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config.log
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by ABySS configure 2.1.4, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --prefix=/s/chopin/a/grad/asharifi/usr/bin CPPFLAGS=-I/s/chopin/a/grad/asharifi/usr/bin/include --with-mpi=/s/chopin/a/grad/asharifi/usr/lib/openmpi
## --------- ##
## Platform. ##
## --------- ##
hostname = oak
uname -m = x86_64
uname -r = 4.18.16-100.fc27.x86_64
uname -s = Linux
uname -v = #1 SMP Sun Oct 21 09:33:00 UTC 2018
/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: ./include/
PATH: /s/chopin/a/grad/asharifi/usr/.openmpi/bin/
PATH: /s/chopin/a/grad/asharifi/usr/.openmpi/bin/
PATH: /s/chopin/a/grad/asharifi/usr/bin/bin/
PATH: ./bin/
PATH: /s/chopin/a/grad/asharifi/usr/bin/
PATH: ../include
PATH: ./sparsehash/m4
PATH: ./sparsehash/lib
PATH: ./sparsehash
PATH: /usr/local/anaconda3-4.4.0/bin
PATH: ../openmpi-2.1.5/bin
PATH: ./sparsehash/
PATH: ./openmpi-2.1.5/bin/
PATH: /usr/local/anaconda/bin/
PATH: /usr/local/anaconda/bin/
PATH: /s/chopin/a/grad/asharifi/bioconda/bin
PATH: /usr/local/cuda_8.0.61-cudnnv5/bin
PATH: /s/chopin/a/grad/asharifi/.nvm/versions/node/v7.5.0/bin
PATH: /s/chopin/a/grad/asharifi/bin
PATH: /s/chopin/a/grad/asharifi/e/bin
PATH: /bin
PATH: /usr/bin
PATH: /sbin
PATH: /usr/sbin
PATH: /usr/local/bin
PATH: /s/damavand/e/asharifi/BS_Aligners/methylcode/bench/gsnap/gmap-2014-12-06/bin
PATH: .
PATH: /s/chopin/a/grad/asharifi/anaconda3/bin
PATH: /usr/local/anaconda/bin/
PATH: /usr/local/anaconda/bin/
PATH: /s/chopin/a/grad/asharifi/bioconda/bin
PATH: /usr/local/cuda_8.0.61-cudnnv5/bin
PATH: /s/chopin/a/grad/asharifi/bin
PATH: /s/chopin/a/grad/asharifi/e/bin
PATH: /bin
PATH: /usr/bin
PATH: /sbin
PATH: /usr/sbin
PATH: /usr/local/bin
PATH: /s/damavand/e/asharifi/BS_Aligners/methylcode/bench/gsnap/gmap-2014-12-06/bin
PATH: .
PATH: /opt/local/bin
PATH: /opt/local/sbin
PATH: ~/f/miniconda3/bin
PATH: /usr/local/anaconda/bin/
PATH: /usr/local/anaconda/bin/
PATH: /s/chopin/a/grad/asharifi/bioconda/bin
PATH: /usr/local/cuda_8.0.61-cudnnv5/bin
PATH: /s/chopin/a/grad/asharifi/bin
PATH: /s/chopin/a/grad/asharifi/e/bin
PATH: /bin
PATH: /usr/bin
PATH: /sbin
PATH: /usr/sbin
PATH: /usr/local/bin
PATH: /s/damavand/e/asharifi/BS_Aligners/methylcode/bench/gsnap/gmap-2014-12-06/bin
PATH: .
PATH: /s/chopin/a/grad/asharifi/anaconda3/bin
PATH: /usr/local/anaconda/bin/
PATH: /usr/local/anaconda/bin/
PATH: /s/chopin/a/grad/asharifi/bioconda/bin
PATH: /usr/local/cuda_8.0.61-cudnnv5/bin
PATH: /s/chopin/a/grad/asharifi/bin
PATH: /s/chopin/a/grad/asharifi/e/bin
PATH: /bin
PATH: /usr/bin
PATH: /sbin
PATH: /usr/sbin
PATH: /usr/local/bin
PATH: /s/damavand/e/asharifi/BS_Aligners/methylcode/bench/gsnap/gmap-2014-12-06/bin
PATH: .
