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 2.3.7, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure ## --------- ## ## Platform. ## ## --------- ## hostname = venus.cc.umanitoba.ca uname -m = x86_64 uname -r = 4.18.0-477.21.1.el8_8.x86_64 uname -s = Linux uname -v = #1 SMP Thu Jul 20 08:38:27 EDT 2023 /usr/bin/uname -p = x86_64 /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /home/psgendb/BIRCHDEV/local/script PATH: /home/psgendb/BIRCHDEV/local/bin-linux-x86_64 PATH: /usr/share/Modules/bin PATH: /usr/local/bin PATH: /usr/bin PATH: /bin PATH: /opt/thinlinc/bin PATH: /usr/bin/X11 PATH: /usr/local/sbin PATH: /usr/sbin PATH: /sbin PATH: /home/psgendb/BIRCHDEV/script PATH: /home/psgendb/BIRCHDEV/bin-linux-x86_64 PATH: /home/psgendb/BIRCHDEV/local/pkg/EMBOSS/linux-x86_64/bin PATH: /home/psgendb/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2962: checking for g++ configure:2978: found /usr/bin/g++ configure:2989: result: g++ configure:3016: checking for C++ compiler version configure:3025: g++ --version >&5 g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-18) Copyright (C) 2018 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:3036: $? = 0 configure:3025: g++ -v >&5 Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-redhat-linux Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 8.5.0 20210514 (Red Hat 8.5.0-18) (GCC) configure:3036: $? = 0 configure:3025: g++ -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:3036: $? = 1 configure:3025: g++ -qversion >&5 g++: error: unrecognized command line option '-qversion'; did you mean '--version'? g++: fatal error: no input files compilation terminated. configure:3036: $? = 1 configure:3056: checking whether the C++ compiler works configure:3078: g++ conftest.cpp >&5 configure:3082: $? = 0 configure:3130: result: yes configure:3133: checking for C++ compiler default output file name configure:3135: result: a.out configure:3141: checking for suffix of executables configure:3148: g++ -o conftest conftest.cpp >&5 configure:3152: $? = 0 configure:3174: result: configure:3196: checking whether we are cross compiling configure:3204: g++ -o conftest conftest.cpp >&5 configure:3208: $? = 0 configure:3215: ./conftest configure:3219: $? = 0 configure:3234: result: no configure:3239: checking for suffix of object files configure:3261: g++ -c conftest.cpp >&5 configure:3265: $? = 0 configure:3286: result: o configure:3290: checking whether we are using the GNU C++ compiler configure:3309: g++ -c conftest.cpp >&5 configure:3309: $? = 0 configure:3318: result: yes configure:3327: checking whether g++ accepts -g configure:3347: g++ -c -g conftest.cpp >&5 configure:3347: $? = 0 configure:3388: result: yes configure:3426: checking whether g++ supports C++11 features with -std=c++11 configure:3722: g++ -std=c++11 -c -g -O2 conftest.cpp >&5 configure:3722: $? = 0 configure:3731: result: yes configure:3816: checking for a BSD-compatible install configure:3884: result: /usr/bin/install -c configure:3895: checking whether build environment is sane configure:3950: result: yes configure:4101: checking for a thread-safe mkdir -p configure:4140: result: /usr/bin/mkdir -p configure:4147: checking for gawk configure:4163: found /usr/bin/gawk configure:4174: result: gawk configure:4185: checking whether make sets $(MAKE) configure:4207: result: yes configure:4237: checking for style of include used by make configure:4265: result: GNU configure:4299: checking whether make supports nested variables configure:4316: result: yes configure:4405: checking whether UID '200530' is supported by ustar format configure:4408: result: yes configure:4415: checking whether GID '202' is supported by ustar format configure:4418: result: yes configure:4426: checking how to create a ustar tar archive configure:4437: tar --version tar (GNU tar) 1.30 Copyright (C) 2017 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later . This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written by John Gilmore and Jay Fenlason. configure:4440: $? = 0 configure:4480: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir" >conftest.tar configure:4483: $? = 0 configure:4487: tar -xf - &5 gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-18) Copyright (C) 2018 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:5015: $? = 0 configure:5004: gcc -v >&5 Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-redhat-linux Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 8.5.0 20210514 (Red Hat 8.5.0-18) (GCC) configure:5015: $? = 0 configure:5004: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:5015: $? = 1 configure:5004: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion'; did you mean '--version'? gcc: fatal error: no input files compilation terminated. configure:5015: $? = 1 configure:5019: checking whether we are using the GNU C compiler configure:5038: gcc -c conftest.c >&5 configure:5038: $? = 0 configure:5047: result: yes configure:5056: checking whether gcc accepts -g configure:5076: gcc -c -g conftest.c >&5 configure:5076: $? = 0 configure:5117: result: yes configure:5134: checking for gcc option to accept ISO C89 configure:5197: gcc -c -g -O2 conftest.c >&5 configure:5197: $? = 0 configure:5210: result: none needed configure:5232: checking dependency style of gcc configure:5343: result: gcc3 configure:5363: checking how to run the C preprocessor configure:5394: gcc -E conftest.c configure:5394: $? = 0 configure:5408: gcc -E conftest.c conftest.c:12:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:5408: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | /* end confdefs.h. */ | #include configure:5433: result: gcc -E configure:5453: gcc -E conftest.c configure:5453: $? = 0 configure:5467: gcc -E conftest.c conftest.c:12:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:5467: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | /* end confdefs.h. */ | #include configure:5607: checking for C++ compiler version configure:5616: g++ -std=c++11 --version >&5 g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-18) Copyright (C) 2018 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:5627: $? = 0 configure:5616: g++ -std=c++11 -v >&5 Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-redhat-linux Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 8.5.0 20210514 (Red Hat 8.5.0-18) (GCC) configure:5627: $? = 0 configure:5616: g++ -std=c++11 -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:5627: $? = 1 configure:5616: g++ -std=c++11 -qversion >&5 g++: error: unrecognized command line option '-qversion'; did you mean '--version'? g++: fatal error: no input files compilation terminated. configure:5627: $? = 1 configure:5631: checking whether we are using the GNU C++ compiler configure:5659: result: yes configure:5668: checking whether g++ -std=c++11 accepts -g configure:5729: result: yes configure:5796: checking for ranlib configure:5812: found /usr/bin/ranlib configure:5823: result: ranlib configure:5888: checking for ghc configure:5918: result: no configure:5947: checking for pandoc configure:5963: found /usr/bin/pandoc configure:5974: result: yes configure:6040: checking for ar configure:6056: found /usr/bin/ar configure:6067: result: ar configure:6093: checking the archiver (ar) interface configure:6103: gcc -c -g -O2 conftest.c >&5 configure:6103: $? = 0 configure:6105: ar cru libconftest.a conftest.o >&5 configure:6108: $? = 0 configure:6131: result: ar configure:6154: checking for grep that handles long lines and -e configure:6212: result: /usr/bin/grep configure:6217: checking for egrep configure:6279: result: /usr/bin/grep -E configure:6284: checking for ANSI C header files configure:6304: gcc -c -g -O2 conftest.c >&5 configure:6304: $? = 0 configure:6377: gcc -o conftest -g -O2 conftest.c >&5 configure:6377: $? = 0 configure:6377: ./conftest configure:6377: $? = 0 configure:6388: result: yes configure:6401: checking for sys/types.h configure:6401: gcc -c -g -O2 conftest.c >&5 configure:6401: $? = 0 configure:6401: result: yes configure:6401: checking for sys/stat.h configure:6401: gcc -c -g -O2 conftest.c >&5 configure:6401: $? = 0 configure:6401: result: yes configure:6401: checking for stdlib.h configure:6401: gcc -c -g -O2 conftest.c >&5 configure:6401: $? = 0 configure:6401: result: yes configure:6401: checking for string.h configure:6401: gcc -c -g -O2 conftest.c >&5 configure:6401: $? = 0 configure:6401: result: yes configure:6401: checking for memory.h configure:6401: gcc -c -g -O2 conftest.c >&5 configure:6401: $? = 0 configure:6401: result: yes configure:6401: checking for strings.h configure:6401: gcc -c -g -O2 conftest.c >&5 configure:6401: $? = 0 configure:6401: result: yes configure:6401: checking for inttypes.h configure:6401: gcc -c -g -O2 conftest.c >&5 configure:6401: $? = 0 configure:6401: result: yes configure:6401: checking for stdint.h configure:6401: gcc -c -g -O2 conftest.c >&5 configure:6401: $? = 0 configure:6401: result: yes configure:6401: checking for unistd.h configure:6401: gcc -c -g -O2 conftest.c >&5 configure:6401: $? = 0 configure:6401: result: yes configure:6417: checking dlfcn.h usability configure:6417: gcc -c -g -O2 conftest.c >&5 configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking dlfcn.h presence configure:6417: gcc -E conftest.c configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking for dlfcn.h configure:6417: result: yes configure:6417: checking fcntl.h usability configure:6417: gcc -c -g -O2 conftest.c >&5 configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking fcntl.h presence configure:6417: gcc -E conftest.c configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking for fcntl.h configure:6417: result: yes configure:6417: checking float.h usability configure:6417: gcc -c -g -O2 conftest.c >&5 configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking float.h presence configure:6417: gcc -E conftest.c configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking for float.h configure:6417: result: yes configure:6417: checking limits.h usability configure:6417: gcc -c -g -O2 conftest.c >&5 configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking limits.h presence configure:6417: gcc -E conftest.c configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking for limits.h configure:6417: result: yes configure:6417: checking stddef.h usability configure:6417: gcc -c -g -O2 conftest.c >&5 configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking stddef.h presence configure:6417: gcc -E conftest.c configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking for stddef.h configure:6417: result: yes configure:6417: checking for stdint.h configure:6417: result: yes configure:6417: checking for stdlib.h configure:6417: result: yes configure:6417: checking sys/param.h usability configure:6417: gcc -c -g -O2 conftest.c >&5 configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking sys/param.h presence configure:6417: gcc -E conftest.c configure:6417: $? = 0 configure:6417: result: yes configure:6417: checking for sys/param.h configure:6417: result: yes configure:6427: checking for stdbool.h that conforms to C99 configure:6494: gcc -c -g -O2 conftest.c >&5 configure:6494: $? = 0 configure:6501: result: yes configure:6503: checking for _Bool configure:6503: gcc -c -g -O2 conftest.c >&5 configure:6503: $? = 0 configure:6503: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:66:20: error: expected expression