301: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6301: $? = 0 configure:6301: result: yes configure:6301: checking for getpagesize configure:6301: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6301: $? = 0 configure:6301: result: yes configure:6301: checking for memset configure:6301: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 conftest.c:63:6: warning: conflicting types for built-in function 'memset' char memset (); ^ configure:6301: $? = 0 configure:6301: result: yes configure:6301: checking for strdup configure:6301: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 conftest.c:64:6: warning: conflicting types for built-in function 'strdup' char strdup (); ^ configure:6301: $? = 0 configure:6301: result: yes configure:6301: checking for strerror configure:6301: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6301: $? = 0 configure:6301: result: yes configure:6301: checking for strtoul configure:6301: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6301: $? = 0 configure:6301: result: yes configure:6312: checking vfork.h usability configure:6312: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 conftest.c:77:19: fatal error: vfork.h: No such file or directory compilation terminated. configure:6312: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6312: result: no configure:6312: checking vfork.h presence configure:6312: x86_64-pc-linux-gnu-gcc -E conftest.c conftest.c:44:19: fatal error: vfork.h: No such file or directory compilation terminated. configure:6312: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6312: result: no configure:6312: checking for vfork.h configure:6312: result: no configure:6325: checking for fork configure:6325: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 conftest.c:67:6: warning: conflicting types for built-in function 'fork' char fork (); ^ configure:6325: $? = 0 configure:6325: result: yes configure:6325: checking for vfork configure:6325: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6325: $? = 0 configure:6325: result: yes configure:6335: checking for working fork configure:6357: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6357: $? = 0 configure:6357: ./conftest configure:6357: $? = 0 configure:6367: result: yes configure:6388: checking for working vfork configure:6498: result: yes configure:6525: checking for stdlib.h configure:6525: result: yes configure:6535: checking for GNU libc compatible malloc configure:6559: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6559: $? = 0 configure:6559: ./conftest configure:6559: $? = 0 configure:6569: result: yes configure:6590: checking for working memcmp configure:6633: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6633: $? = 0 configure:6633: ./conftest configure:6633: $? = 0 configure:6643: result: yes configure:6654: checking for stdlib.h configure:6654: result: yes configure:6664: checking for GNU libc compatible realloc configure:6688: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 configure:6688: $? = 0 configure:6688: ./conftest configure:6688: $? = 0 configure:6698: result: yes configure:6728: checking for vprintf configure:6728: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 conftest.c:75:6: warning: conflicting types for built-in function 'vprintf' char vprintf (); ^ configure:6728: $? = 0 configure:6728: result: yes configure:6734: checking for _doprnt configure:6734: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wl,--as-needed conftest.c >&5 /apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/temp/ccIYmm72.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_doprnt' collect2: error: ld returned 1 exit status configure:6734: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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:6734: result: no configure:6747: checking whether HOST_NAME_MAX is declared configure:6747: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize conftest.c >&5 configure:6747: $? = 0 configure:6747: result: yes configure:6881: checking build system type configure:6895: result: x86_64-pc-linux-gnu configure:6915: checking host system type configure:6928: result: x86_64-pc-linux-gnu configure:7060: checking if compiler needs -Werror to reject unknown flags configure:7076: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Werror -Wunknown-warning-option -Wsizeof-array-argument -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.c >&5 x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-Wunknown-warning-option' configure:7076: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | /* end confdefs.h. */ | int foo(void); | int | main () | { | foo() | ; | return 0; | } configure:7081: result: no configure:7147: checking for the pthreads library -lpthreads configure:7185: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -lpthreads >&5 /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lpthreads collect2: error: ld returned 1 exit status configure:7185: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #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:7194: result: no configure:7092: checking whether pthreads work without any flags configure:7185: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c >&5 /apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/temp/ccvCNaix.o: In function `main': conftest.c:(.text.startup+0x29): undefined reference to `pthread_create' conftest.c:(.text.startup+0x35): undefined reference to `pthread_join' conftest.c:(.text.startup+0x59): undefined reference to `__pthread_register_cancel' conftest.c:(.text.startup+0x63): undefined reference to `__pthread_unregister_cancel' collect2: error: ld returned 1 exit status configure:7185: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #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:7194: result: no configure:7097: checking whether