PATH: /opt/local/bin
PATH: /opt/local/sbin
PATH: ~/f/miniconda3/bin
PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/lib64/ccache
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /s/chopin/a/grad/asharifi/.composer/vendor/bin
PATH: /s/chopin/a/grad/asharifi/bin
PATH: /s/chopin/a/grad/asharifi/S
PATH: /s/chopin/a/grad/asharifi/.local/bin
PATH: /s/chopin/a/grad/asharifi/e/Applications/weblogo
PATH: /s/chopin/a/grad/asharifi/e/Applications/gurobi652/linux64/bin
PATH: /s/chopin/a/grad/asharifi/f/miniconda3/bin
PATH: /s/chopin/a/grad/asharifi/e/Applications/Torch/bin
PATH: /usr/local/torch/install/bin
PATH: /s/chopin/a/grad/asharifi/f/Saberi/pg/gsutil
PATH: /s/chopin/a/grad/asharifi/e/Applications/gurobi652/linux64/bin
PATH: /s/chopin/a/grad/asharifi/f/miniconda3/bin
PATH: /s/chopin/a/grad/asharifi/e/Applications/Torch/bin
PATH: /usr/local/torch/install/bin
PATH: /s/chopin/a/grad/asharifi/f/Saberi/pg/gsutil
PATH: /s/chopin/a/grad/asharifi/bin
PATH: /s/chopin/a/grad/asharifi/S
PATH: /s/chopin/a/grad/asharifi/.local/bin
PATH: /s/chopin/a/grad/asharifi/e/Applications/weblogo
PATH: /s/chopin/a/grad/asharifi/e/Applications/gurobi652/linux64/bin
PATH: /s/chopin/a/grad/asharifi/f/miniconda3/bin
PATH: /s/chopin/a/grad/asharifi/e/Applications/Torch/bin
PATH: /usr/local/torch/install/bin
PATH: /s/chopin/a/grad/asharifi/f/Saberi/pg/gsutil
PATH: /s/chopin/a/grad/asharifi/e/Applications/gurobi652/linux64/bin
PATH: /s/chopin/a/grad/asharifi/f/miniconda3/bin
PATH: /s/chopin/a/grad/asharifi/e/Applications/Torch/bin
PATH: /usr/local/torch/install/bin
PATH: /s/chopin/a/grad/asharifi/f/Saberi/pg/gsutil
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2873: checking for a BSD-compatible install
configure:2941: result: /bin/install -c
configure:2952: checking whether build environment is sane
configure:3007: result: yes
configure:3158: checking for a thread-safe mkdir -p
configure:3197: result: /bin/mkdir -p
configure:3204: checking for gawk
configure:3220: found /bin/gawk
configure:3231: result: gawk
configure:3242: checking whether make sets $(MAKE)
configure:3264: result: yes
configure:3293: checking whether make supports nested variables
configure:3310: result: yes
configure:3445: checking for gawk
configure:3472: result: gawk
configure:3531: checking for gcc
configure:3547: found /bin/gcc
configure:3558: result: gcc
configure:3787: checking for C compiler version
configure:3796: gcc --version >&5
gcc (GCC) 7.3.1 20180712 (Red Hat 7.3.1-6)
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3807: $? = 0
configure:3796: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/7/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++,objc,obj-c++,fortran,ada,go,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 --enable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 7.3.1 20180712 (Red Hat 7.3.1-6) (GCC)
configure:3807: $? = 0
configure:3796: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3807: $? = 1
configure:3796: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'; did you mean '--version'?
gcc: fatal error: no input files
compilation terminated.
configure:3807: $? = 1
configure:3827: checking whether the C compiler works
configure:3849: gcc -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:3853: $? = 0
configure:3901: result: yes
configure:3904: checking for C compiler default output file name
configure:3906: result: a.out
configure:3912: checking for suffix of executables
configure:3919: gcc -o conftest -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:3923: $? = 0
configure:3945: result:
configure:3967: checking whether we are cross compiling
configure:3975: gcc -o conftest -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:3979: $? = 0
configure:3986: ./conftest
configure:3990: $? = 0
configure:4005: result: no
configure:4010: checking for suffix of object files
configure:4032: gcc -c -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:4036: $? = 0
configure:4057: result: o
configure:4061: checking whether we are using the GNU C compiler
configure:4080: gcc -c -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:4080: $? = 0
configure:4089: result: yes
configure:4098: checking whether gcc accepts -g
configure:4118: gcc -c -g -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:4118: $? = 0
configure:4159: result: yes
configure:4176: checking for gcc option to accept ISO C89
configure:4239: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:4239: $? = 0
configure:4252: result: none needed
configure:4277: checking whether gcc understands -c and -o together
configure:4299: gcc -c conftest.c -o conftest2.o
configure:4302: $? = 0
configure:4299: gcc -c conftest.c -o conftest2.o
configure:4302: $? = 0
configure:4314: result: yes
configure:4342: checking for style of include used by make
configure:4370: result: GNU
configure:4396: checking dependency style of gcc
configure:4507: result: gcc3
configure:4527: checking how to run the C preprocessor
configure:4558: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
configure:4558: $? = 0
configure:4572: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
conftest.c:11:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:4572: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4597: result: gcc -E
configure:4617: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
configure:4617: $? = 0
configure:4631: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
conftest.c:11:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:4631: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4717: checking for g++
configure:4733: found /bin/g++
configure:4744: result: g++
configure:4771: checking for C++ compiler version
configure:4780: g++ --version >&5
g++ (GCC) 7.3.1 20180712 (Red Hat 7.3.1-6)
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:4791: $? = 0
configure:4780: g++ -v >&5
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/7/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++,objc,obj-c++,fortran,ada,go,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 --enable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 7.3.1 20180712 (Red Hat 7.3.1-6) (GCC)
configure:4791: $? = 0
configure:4780: g++ -V >&5
g++: error: unrecognized command line option '-V'
g++: fatal error: no input files
compilation terminated.