before ')' token if (sizeof ((_Bool))) ^ configure:6503: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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:6503: result: yes configure:6522: checking whether byte ordering is bigendian configure:6537: gcc -c -g -O2 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:6537: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 | /* end confdefs.h. */ | #ifndef __APPLE_CC__ | not a universal capable compiler | #endif | typedef int dummy; | configure:6582: gcc -c -g -O2 conftest.c >&5 configure:6582: $? = 0 configure:6600: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:39:4: error: unknown type name 'not'; did you mean 'ino_t'? not big endian ^~~ ino_t conftest.c:39:12: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'endian' not big endian ^~~~~~ configure:6600: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 | /* end confdefs.h. */ | #include | #include | | int | main () | { | #if BYTE_ORDER != BIG_ENDIAN | not big endian | #endif | | ; | return 0; | } configure:6728: result: no configure:6746: checking for an ANSI C-conforming const configure:6812: gcc -c -g -O2 conftest.c >&5 configure:6812: $? = 0 configure:6819: result: yes configure:6827: checking for inline configure:6843: gcc -c -g -O2 conftest.c >&5 configure:6843: $? = 0 configure:6851: result: inline configure:6869: checking for ptrdiff_t configure:6869: gcc -c -g -O2 conftest.c >&5 configure:6869: $? = 0 configure:6869: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:68:24: error: expected expression before ')' token if (sizeof ((ptrdiff_t))) ^ configure:6869: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 | /* 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:6869: result: yes configure:6879: checking for mode_t configure:6879: gcc -c -g -O2 conftest.c >&5 configure:6879: $? = 0 configure:6879: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:69:21: error: expected expression before ')' token if (sizeof ((mode_t))) ^ configure:6879: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 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:6879: result: yes configure:6890: checking for pid_t configure:6890: gcc -c -g -O2 conftest.c >&5 configure:6890: $? = 0 configure:6890: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:69:20: error: expected expression before ')' token if (sizeof ((pid_t))) ^ configure:6890: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 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:6890: result: yes configure:6901: checking for size_t configure:6901: gcc -c -g -O2 conftest.c >&5 configure:6901: $? = 0 configure:6901: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:69:21: error: expected expression before ')' token if (sizeof ((size_t))) ^ configure:6901: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 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:6901: result: yes configure:6912: checking for ssize_t configure:6912: gcc -c -g -O2 conftest.c >&5 configure:6912: $? = 0 configure:6912: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:69:22: error: expected expression before ')' token if (sizeof ((ssize_t))) ^ configure:6912: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 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:6912: result: yes configure:6923: checking for int64_t configure:6923: gcc -c -g -O2 conftest.c >&5 configure:6923: $? = 0 configure:6923: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:71:53: warning: integer overflow in expression of type 'long int' results in '-9223372036854775808' [-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:6923: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 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:6923: result: yes configure:6934: checking for uint8_t configure:6934: gcc -c -g -O2 conftest.c >&5 configure:6934: $? = 0 configure:6934: result: yes configure:6948: checking for uint16_t configure:6948: gcc -c -g -O2 conftest.c >&5 configure:6948: $? = 0 configure:6948: result: yes configure:6960: checking for uint32_t configure:6960: gcc -c -g -O2 conftest.c >&5 configure:6960: $? = 0 configure:6960: result: yes configure:6974: checking for uint64_t configure:6974: gcc -c -g -O2 conftest.c >&5 configure:6974: $? = 0 configure:6974: result: yes configure:6997: checking for std::hash configure:6997: g++ -std=c++11 -c -g -O2 conftest.cpp >&5 configure:6997: $? = 0 configure:6997: g++ -std=c++11 -c -g -O2 conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:43:28: error: expected primary-expression before ')' token if (sizeof ((std::hash))) ^ configure:6997: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | /* end confdefs.h. */ | | #ifdef __FUJITSU | #include | #else | #include | #endif | | int | main () | { | if (sizeof ((std::hash))) | return 0; | ; | return 0; | } configure:6997: result: yes configure:7011: checking for std::tr1::hash configure:7011: g++ -std=c++11 -c -g -O2 conftest.cpp >&5 configure:7011: $? = 0 configure:7011: g++ -std=c++11 -c -g -O2 conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:39:33: error: expected primary-expression before ')' token if (sizeof ((std::tr1::hash))) ^ configure:7011: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 1 | /* end confdefs.h. */ | #include | | int | main () | { | if (sizeof ((std::tr1::hash))) | return 0; | ; | return 0; | } configure:7011: result: yes configure:7020: checking for std::tr1::tuple configure:7020: g++ -std=c++11 -c -g -O2 conftest.cpp >&5 configure:7020: $? = 0 configure:7020: g++ -std=c++11 -c -g -O2 conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:40:34: error: expected primary-expression before ')' token if (sizeof ((std::tr1::tuple))) ^ configure:7020: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 1 | #define HAVE_STD_TR1_HASH 1 | /* end confdefs.h. */ | #include | | int | main () | { | if (sizeof ((std::tr1::tuple))) | return 0; | ; | return 0; | } configure:7020: result: yes configure:7056: checking for dup2 configure:7056: gcc -o conftest -g -O2 conftest.c >&5 configure:7056: $? = 0 configure:7056: result: yes configure:7056: checking for gethostname configure:7056: gcc -o conftest -g -O2 conftest.c >&5 configure:7056: $? = 0 configure:7056: result: yes configure:7056: checking for getopt_long configure:7056: gcc -o conftest -g -O2 conftest.c >&5 configure:7056: $? = 0 configure:7056: result: yes configure:7056: checking for getpagesize configure:7056: gcc -o conftest -g -O2 conftest.c >&5 configure:7056: $? = 0 configure:7056: result: yes configure:7056: checking for memset configure:7056: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:64:6: warning: conflicting types for built-in function 'memset' [-Wbuiltin-declaration-mismatch] char memset (); ^~~~~~ configure:7056: $? = 0 configure:7056: result: yes configure:7056: checking for strdup configure:7056: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:65:6: warning: conflicting types for built-in function 'strdup' [-Wbuiltin-declaration-mismatch] char strdup (); ^~~~~~ configure:7056: $? = 0 configure:7056: result: yes configure:7056: checking for strerror configure:7056: gcc -o conftest -g -O2 conftest.c >&5 configure:7056: $? = 0 configure:7056: result: yes configure:7056: checking for strtoul configure:7056: gcc -o conftest -g -O2 conftest.c >&5 configure:7056: $? = 0 configure:7056: result: yes configure:7067: checking vfork.h usability configure:7067: gcc -c -g -O2 conftest.c >&5 conftest.c:78:10: fatal error: vfork.h: No such file or directory #include ^~~~~~~~~ compilation terminated. configure:7067: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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:7067: result: no configure:7067: checking vfork.h presence configure:7067: gcc -E conftest.c conftest.c:45:10: fatal error: vfork.h: No such file or directory #include ^~~~~~~~~ compilation terminated. configure:7067: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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:7067: result: no configure:7067: checking for vfork.h configure:7067: result: no configure:7080: checking for fork configure:7080: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:68:6: warning: conflicting types for built-in function 'fork' [-Wbuiltin-declaration-mismatch] char fork (); ^~~~ configure:7080: $? = 0 configure:7080: result: yes configure:7080: checking for vfork configure:7080: gcc -o conftest -g -O2 conftest.c >&5 configure:7080: $? = 0 configure:7080: result: yes configure:7090: checking for working fork configure:7112: gcc -o conftest -g -O2 conftest.c >&5 configure:7112: $? = 0 configure:7112: ./conftest configure:7112: $? = 0 configure:7122: result: yes configure:7143: checking for working vfork configure:7253: result: yes configure:7280: checking for stdlib.h configure:7280: result: yes configure:7290: checking for GNU libc compatible malloc configure:7314: gcc -o conftest -g -O2 conftest.c >&5 configure:7314: $? = 0 configure:7314: ./conftest configure:7314: $? = 0 configure:7324: result: yes configure:7345: checking for working memcmp configure:7388: gcc -o conftest -g -O2 conftest.c >&5 configure:7388: $? = 0 configure:7388: ./conftest configure:7388: $? = 0 configure:7398: result: yes configure:7409: checking for stdlib.h configure:7409: result: yes configure:7419: checking for GNU libc compatible realloc configure:7443: gcc -o conftest -g -O2 conftest.c >&5 configure:7443: $? = 0 configure:7443: ./conftest configure:7443: $? = 0 configure:7453: result: yes configure:7476: checking for vprintf configure:7476: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:76:6: warning: conflicting types for built-in function 'vprintf' [-Wbuiltin-declaration-mismatch] char vprintf (); ^~~~~~~ configure:7476: $? = 0 configure:7476: result: yes configure:7482: checking for _doprnt configure:7482: gcc -o conftest -g -O2 conftest.c >&5 /tmp/ccXkJ8Sf.o: In function `main': /home/psgendb/BIRCHDEV/install/abyss-2.3.7/conftest.c:88: undefined reference to `_doprnt' collect2: error: ld returned 1 exit status configure:7482: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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:7482: result: no configure:7495: checking whether HOST_NAME_MAX is declared configure:7495: gcc -c -g -O2 conftest.c >&5 configure:7495: $? = 0 configure:7495: result: yes configure:7641: checking build system type configure:7655: result: x86_64-unknown-linux-gnu configure:7675: checking host system type configure:7688: result: x86_64-unknown-linux-gnu configure:7820: checking if compiler needs -Werror to reject unknown flags configure:7836: gcc -c -g -O2 -Werror -Wunknown-warning-option -Wsizeof-array-argument -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c >&5 gcc: error: unrecognized command line option '-Wunknown-warning-option' configure:7836: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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:7841: result: no configure:7907: checking for the pthreads library -lpthreads configure:7945: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c -lpthreads >&5 /usr/bin/ld: cannot find -lpthreads collect2: error: ld returned 1 exit status configure:7945: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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:7954: result: no configure:7852: checking whether pthreads work without any flags configure:7945: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c >&5 /tmp/ccOilnu7.o: In function `main': /home/psgendb/BIRCHDEV/install/abyss-2.3.7/conftest.c:64: undefined reference to `pthread_create' /home/psgendb/BIRCHDEV/install/abyss-2.3.7/conftest.c:65: undefined reference to `pthread_join' /home/psgendb/BIRCHDEV/install/abyss-2.3.7/conftest.c:67: undefined reference to `__pthread_register_cancel' /home/psgendb/BIRCHDEV/install/abyss-2.3.7/conftest.c:68: undefined reference to `__pthread_unregister_cancel' collect2: error: ld returned 1 exit status configure:7945: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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:7954: result: no configure:7857: checking whether pthreads work with -Kthread configure:7945: gcc -o conftest -g -O2 -Kthread -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c >&5 gcc: error: unrecognized command line option '-Kthread'; did you mean '-pthread'? configure:7945: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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:7954: result: no configure:7857: checking whether pthreads work with -kthread configure:7945: gcc -o conftest -g -O2 -kthread -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c >&5 gcc: error: unrecognized command line option '-kthread'; did you mean '-pthread'? configure:7945: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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:7954: result: no configure:7907: checking for the pthreads library -llthread configure:7945: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c -llthread >&5 /usr/bin/ld: cannot find -llthread collect2: error: ld returned 1 exit status configure:7945: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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:7954: result: no configure:7857: checking whether pthreads work with -pthread configure:7945: gcc -o conftest -g -O2 -pthread -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c >&5 configure:7945: $? = 0 configure:7954: result: yes configure:7973: checking for joinable pthread attribute configure:7988: gcc -o conftest -g -O2 -pthread -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c >&5 configure:7988: $? = 0 configure:7994: result: PTHREAD_CREATE_JOINABLE configure:8004: checking if more special flags are required for pthreads configure:8019: result: no configure:8025: checking for PTHREAD_PRIO_INHERIT configure:8042: gcc -o conftest -g -O2 -pthread -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c >&5 configure:8042: $? = 0 configure:8051: result: yes configure:8167: checking mpi.h usability configure:8167: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c >&5 conftest.c:93:10: fatal error: mpi.h: No such file or directory #include ^~~~~~~ compilation terminated. configure:8167: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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 | /* 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:8167: result: no configure:8167: checking mpi.h presence configure:8167: gcc -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c conftest.c:60:10: fatal error: mpi.h: No such file or directory #include ^~~~~~~ compilation terminated. configure:8167: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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 | /* end confdefs.h. */ | #include configure:8167: result: no configure:8167: checking for mpi.h configure:8167: result: no configure:8547: checking for MPI_Init in -lmpi configure:8572: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c -lmpi >&5 /usr/bin/ld: cannot find -lmpi collect2: error: ld returned 1 exit status configure:8572: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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 | /* 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:8581: result: no configure:8606: checking for sqrt in -lm configure:8631: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c -lm >&5 conftest.c:67:6: warning: conflicting types for built-in function 'sqrt' [-Wbuiltin-declaration-mismatch] char sqrt (); ^~~~ configure:8631: $? = 0 configure:8640: result: yes configure:8654: checking for pow configure:8654: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c -lm >&5 conftest.c:84:6: warning: conflicting types for built-in function 'pow' [-Wbuiltin-declaration-mismatch] char pow (); ^~~ configure:8654: $? = 0 configure:8654: result: yes configure:8654: checking for sqrt configure:8654: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c -lm >&5 conftest.c:85:6: warning: conflicting types for built-in function 'sqrt' [-Wbuiltin-declaration-mismatch] char sqrt (); ^~~~ configure:8654: $? = 0 configure:8654: result: yes configure:8663: checking for ceilf configure:8663: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c -lm >&5 conftest.c:86:6: warning: conflicting types for built-in function 'ceilf' [-Wbuiltin-declaration-mismatch] char ceilf (); ^~~~~ configure:8663: $? = 0 configure:8663: result: yes configure:8674: checking for dlsym in -ldl configure:8699: gcc -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c -ldl -lm >&5 configure:8699: $? = 0 configure:8708: result: yes configure:8733: gcc -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.c >&5 conftest.c:64:20: warning: extra tokens at end of #include directive #include , ^ configure:8733: $? = 0 configure:8756: checking how to run the C++ preprocessor configure:8783: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8783: $? = 0 configure:8797: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp conftest.cpp:65:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:8797: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_LIBM 1 | #define HAVE_POW 1 | #define HAVE_SQRT 1 | #define HAVE_LIBDL 1 | #define HAVE_POPCNT 1 | /* end confdefs.h. */ | #include configure:8822: result: g++ -std=c++11 -E configure:8842: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8842: $? = 0 configure:8856: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp conftest.cpp:65:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:8856: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_LIBM 1 | #define HAVE_POW 1 | #define HAVE_SQRT 1 | #define HAVE_LIBDL 1 | #define HAVE_POPCNT 1 | /* end confdefs.h. */ | #include configure:8898: checking functional usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking functional presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking for functional configure:8898: result: yes configure:8898: checking tr1/functional usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking tr1/functional presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking for tr1/functional configure:8898: result: yes configure:8898: checking boost/functional/hash.hpp usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking boost/functional/hash.hpp presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking for boost/functional/hash.hpp configure:8898: result: yes configure:8898: checking boost/property_map/property_map.hpp usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking boost/property_map/property_map.hpp presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking for boost/property_map/property_map.hpp configure:8898: result: yes configure:8898: checking google/sparse_hash_map usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 conftest.cpp:102:10: fatal error: google/sparse_hash_map: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. configure:8898: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_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:8898: result: no configure:8898: checking google/sparse_hash_map presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp conftest.cpp:69:10: fatal error: google/sparse_hash_map: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. configure:8898: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_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:8898: result: no configure:8898: checking for google/sparse_hash_map configure:8898: result: no configure:8898: checking unordered_map usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking unordered_map presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking for unordered_map configure:8898: result: yes configure:8898: checking tr1/unordered_map usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking tr1/unordered_map presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking for tr1/unordered_map configure:8898: result: yes configure:8898: checking unordered_set usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking unordered_set presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking for unordered_set configure:8898: result: yes configure:8898: checking tr1/unordered_set usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking tr1/unordered_set presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking for tr1/unordered_set configure:8898: result: yes configure:8898: checking boost/unordered_set.hpp usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking boost/unordered_set.hpp presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp configure:8898: $? = 0 configure:8898: result: yes configure:8898: checking for boost/unordered_set.hpp configure:8898: result: yes configure:8898: checking btllib/bloom_filter.hpp usability configure:8898: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 conftest.cpp:107:10: fatal error: btllib/bloom_filter.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. configure:8898: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_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_UNORDERED_MAP 1 | #define HAVE_TR1_UNORDERED_MAP 1 | #define HAVE_UNORDERED_SET 1 | #define HAVE_TR1_UNORDERED_SET 1 | #define HAVE_BOOST_UNORDERED_SET_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:8898: result: no configure:8898: checking btllib/bloom_filter.hpp presence configure:8898: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp conftest.cpp:74:10: fatal error: btllib/bloom_filter.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. configure:8898: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_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_UNORDERED_MAP 1 | #define HAVE_TR1_UNORDERED_MAP 1 | #define HAVE_UNORDERED_SET 1 | #define HAVE_TR1_UNORDERED_SET 1 | #define HAVE_BOOST_UNORDERED_SET_HPP 1 | /* end confdefs.h. */ | #include configure:8898: result: no configure:8898: checking for btllib/bloom_filter.hpp configure:8898: result: no configure:8926: checking sqlite3.h usability configure:8926: g++ -std=c++11 -c -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp >&5 conftest.cpp:107:10: fatal error: sqlite3.h: No such file or directory #include ^~~~~~~~~~~ compilation terminated. configure:8926: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_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_UNORDERED_MAP 1 | #define HAVE_TR1_UNORDERED_MAP 1 | #define HAVE_UNORDERED_SET 1 | #define HAVE_TR1_UNORDERED_SET 1 | #define HAVE_BOOST_UNORDERED_SET_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:8926: result: no configure:8926: checking sqlite3.h presence configure:8926: g++ -std=c++11 -E -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp conftest.cpp:74:10: fatal error: sqlite3.h: No such file or directory #include ^~~~~~~~~~~ compilation terminated. configure:8926: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_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_UNORDERED_MAP 