pthreads work with -Kthread configure:7185: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Kthread -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c >&5 x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-Kthread' configure:7185: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #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:7194: result: no configure:7097: checking whether pthreads work with -kthread configure:7185: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -kthread -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c >&5 x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-kthread' configure:7185: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #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:7194: result: no configure:7147: checking for the pthreads library -llthread configure:7185: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -llthread >&5 /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -llthread collect2: error: ld returned 1 exit status configure:7185: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #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:7194: result: no configure:7097: checking whether pthreads work with -pthread configure:7185: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -pthread -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c >&5 configure:7185: $? = 0 configure:7194: result: yes configure:7213: checking for joinable pthread attribute configure:7228: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -pthread -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c >&5 configure:7228: $? = 0 configure:7234: result: PTHREAD_CREATE_JOINABLE configure:7244: checking if more special flags are required for pthreads configure:7259: result: no configure:7265: checking for PTHREAD_PRIO_INHERIT configure:7282: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -pthread -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c >&5 configure:7282: $? = 0 configure:7291: result: yes configure:7407: checking mpi.h usability configure:7407: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.c >&5 configure:7407: $? = 0 configure:7407: result: yes configure:7407: checking mpi.h presence configure:7407: x86_64-pc-linux-gnu-gcc -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.c configure:7407: $? = 0 configure:7407: result: yes configure:7407: checking for mpi.h configure:7407: result: yes configure:7418: checking for pthread_create in -lpthread configure:7443: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -lpthread >&5 configure:7443: $? = 0 configure:7452: result: yes configure:7463: checking for MPL_env2int in -lmpl configure:7488: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -lmpl -lpthread >&5 /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lmpl collect2: error: ld returned 1 exit status configure:7488: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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 MPL_env2int (); | int | main () | { | return MPL_env2int (); | ; | return 0; | } configure:7497: result: no configure:7508: checking for MPI_Init in -lmpich configure:7533: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -lmpich -lpthread >&5 /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lmpich collect2: error: ld returned 1 exit status configure:7533: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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:7542: result: no configure:7846: checking for sqrt in -lm configure:7871: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -lm >&5 conftest.c:68:6: warning: conflicting types for built-in function 'sqrt' char sqrt (); ^ configure:7871: $? = 0 configure:7880: result: yes configure:7894: checking for pow configure:7894: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -lm >&5 conftest.c:85:6: warning: conflicting types for built-in function 'pow' char pow (); ^ configure:7894: $? = 0 configure:7894: result: yes configure:7894: checking for sqrt configure:7894: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -lm >&5 conftest.c:86:6: warning: conflicting types for built-in function 'sqrt' char sqrt (); ^ configure:7894: $? = 0 configure:7894: result: yes configure:7903: checking for ceilf configure:7903: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -lm >&5 conftest.c:87:6: warning: conflicting types for built-in function 'ceilf' char ceilf (); ^ configure:7903: $? = 0 configure:7903: result: yes configure:7914: checking for dlsym in -ldl configure:7939: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.c -ldl -lm >&5 configure:7939: $? = 0 configure:7948: result: yes configure:7973: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.c >&5 conftest.c:65:20: warning: extra tokens at end of #include directive #include , ^ configure:7973: $? = 0 configure:7996: checking how to run the C++ preprocessor configure:8023: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8023: $? = 0 configure:8037: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp conftest.cpp:66:28: fatal error: ac_nonexistent.h: No such file or directory compilation terminated. configure:8037: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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:8062: result: x86_64-pc-linux-gnu-g++ -E configure:8082: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8082: $? = 0 configure:8096: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp conftest.cpp:66:28: fatal error: ac_nonexistent.h: No such file or directory compilation terminated. configure:8096: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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:8137: checking functional usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking functional presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking for functional configure:8137: result: yes configure:8137: checking tr1/functional usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking tr1/functional presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking for tr1/functional configure:8137: result: yes configure:8137: checking boost/functional/hash.hpp usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking boost/functional/hash.hpp presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking for boost/functional/hash.hpp configure:8137: result: yes configure:8137: checking boost/property_map/property_map.hpp usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking boost/property_map/property_map.hpp presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking for boost/property_map/property_map.hpp configure:8137: result: yes configure:8137: checking google/sparse_hash_map usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 In file included from /apps/gentoo/usr/include/sparsehash/sparsetable:227:0, from /apps/gentoo/usr/include/sparsehash/internal/sparsehashtable.h:106, from /apps/gentoo/usr/include/sparsehash/sparse_hash_map:93, from /apps/gentoo/usr/include/google/sparse_hash_map:34, from conftest.cpp:103: /apps/gentoo/usr/include/sparsehash/sparse_hash_map:98:27: error: 'hash' in namespace 'std' does not name a template type class HashFcn = SPARSEHASH_HASH, // defined in sparseconfig.h ^ In file included from /apps/gentoo/usr/include/google/sparse_hash_map:34:0, from conftest.cpp:103: /apps/gentoo/usr/include/sparsehash/sparse_hash_map:98:42: error: expected '>' before '<' token class HashFcn = SPARSEHASH_HASH, // defined in sparseconfig.h ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:128:36: error: 'EqualKey' was not declared in this scope SetKey, EqualKey, Alloc> ht; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:128:46: error: 'Alloc' was not declared in this scope SetKey, EqualKey, Alloc> ht; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:128:51: error: template argument 6 is invalid SetKey, EqualKey, Alloc> ht; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:128:51: error: template argument 7 is invalid /apps/gentoo/usr/include/sparsehash/sparse_hash_map:132:20: error: 'ht' is not a class or namespace typedef typename ht::key_type key_type; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:135:20: error: 'ht' is not a class or namespace typedef typename ht::value_type value_type; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:136:20: error: 'ht' is not a class or namespace typedef typename ht::hasher hasher; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:137:20: error: 'ht' is not a class or namespace typedef typename ht::key_equal key_equal; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:138:11: error: 'Alloc' does not name a type typedef Alloc allocator_type; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:140:20: error: 'ht' is not a class or namespace typedef typename ht::size_type size_type; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:141:20: error: 'ht' is not a class or namespace typedef typename ht::difference_type difference_type; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:142:20: error: 'ht' is not a class or namespace typedef typename ht::pointer pointer; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:143:20: error: 'ht' is not a class or namespace typedef typename ht::const_pointer const_pointer; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:144:20: error: 'ht' is not a class or namespace typedef typename ht::reference reference; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:145:20: error: 'ht' is not a class or namespace typedef typename ht::const_reference const_reference; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:147:20: error: 'ht' is not a class or namespace typedef typename ht::iterator iterator; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:148:20: error: 'ht' is not a class or namespace typedef typename ht::const_iterator const_iterator; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:149:20: error: 'ht' is not a class or namespace typedef typename ht::local_iterator local_iterator; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:150:20: error: 'ht' is not a class or namespace typedef typename ht::const_local_iterator const_local_iterator; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:165:3: error: 'allocator_type' does not name a type allocator_type get_allocator() const { return rep.get_allocator(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:175:34: error: 'allocator_type' does not name a type const allocator_type& alloc = allocator_type()) ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:184:25: error: 'allocator_type' does not name a type const allocator_type& alloc = allocator_type()) ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:305:20: error: 'ht' is not a class or namespace typedef typename ht::NopointerSerializer NopointerSerializer; ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:175:73: error: there are no arguments to 'allocator_type' that depend on a template parameter, so a declaration of 'allocator_type' must be available [-fpermissive] const allocator_type& alloc = allocator_type()) ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:175:73: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated) /apps/gentoo/usr/include/sparsehash/sparse_hash_map:184:64: error: there are no arguments to 'allocator_type' that depend on a template parameter, so a declaration of 'allocator_type' must be available [-fpermissive] const allocator_type& alloc = allocator_type()) ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::iterator google::sparse_hash_map::begin()': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:153:63: error: request for member 