configure:4791: $? = 1
configure:4780: g++ -qversion >&5
g++: error: unrecognized command line option '-qversion'; did you mean '--version'?
g++: fatal error: no input files
compilation terminated.
configure:4791: $? = 1
configure:4795: checking whether we are using the GNU C++ compiler
configure:4814: g++ -c -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.cpp >&5
configure:4814: $? = 0
configure:4823: result: yes
configure:4832: checking whether g++ accepts -g
configure:4852: g++ -c -g -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.cpp >&5
configure:4852: $? = 0
configure:4893: result: yes
configure:4918: checking dependency style of g++
configure:5029: result: gcc3
configure:5088: checking for ranlib
configure:5104: found /bin/ranlib
configure:5115: result: ranlib
configure:5180: checking for ghc
configure:5196: found /bin/ghc
configure:5207: result: ghc
configure:5239: checking for pandoc
configure:5255: found /bin/pandoc
configure:5266: result: yes
configure:5286: checking for grep that handles long lines and -e
configure:5344: result: /bin/grep
configure:5349: checking for egrep
configure:5411: result: /bin/grep -E
configure:5416: checking for ANSI C header files
configure:5436: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5436: $? = 0
configure:5509: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5509: $? = 0
configure:5509: ./conftest
configure:5509: $? = 0
configure:5520: result: yes
configure:5533: checking for sys/types.h
configure:5533: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for sys/stat.h
configure:5533: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for stdlib.h
configure:5533: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for string.h
configure:5533: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for memory.h
configure:5533: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for strings.h
configure:5533: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for inttypes.h
configure:5533: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for stdint.h
configure:5533: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5533: checking for unistd.h
configure:5533: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5533: $? = 0
configure:5533: result: yes
configure:5549: checking dlfcn.h usability
configure:5549: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking dlfcn.h presence
configure:5549: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for dlfcn.h
configure:5549: result: yes
configure:5549: checking fcntl.h usability
configure:5549: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking fcntl.h presence
configure:5549: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for fcntl.h
configure:5549: result: yes
configure:5549: checking float.h usability
configure:5549: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking float.h presence
configure:5549: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for float.h
configure:5549: result: yes
configure:5549: checking limits.h usability
configure:5549: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking limits.h presence
configure:5549: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for limits.h
configure:5549: result: yes
configure:5549: checking stddef.h usability
configure:5549: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking stddef.h presence
configure:5549: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for stddef.h
configure:5549: result: yes
configure:5549: checking for stdint.h
configure:5549: result: yes
configure:5549: checking for stdlib.h
configure:5549: result: yes
configure:5549: checking sys/param.h usability
configure:5549: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking sys/param.h presence
configure:5549: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
configure:5549: $? = 0
configure:5549: result: yes
configure:5549: checking for sys/param.h
configure:5549: result: yes
configure:5559: checking for stdbool.h that conforms to C99
configure:5626: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5626: $? = 0
configure:5633: result: yes
configure:5635: checking for _Bool
configure:5635: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5635: $? = 0
configure:5635: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:65:20: error: expected expression before ')' token
if (sizeof ((_Bool)))
^
configure:5635: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #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 <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((_Bool)))
| return 0;
| ;
| return 0;
| }
configure:5635: result: yes
configure:5652: checking for ANSI C header files
configure:5756: result: yes
configure:5766: checking whether byte ordering is bigendian
configure:5781: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c:33:9: error: unknown type name 'not'
not a universal capable compiler
^~~
conftest.c:33:15: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'universal'
not a universal capable compiler
^~~~~~~~~
conftest.c:33:15: error: unknown type name 'universal'
configure:5781: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| /* end confdefs.h. */
| #ifndef __APPLE_CC__
| not a universal capable compiler
| #endif
| typedef int dummy;
|
configure:5826: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:5826: $? = 0
configure:5844: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include 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:5844: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| /* end confdefs.h. */
| #include <sys/types.h>
| #include <sys/param.h>
|
| int
| main ()
| {
| #if BYTE_ORDER != BIG_ENDIAN
| not big endian
| #endif
|
| ;
| return 0;
| }
configure:5972: result: no
configure:5990: checking for an ANSI C-conforming const
configure:6056: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6056: $? = 0
configure:6063: result: yes
configure:6071: checking for inline
configure:6087: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6087: $? = 0
configure:6095: result: inline
configure:6113: checking for ptrdiff_t
configure:6113: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6113: $? = 0
configure:6113: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:68:24: error: expected expression before ')' token