1 | #define HAVE_TR1_UNORDERED_MAP 1 | #define HAVE_UNORDERED_SET 1 | #define HAVE_TR1_UNORDERED_SET 1 | #define HAVE_BOOST_UNORDERED_SET_HPP 1 | /* end confdefs.h. */ | #include configure:8926: result: no configure:8926: checking for sqlite3.h configure:8926: result: no configure:8936: checking for main in -lsqlite3 configure:8955: g++ -std=c++11 -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp -lsqlite3 -ldl -lm >&5 /usr/bin/ld: cannot find -lsqlite3 collect2: error: ld returned 1 exit status configure:8955: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_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_UNORDERED_MAP 1 | #define HAVE_TR1_UNORDERED_MAP 1 | #define HAVE_UNORDERED_SET 1 | #define HAVE_TR1_UNORDERED_SET 1 | #define HAVE_BOOST_UNORDERED_SET_HPP 1 | /* end confdefs.h. */ | | | int | main () | { | return main (); | ; | return 0; | } configure:8964: result: no configure:9002: checking for g++ -std=c++11 option to support OpenMP configure:9017: g++ -std=c++11 -o conftest -g -O2 -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp -ldl -lm >&5 conftest.cpp:76:2: error: 'choke' does not name a type choke me ^~~~~ In file included from conftest.cpp:78: /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:39:3: error: 'omp_lock_t' does not name a type } omp_lock_t; ^~~~~~~~~~ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:95:28: error: variable or field 'omp_init_lock' declared void extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:95:28: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:95:28: note: suggested alternative: 'omp_lock_hint_t' extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ omp_lock_hint_t /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:95:40: error: expected primary-expression before ')' token extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:96:38: error: variable or field 'omp_init_lock_with_hint' declared void extern void omp_init_lock_with_hint (omp_lock_t *, omp_lock_hint_t) ^~~~~~~~~~ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:96:38: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:96:38: note: suggested alternative: 'omp_lock_hint_t' extern void omp_init_lock_with_hint (omp_lock_t *, omp_lock_hint_t) ^~~~~~~~~~ omp_lock_hint_t /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:96:50: error: expected primary-expression before ',' token extern void omp_init_lock_with_hint (omp_lock_t *, omp_lock_hint_t) ^ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:96:67: error: expected primary-expression before ')' token extern void omp_init_lock_with_hint (omp_lock_t *, omp_lock_hint_t) ^ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:98:31: error: variable or field 'omp_destroy_lock' declared void extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:98:31: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:98:31: note: suggested alternative: 'omp_lock_hint_t' extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ omp_lock_hint_t /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:98:43: error: expected primary-expression before ')' token extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:99:27: error: variable or field 'omp_set_lock' declared void extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:99:27: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:99:27: note: suggested alternative: 'omp_lock_hint_t' extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ omp_lock_hint_t /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:99:39: error: expected primary-expression before ')' token extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:100:29: error: variable or field 'omp_unset_lock' declared void extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:100:29: error: 'omp_lock_t' was not declared in this scope /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:100:29: note: suggested alternative: 'omp_lock_hint_t' extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ omp_lock_hint_t /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:100:41: error: expected primary-expression before ')' token extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW; ^ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:101:27: error: 'omp_lock_t' was not declared in this scope extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:101:27: note: suggested alternative: 'omp_lock_hint_t' extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW; ^~~~~~~~~~ omp_lock_hint_t /usr/lib/gcc/x86_64-redhat-linux/8/include/omp.h:101:39: error: expected primary-expression before ')' token extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW; ^ configure:9017: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ABySS" | #define PACKAGE_TARNAME "abyss" | #define PACKAGE_VERSION "2.3.7" | #define PACKAGE_STRING "ABySS 2.3.7" | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | #define HAVE_CXX11 1 | #define PACKAGE "abyss" | #define VERSION "2.3.7" | #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 HAVE_PTRDIFF_T 1 | #define HAVE_STD_HASH 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_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_UNORDERED_MAP 1 | #define HAVE_TR1_UNORDERED_MAP 1 | #define HAVE_UNORDERED_SET 1 | #define HAVE_TR1_UNORDERED_SET 1 | #define HAVE_BOOST_UNORDERED_SET_HPP 1 | /* end confdefs.h. */ | | #ifndef _OPENMP | choke me | #endif | #include | int main () { return omp_get_num_threads (); } | configure:9035: g++ -std=c++11 -o conftest -g -O2 -fopenmp -I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0 conftest.cpp -ldl -lm >&5 configure:9035: $? = 0 configure:9049: result: -fopenmp configure:9066: error: ABySS requires the btllib C++ libraries, which may be downloaded from here: https://github.com/bcgsc/btllib It is necessary to compile btllib. The readme in the GitHub repo contains instructs to compile btllib. ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-unknown-linux-gnu ac_cv_c_bigendian=no ac_cv_c_compiler_gnu=yes ac_cv_c_const=yes ac_cv_c_inline=inline ac_cv_c_int64_t=yes ac_cv_c_uint16_t=yes ac_cv_c_uint32_t=yes ac_cv_c_uint64_t=yes ac_cv_c_uint8_t=yes ac_cv_cxx_compiler_gnu=yes ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= 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= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_func__doprnt=no ac_cv_func_ceilf=yes ac_cv_func_dup2=yes ac_cv_func_fork=yes ac_cv_func_fork_works=yes ac_cv_func_gethostname=yes ac_cv_func_getopt_long=yes ac_cv_func_getpagesize=yes ac_cv_func_malloc_0_nonnull=yes ac_cv_func_memcmp_working=yes ac_cv_func_memset=yes ac_cv_func_pow=yes ac_cv_func_realloc_0_nonnull=yes ac_cv_func_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_btllib_bloom_filter_hpp=no 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=no ac_cv_header_sqlite3_h=no 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=yes ac_cv_header_unordered_set=yes ac_cv_header_vfork_h=no ac_cv_host=x86_64-unknown-linux-gnu ac_cv_lib_dl_dlsym=yes ac_cv_lib_m_sqrt=yes ac_cv_lib_mpi_MPI_Init=no ac_cv_lib_sqlite3_main=no ac_cv_objext=o ac_cv_path_EGREP='/usr/bin/grep -E' ac_cv_path_GREP=/usr/bin/grep ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/usr/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_CPP='gcc -E' ac_cv_prog_CXXCPP='g++ -std=c++11 -E' ac_cv_prog_PANDOC=yes ac_cv_prog_ac_ct_AR=ar ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_CXX=g++ ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_cc_c89= ac_cv_prog_cc_g=yes ac_cv_prog_cxx_g=yes ac_cv_prog_cxx_openmp=-fopenmp ac_cv_prog_make_make_set=yes ac_cv_type__Bool=yes ac_cv_type_mode_t=yes ac_cv_type_pid_t=yes ac_cv_type_ptrdiff_t=yes ac_cv_type_size_t=yes ac_cv_type_ssize_t=yes ac_cv_type_std__hash_int_=yes ac_cv_type_std__tr1__hash_int_=yes ac_cv_type_std__tr1__tuple_int_=yes am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 am_cv_ar_interface=ar am_cv_make_support_nested_variables=yes am_cv_prog_tar_ustar=gnutar ax_cv_PTHREAD_PRIO_INHERIT=yes ax_cv_cxx_compile_cxx11__std_cpp11=yes ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-2.3.7/missing aclocal-1.13' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_CXXFLAGS='' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='1' AM_V='$(V)' AR='ar' AUTOCONF='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-2.3.7/missing autoconf' AUTOHEADER='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-2.3.7/missing autoheader' AUTOMAKE='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-2.3.7/missing automake-1.13' AWK='gawk' CC='gcc' CCDEPMODE='depmode=gcc3' CFLAGS='-g -O2' CPP='gcc -E' CPPFLAGS='-I/home/psgendb/BIRCHDEV/install/abyss-2.3.7 -isystem/home/psgendb/BIRCHDEV/install/abyss-2.3.7/boost_1_56_0' CXX='g++ -std=c++11' CXXCPP='g++ -std=c++11 -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-g -O2' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/usr/bin/grep -E' EXEEXT='' GHC='' GREP='/usr/bin/grep' HAVE_CXX11='1' HAVE_GHC_FALSE='' HAVE_GHC_TRUE='#' HAVE_LIBMPI_FALSE='' HAVE_LIBMPI_TRUE='#' HAVE_PANDOC_FALSE='#' HAVE_PANDOC_TRUE='' HAVE_PTHREAD_FALSE='#' HAVE_PTHREAD_TRUE='' HAVE_SQLITE3_FALSE='' HAVE_SQLITE3_TRUE='#' HAVE_TR1_TUPLE_FALSE='#' HAVE_TR1_TUPLE_TRUE='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS=' ' LIBOBJS='' LIBS='-ldl -lm ' LTLIBOBJS='' MAKEINFO='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-2.3.7/missing makeinfo' MKDIR_P='/usr/bin/mkdir -p' MPI_LIBS='' OBJEXT='o' OPENMP_CXXFLAGS='-fopenmp' PACKAGE='abyss' PACKAGE_BUGREPORT='abyss-users@bcgsc.ca' PACKAGE_NAME='ABySS' PACKAGE_STRING='ABySS 2.3.7' PACKAGE_TARNAME='abyss' PACKAGE_URL='http://www.bcgsc.ca/platform/bioinfo/software/abyss' PACKAGE_VERSION='2.3.7' PAIRED_DBG_FALSE='' PAIRED_DBG_TRUE='' PANDOC='yes' PATH_SEPARATOR=':' PTHREAD_CC='gcc' PTHREAD_CFLAGS='-pthread' PTHREAD_LIBS='' RANLIB='ranlib' SET_MAKE='' SHELL='/bin/sh' SQLITE_LIBS='-ldl -lm ' STRIP='' VERSION='2.3.7' ac_ct_AR='ar' ac_ct_CC='gcc' ac_ct_CXX='g++' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='' am__fastdepCC_FALSE='#' am__fastdepCC_TRUE='' am__fastdepCXX_FALSE='#' am__fastdepCXX_TRUE='' am__include='include' am__isrc='' am__leading_dot='.' am__nodep='_no' am__quote='' am__tar='tar --format=ustar -chf - "$$tardir"' am__untar='tar -xf -' ax_pthread_config='' bindir='${exec_prefix}/bin' build='x86_64-unknown-linux-gnu' build_alias='' build_cpu='x86_64' build_os='linux-gnu' build_vendor='unknown' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host='x86_64-unknown-linux-gnu' host_alias='' host_cpu='x86_64' host_os='linux-gnu' host_vendor='unknown' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /home/psgendb/BIRCHDEV/install/abyss-2.3.7/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='$(MKDIR_P)' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='NONE' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "ABySS" #define PACKAGE_TARNAME "abyss" #define PACKAGE_VERSION "2.3.7" #define PACKAGE_STRING "ABySS 2.3.7" #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" #define HAVE_CXX11 1 #define PACKAGE "abyss" #define VERSION "2.3.7" #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 HAVE_PTRDIFF_T 1 #define HAVE_STD_HASH 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_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_UNORDERED_MAP 1 #define HAVE_TR1_UNORDERED_MAP 1 #define HAVE_UNORDERED_SET 1 #define HAVE_TR1_UNORDERED_SET 1 #define HAVE_BOOST_UNORDERED_SET_HPP 1 configure: exit 1