'begin' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' iterator begin() { return rep.begin(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::iterator google::sparse_hash_map::end()': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:154:63: error: request for member 'end' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' iterator end() { return rep.end(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::const_iterator google::sparse_hash_map::begin() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:155:63: error: request for member 'begin' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' const_iterator begin() const { return rep.begin(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::const_iterator google::sparse_hash_map::end() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:156:63: error: request for member 'end' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' const_iterator end() const { return rep.end(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::local_iterator google::sparse_hash_map::begin(google::sparse_hash_map::size_type)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:159:63: error: request for member 'begin' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' local_iterator begin(size_type i) { return rep.begin(i); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::local_iterator google::sparse_hash_map::end(google::sparse_hash_map::size_type)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:160:63: error: request for member 'end' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' local_iterator end(size_type i) { return rep.end(i); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::const_local_iterator google::sparse_hash_map::begin(google::sparse_hash_map::size_type) const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:161:63: error: request for member 'begin' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' const_local_iterator begin(size_type i) const { return rep.begin(i); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::const_local_iterator google::sparse_hash_map::end(google::sparse_hash_map::size_type) const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:162:63: error: request for member 'end' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' const_local_iterator end(size_type i) const { return rep.end(i); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::hasher google::sparse_hash_map::hash_funct() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:166:63: error: request for member 'hash_funct' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' hasher hash_funct() const { return rep.hash_funct(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::key_equal google::sparse_hash_map::key_eq() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:168:63: error: request for member 'key_eq' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' key_equal key_eq() const { return rep.key_eq(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In constructor 'google::sparse_hash_map::sparse_hash_map(InputIterator, InputIterator, google::sparse_hash_map::size_type, const hasher&, const key_equal&, const int&)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:186:9: error: request for member 'insert' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' rep.insert(f, l); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::clear()': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:192:45: error: request for member 'clear' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' void clear() { rep.clear(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::swap(google::sparse_hash_map&)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:193:45: error: request for member 'swap' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' void swap(sparse_hash_map& hs) { rep.swap(hs.rep); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::size_type google::sparse_hash_map::size() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:197:52: error: request for member 'size' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' size_type size() const { return rep.size(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::size_type google::sparse_hash_map::max_size() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:198:52: error: request for member 'max_size' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' size_type max_size() const { return rep.max_size(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'bool google::sparse_hash_map::empty() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:199:52: error: request for member 'empty' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' bool empty() const { return rep.empty(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::size_type google::sparse_hash_map::bucket_count() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:200:52: error: request for member 'bucket_count' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' size_type bucket_count() const { return rep.bucket_count(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::size_type google::sparse_hash_map::max_bucket_count() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:201:52: error: request for member 'max_bucket_count' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' size_type max_bucket_count() const { return rep.max_bucket_count(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::size_type google::sparse_hash_map::bucket_size(google::sparse_hash_map::size_type) const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:204:60: error: request for member 'bucket_size' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' size_type bucket_size(size_type i) const { return rep.bucket_size(i); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::size_type google::sparse_hash_map::bucket(const