if (sizeof ((ptrdiff_t)))
^
configure:6113: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((ptrdiff_t)))
| return 0;
| ;
| return 0;
| }
configure:6113: result: yes
configure:6123: checking for mode_t
configure:6123: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6123: $? = 0
configure:6123: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:69:21: error: expected expression before ')' token
if (sizeof ((mode_t)))
^
configure:6123: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((mode_t)))
| return 0;
| ;
| return 0;
| }
configure:6123: result: yes
configure:6134: checking for pid_t
configure:6134: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6134: $? = 0
configure:6134: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:69:20: error: expected expression before ')' token
if (sizeof ((pid_t)))
^
configure:6134: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((pid_t)))
| return 0;
| ;
| return 0;
| }
configure:6134: result: yes
configure:6145: checking for size_t
configure:6145: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6145: $? = 0
configure:6145: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:69:21: error: expected expression before ')' token
if (sizeof ((size_t)))
^
configure:6145: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((size_t)))
| return 0;
| ;
| return 0;
| }
configure:6145: result: yes
configure:6156: checking for ssize_t
configure:6156: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6156: $? = 0
configure:6156: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:69:22: error: expected expression before ')' token
if (sizeof ((ssize_t)))
^
configure:6156: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((ssize_t)))
| return 0;
| ;
| return 0;
| }
configure:6156: result: yes
configure:6167: checking for int64_t
configure:6167: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6167: $? = 0
configure:6167: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:71:53: warning: integer overflow in expression [-Woverflow]
< (int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 2))];
^
conftest.c:70:12: error: storage size of 'test_array' isn't constant
static int test_array [1 - 2 * !((int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 1)
^~~~~~~~~~
configure:6167: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| enum { N = 64 / 2 - 1 };
| int
| main ()
| {
| static int test_array [1 - 2 * !((int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 1)
| < (int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 2))];
| test_array [0] = 0;
| return test_array [0];
|
| ;
| return 0;
| }
configure:6167: result: yes
configure:6178: checking for uint8_t
configure:6178: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6178: $? = 0
configure:6178: result: yes
configure:6192: checking for uint16_t
configure:6192: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6192: $? = 0
configure:6192: result: yes
configure:6204: checking for uint32_t
configure:6204: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6204: $? = 0
configure:6204: result: yes
configure:6218: checking for uint64_t
configure:6218: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6218: $? = 0
configure:6218: result: yes
configure:6242: checking for std::hash<int>
configure:6242: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.cpp >&5
configure:6242: $? = 0
configure:6242: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:43:28: error: expected primary-expression before ')' token
if (sizeof ((std::hash<int>)))
^
configure:6242: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| /* end confdefs.h. */
|
| #ifdef __FUJITSU
| #include <string>
| #else
| #include <functional>
| #endif
|
| int
| main ()
| {
| if (sizeof ((std::hash<int>)))
| return 0;
| ;
| return 0;
| }
configure:6242: result: yes
configure:6256: checking for std::tr1::hash<int>
configure:6256: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.cpp >&5
configure:6256: $? = 0
configure:6256: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:39:33: error: expected primary-expression before ')' token
if (sizeof ((std::tr1::hash<int>)))
^
configure:6256: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| /* end confdefs.h. */
| #include <tr1/functional>
|
| int
| main ()
| {
| if (sizeof ((std::tr1::hash<int>)))
| return 0;
| ;
| return 0;
| }
configure:6256: result: yes
configure:6265: checking for std::tr1::tuple<int>
configure:6265: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.cpp >&5
configure:6265: $? = 0
configure:6265: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:40:34: error: expected primary-expression before ')' token
if (sizeof ((std::tr1::tuple<int>)))
^
configure:6265: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_HASH 1
| #define HAVE_STD_TR1_HASH 1
| /* end confdefs.h. */
| #include <tr1/tuple>
|
| int
| main ()
| {
| if (sizeof ((std::tr1::tuple<int>)))
| return 0;
| ;
| return 0;
| }
configure:6265: result: yes
configure:6301: checking for dup2
configure:6301: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for gethostname
configure:6301: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for getopt_long
configure:6301: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for getpagesize
configure:6301: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for memset
configure:6301: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c:64:6: warning: conflicting types for built-in function 'memset' [-Wbuiltin-declaration-mismatch]
char memset ();
^~~~~~
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for strdup
configure:6301: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c:65:6: warning: conflicting types for built-in function 'strdup' [-Wbuiltin-declaration-mismatch]
char strdup ();
^~~~~~
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for strerror
configure:6301: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6301: checking for strtoul
configure:6301: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6301: $? = 0
configure:6301: result: yes
configure:6312: checking vfork.h usability
configure:6312: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c:78:10: fatal error: vfork.h: No such file or directory
#include <vfork.h>
^~~~~~~~~
compilation terminated.