key_type&) const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:205:60: error: request for member 'bucket' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' size_type bucket(const key_type& key) const { return rep.bucket(key); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'float google::sparse_hash_map::max_load_factor() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:211:9: error: request for member 'get_resizing_parameters' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' rep.get_resizing_parameters(&shrink, &grow); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::max_load_factor(float)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:216:9: error: request for member 'get_resizing_parameters' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' rep.get_resizing_parameters(&shrink, &grow); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:217:9: error: request for member 'set_resizing_parameters' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' rep.set_resizing_parameters(shrink, new_grow); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'float google::sparse_hash_map::min_load_factor() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:222:9: error: request for member 'get_resizing_parameters' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' rep.get_resizing_parameters(&shrink, &grow); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::min_load_factor(float)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:227:9: error: request for member 'get_resizing_parameters' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' rep.get_resizing_parameters(&shrink, &grow); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:228:9: error: request for member 'set_resizing_parameters' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' rep.set_resizing_parameters(new_shrink, grow); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::set_resizing_parameters(float, float)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:232:9: error: request for member 'set_resizing_parameters' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' rep.set_resizing_parameters(shrink, grow); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::resize(google::sparse_hash_map::size_type)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:235:45: error: request for member 'resize' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' void resize(size_type hint) { rep.resize(hint); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::iterator google::sparse_hash_map::find(const key_type&)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:239:67: error: request for member 'find' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' iterator find(const key_type& key) { return rep.find(key); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::const_iterator google::sparse_hash_map::find(const key_type&) const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:240:67: error: request for member 'find' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' const_iterator find(const key_type& key) const { return rep.find(key); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::size_type google::sparse_hash_map::count(const key_type&) const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:249:67: error: request for member 'count' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' size_type count(const key_type& key) const { return rep.count(key); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'std::pair google::sparse_hash_map::equal_range(const key_type&)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:252:16: error: request for member 'equal_range' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' return rep.equal_range(key); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'std::pair google::sparse_hash_map::equal_range(const key_type&) const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:256:16: error: request for member 'equal_range' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' return rep.equal_range(key); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'std::pair google::sparse_hash_map::insert(const value_type&)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:261:16: error: request for member 'insert' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' return rep.insert(obj); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::insert(InputIterator, InputIterator)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:264:9: error: request for member 'insert' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' rep.insert(f, l); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::insert(google::sparse_hash_map::const_iterator, google::sparse_hash_map::const_iterator)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:267:9: error: request for member 'insert' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' rep.insert(f, l); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::set_deleted_key(const key_type&)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:279:9: error: request for member 'set_deleted_key' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' rep.set_deleted_key(key); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::clear_deleted_key()': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:281:53: error: request for member 'clear_deleted_key' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' void clear_deleted_key() { rep.clear_deleted_key(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::key_type google::sparse_hash_map::deleted_key() const': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:282:60: error: request for member 'deleted_key' in '((const google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'const ht {aka const int}' key_type deleted_key() const { return rep.deleted_key(); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'google::sparse_hash_map::size_type google::sparse_hash_map::erase(const key_type&)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:285:67: error: request for member 'erase' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' size_type erase(const key_type& key) { return rep.erase(key); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::erase(google::sparse_hash_map::iterator)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:286:60: error: request for member 'erase' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' void erase(iterator it) { rep.erase(it); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'void google::sparse_hash_map::erase(google::sparse_hash_map::iterator, google::sparse_hash_map::iterator)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:287:60: error: request for member 'erase' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' void erase(iterator f, iterator l) { rep.erase(f, l); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'bool google::sparse_hash_map::serialize(ValueSerializer, OUTPUT*)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:317:16: error: request for member 'serialize' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' return rep.serialize(serializer, fp); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'bool google::sparse_hash_map::unserialize(ValueSerializer, INPUT*)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:336:16: error: request for member 'unserialize' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' return rep.unserialize(serializer, fp); ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'bool google::sparse_hash_map::write_metadata(OUTPUT*)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:342:54: error: request for member 'write_metadata' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' bool write_metadata(OUTPUT *fp) { return rep.write_metadata(fp); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'bool google::sparse_hash_map::read_metadata(INPUT*)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:345:54: error: request for member 'read_metadata' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' bool read_metadata(INPUT *fp) { return rep.read_metadata(fp); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'bool google::sparse_hash_map::write_nopointer_data(OUTPUT*)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:348:54: error: request for member 'write_nopointer_data' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' bool write_nopointer_data(OUTPUT *fp) { return rep.write_nopointer_data(fp); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In member function 'bool google::sparse_hash_map::read_nopointer_data(INPUT*)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:351:54: error: request for member 'read_nopointer_data' in '((google::sparse_hash_map*)this)->google::sparse_hash_map::rep', which is of non-class type 'google::sparse_hash_map::ht {aka int}' bool read_nopointer_data(INPUT *fp) { return rep.read_nopointer_data(fp); } ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: At global scope: /apps/gentoo/usr/include/sparsehash/sparse_hash_map:356:66: error: wrong number of template arguments (5, should be at least 2) inline void swap(sparse_hash_map& hm1, ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:101:7: note: provided for 'template class google::sparse_hash_map' class sparse_hash_map { ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:357:66: error: wrong number of template arguments (5, should be at least 2) sparse_hash_map& hm2) { ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map:101:7: note: provided for 'template class google::sparse_hash_map' class sparse_hash_map { ^ /apps/gentoo/usr/include/sparsehash/sparse_hash_map: In function 'void google::swap(int&, int&)': /apps/gentoo/usr/include/sparsehash/sparse_hash_map:358:7: error: request for member 'swap' in 'hm1', which is of non-class type 'int' hm1.swap(hm2); ^ configure:8137: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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 | /* 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:8137: result: no configure:8137: checking google/sparse_hash_map presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8137: $? = 0 configure:8137: result: yes configure:8137: WARNING: google/sparse_hash_map: present but cannot be compiled configure:8137: WARNING: google/sparse_hash_map: check for missing prerequisite headers? configure:8137: WARNING: google/sparse_hash_map: see the Autoconf documentation configure:8137: WARNING: google/sparse_hash_map: section "Present But Cannot Be Compiled" configure:8137: WARNING: google/sparse_hash_map: proceeding with the compiler's result configure:8137: checking for google/sparse_hash_map configure:8137: result: no configure:8137: checking unordered_map usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 In file included from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/unordered_map:35:0, from conftest.cpp:103: /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options. #error This file requires compiler and library support \ ^ configure:8137: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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 | /* 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:8137: result: no configure:8137: checking unordered_map presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp In file included from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/unordered_map:35:0, from conftest.cpp:70: /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options. #error This file requires compiler and library support \ ^ configure:8137: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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 | /* end confdefs.h. */ | #include configure:8137: result: no configure:8137: checking for unordered_map configure:8137: result: no configure:8137: checking tr1/unordered_map usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking tr1/unordered_map presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking for tr1/unordered_map configure:8137: result: yes configure:8137: checking unordered_set usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 In file included from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/unordered_set:35:0, from conftest.cpp:104: /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options. #error This file requires compiler and library support \ ^ configure:8137: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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_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:8137: result: no configure:8137: checking unordered_set presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp In file included from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/unordered_set:35:0, from conftest.cpp:71: /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options. #error This file requires compiler and library support \ ^ configure:8137: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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_TR1_UNORDERED_MAP 1 | /* end confdefs.h. */ | #include configure:8137: result: no configure:8137: checking for unordered_set configure:8137: result: no configure:8137: checking tr1/unordered_set usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking tr1/unordered_set presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking for tr1/unordered_set configure:8137: result: yes configure:8137: checking boost/unordered_set.hpp usability configure:8137: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking boost/unordered_set.hpp presence configure:8137: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8137: $? = 0 configure:8137: result: yes configure:8137: checking for boost/unordered_set.hpp configure:8137: result: yes configure:8165: checking sqlite3.h usability configure:8165: x86_64-pc-linux-gnu-g++ -c -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp >&5 configure:8165: $? = 0 configure:8165: result: yes configure:8165: checking sqlite3.h presence configure:8165: x86_64-pc-linux-gnu-g++ -E -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 conftest.cpp configure:8165: $? = 0 configure:8165: result: yes configure:8165: checking for sqlite3.h configure:8165: result: yes configure:8175: checking for main in -lsqlite3 configure:8194: x86_64-pc-linux-gnu-g++ -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.cpp -lsqlite3 -ldl -lm >&5 configure:8194: $? = 0 configure:8203: result: yes configure:8241: checking for x86_64-pc-linux-gnu-g++ option to support OpenMP configure:8256: x86_64-pc-linux-gnu-g++ -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.cpp -ldl -lm >&5 conftest.cpp:78:2: error: 'choke' does not name a type choke me ^ In file included from conftest.cpp:80:0: /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:39:3: error: 'omp_lock_t' does not name a type } omp_lock_t; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:86:28: error: variable or field 'omp_init_lock' declared void extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:86:28: error: 'omp_lock_t' was not declared in this scope /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:86:40: error: expected primary-expression before ')' token extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:87:31: error: variable or field 'omp_destroy_lock' declared void extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:87:31: error: 'omp_lock_t' was not declared in this scope /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:87:43: error: expected primary-expression before ')' token extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:88:27: error: variable or field 'omp_set_lock' declared void extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:88:27: error: 'omp_lock_t' was not declared in this scope /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:88:39: error: expected primary-expression before ')' token extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:89:29: error: variable or field 'omp_unset_lock' declared void extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:89:29: error: 'omp_lock_t' was not declared in this scope /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:89:41: error: expected primary-expression before ')' token extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:90:27: error: 'omp_lock_t' was not declared in this scope extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:90:39: error: expected primary-expression before ')' token extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/omp.h:90:41: error: expected ',' or ';' before 'throw' extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW; ^ configure:8256: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.1.0" | #define PACKAGE_STRING "ABySS 2.1.0" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define PACKAGE "abyss" | #define VERSION "2.1.0" | #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 192 | #define MAX_HASHES 32 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define MPICH_SKIP_MPICXX 1 | #define OMPI_SKIP_MPICXX 1 | #define HAVE_MPI_H 1 | #define HAVE_LIBPTHREAD 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_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 | /* end confdefs.h. */ | | #ifndef _OPENMP | choke me | #endif | #include | int main () { return omp_get_num_threads (); } | configure:8274: x86_64-pc-linux-gnu-g++ -o conftest -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -fopenmp -I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0 -Wl,--as-needed conftest.cpp -ldl -lm >&5 configure:8274: $? = 0 configure:8288: result: -fopenmp configure:8337: error: ABySS should be compiled with Google sparsehash to reduce memory usage. It may be downloaded here: https://code.google.com/p/sparsehash/ If you do not wish to use sparsehash, specify --without-sparsehash. ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-pc-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=set ac_cv_env_CFLAGS_value='-O2 -pipe -O2 -pipe -march=native -ftree-vectorize' ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= 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=set ac_cv_env_CXXFLAGS_value='-O2 -pipe -O2 -pipe -march=native -ftree-vectorize' ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_LDFLAGS_set=set ac_cv_env_LDFLAGS_value=-Wl,--as-needed ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_build_alias_set=set ac_cv_env_build_alias_value=x86_64-pc-linux-gnu ac_cv_env_host_alias_set=set ac_cv_env_host_alias_value=x86_64-pc-linux-gnu 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_getentropy=no 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=no ac_cv_header_inttypes_h=yes ac_cv_header_limits_h=yes ac_cv_header_memory_h=yes ac_cv_header_mpi_h=yes 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-pc-linux-gnu ac_cv_lib_dl_dlsym=yes ac_cv_lib_m_sqrt=yes ac_cv_lib_mpi_MPI_Init=no ac_cv_lib_mpich_MPI_Init=no ac_cv_lib_mpl_MPL_env2int=no ac_cv_lib_pthread_pthread_create=yes ac_cv_lib_sqlite3_main=yes ac_cv_objext=o ac_cv_path_EGREP='/apps/gentoo/bin/grep -E' ac_cv_path_GREP=/apps/gentoo/bin/grep ac_cv_path_install='/apps/gentoo/usr/bin/install -c' ac_cv_path_mkdir=/apps/gentoo/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_CC=x86_64-pc-linux-gnu-gcc ac_cv_prog_CPP='x86_64-pc-linux-gnu-gcc -E' ac_cv_prog_CXX=x86_64-pc-linux-gnu-g++ ac_cv_prog_CXXCPP='x86_64-pc-linux-gnu-g++ -E' ac_cv_prog_RANLIB=x86_64-pc-linux-gnu-ranlib ac_cv_prog_ac_ct_GHC= 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=none am_cv_CXX_dependencies_compiler_type=none am_cv_make_support_nested_variables=yes am_cv_prog_cc_c_o=yes ax_cv_PTHREAD_PRIO_INHERIT=yes ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/missing aclocal-1.16' AMDEPBACKSLASH='' AMDEP_FALSE='' AMDEP_TRUE='#' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_CXXFLAGS='-Wall -Wextra' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='1' AM_V='$(V)' AUTOCONF='${SHELL} /apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/missing autoconf' AUTOHEADER='${SHELL} /apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/missing autoheader' AUTOMAKE='${SHELL} /apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/missing automake-1.16' AWK='gawk' CC='x86_64-pc-linux-gnu-gcc' CCDEPMODE='depmode=none' CFLAGS='-O2 -pipe -O2 -pipe -march=native -ftree-vectorize' CPP='x86_64-pc-linux-gnu-gcc -E' CPPFLAGS='-I/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0 -isystem/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/boost_1_56_0' CXX='x86_64-pc-linux-gnu-g++' CXXCPP='x86_64-pc-linux-gnu-g++ -E' CXXDEPMODE='depmode=none' CXXFLAGS='-O2 -pipe -O2 -pipe -march=native -ftree-vectorize' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/apps/gentoo/bin/grep -E' EXEEXT='' GHC='' GREP='/apps/gentoo/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=' -Wl,--as-needed' LIBOBJS='' LIBS='-ldl -lm ' LTLIBOBJS='' MAKEINFO='${SHELL} /apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/missing makeinfo' MKDIR_P='/apps/gentoo/bin/mkdir -p' MPI_LIBS='-lpthread ' OBJEXT='o' OPENMP_CXXFLAGS='-fopenmp' PACKAGE='abyss' PACKAGE_BUGREPORT='abyss-users@bcgsc.ca' PACKAGE_NAME='ABySS' PACKAGE_STRING='ABySS 2.1.0' PACKAGE_TARNAME='abyss' PACKAGE_URL='http://www.bcgsc.ca/platform/bioinfo/software/abyss' PACKAGE_VERSION='2.1.0' PAIRED_DBG_FALSE='#' PAIRED_DBG_TRUE='' PANDOC='' PATH_SEPARATOR=':' PTHREAD_CC='x86_64-pc-linux-gnu-gcc' PTHREAD_CFLAGS='-pthread' PTHREAD_LIBS='' RANLIB='x86_64-pc-linux-gnu-ranlib' SET_MAKE='' SHELL='/apps/gentoo/bin/bash' SQLITE_LIBS='-lsqlite3 -ldl -lm ' STRIP='' VERSION='2.1.0' ac_ct_CC='' ac_ct_CXX='' 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__nodep='' am__quote='' am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -' ax_pthread_config='' bindir='${exec_prefix}/bin' build='x86_64-pc-linux-gnu' build_alias='x86_64-pc-linux-gnu' build_cpu='x86_64' build_os='linux-gnu' build_vendor='pc' datadir='/apps/gentoo/usr/share' datarootdir='${prefix}/share' docdir='/apps/gentoo/usr/share/doc/abyss-2.1.0' dvidir='${docdir}' exec_prefix='NONE' host='x86_64-pc-linux-gnu' host_alias='x86_64-pc-linux-gnu' host_cpu='x86_64' host_os='linux-gnu' host_vendor='pc' htmldir='/apps/gentoo/usr/share/doc/abyss-2.1.0/html' includedir='${prefix}/include' infodir='/apps/gentoo/usr/share/info' install_sh='${SHELL} /apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.0/work/abyss-2.1.0/install-sh' libdir='/apps/gentoo/usr/lib64' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='/apps/gentoo/var/lib' mandir='/apps/gentoo/usr/share/man' mkdir_p='$(MKDIR_P)' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='/apps/gentoo/usr' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='/apps/gentoo/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "ABySS" #define PACKAGE_TARNAME "abyss" #define PACKAGE_VERSION "2.1.0" #define PACKAGE_STRING "ABySS 2.1.0" #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" #define PACKAGE "abyss" #define VERSION "2.1.0" #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 192 #define MAX_HASHES 32 #define HAVE_PTHREAD_PRIO_INHERIT 1 #define MPICH_SKIP_MPICXX 1 #define OMPI_SKIP_MPICXX 1 #define HAVE_MPI_H 1 #define HAVE_LIBPTHREAD 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_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 1