configure:6312: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| #include <vfork.h>
configure:6312: result: no
configure:6312: checking vfork.h presence
configure:6312: gcc -E -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c
conftest.c:45:10: fatal error: vfork.h: No such file or directory
#include <vfork.h>
^~~~~~~~~
compilation terminated.
configure:6312: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 <vfork.h>
configure:6312: result: no
configure:6312: checking for vfork.h
configure:6312: result: no
configure:6325: checking for fork
configure:6325: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c:68:6: warning: conflicting types for built-in function 'fork' [-Wbuiltin-declaration-mismatch]
char fork ();
^~~~
configure:6325: $? = 0
configure:6325: result: yes
configure:6325: checking for vfork
configure:6325: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6325: $? = 0
configure:6325: result: yes
configure:6335: checking for working fork
configure:6357: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6357: $? = 0
configure:6357: ./conftest
configure:6357: $? = 0
configure:6367: result: yes
configure:6388: checking for working vfork
configure:6498: result: yes
configure:6525: checking for stdlib.h
configure:6525: result: yes
configure:6535: checking for GNU libc compatible malloc
configure:6559: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6559: $? = 0
configure:6559: ./conftest
configure:6559: $? = 0
configure:6569: result: yes
configure:6590: checking for working memcmp
configure:6633: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6633: $? = 0
configure:6633: ./conftest
configure:6633: $? = 0
configure:6643: result: yes
configure:6654: checking for stdlib.h
configure:6654: result: yes
configure:6664: checking for GNU libc compatible realloc
configure:6688: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6688: $? = 0
configure:6688: ./conftest
configure:6688: $? = 0
configure:6698: result: yes
configure:6728: checking for vprintf
configure:6728: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
conftest.c:76:6: warning: conflicting types for built-in function 'vprintf' [-Wbuiltin-declaration-mismatch]
char vprintf ();
^~~~~~~
configure:6728: $? = 0
configure:6728: result: yes
configure:6734: checking for _doprnt
configure:6734: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
/tmp/cc60JINc.o: In function `main':
/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/conftest.c:88: undefined reference to `_doprnt'
collect2: error: ld returned 1 exit status
configure:6734: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 <limits.h> declares _doprnt.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define _doprnt innocuous__doprnt
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char _doprnt (); below.
| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
| <limits.h> exists even on freestanding compilers. */
|
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|
| #undef _doprnt
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char _doprnt ();
| /* The GNU C library defines this for functions which it implements
| to always fail with ENOSYS. Some functions are actually named
| something starting with __ and the normal name is an alias. */
| #if defined __stub__doprnt || defined __stub____doprnt
| choke me
| #endif
|
| int
| main ()
| {
| return _doprnt ();
| ;
| return 0;
| }
configure:6734: result: no
configure:6747: checking whether HOST_NAME_MAX is declared
configure:6747: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/usr/bin/include conftest.c >&5
configure:6747: $? = 0
configure:6747: result: yes
configure:6881: checking build system type
configure:6895: result: x86_64-pc-linux-gnu
configure:6915: checking host system type
configure:6928: result: x86_64-pc-linux-gnu
configure:7060: checking if compiler needs -Werror to reject unknown flags
configure:7076: gcc -c -g -O2 -Werror -Wunknown-warning-option -Wsizeof-array-argument -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.c >&5
gcc: error: unrecognized command line option '-Wunknown-warning-option'
configure:7076: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #define MAX_HASHES 32
| /* end confdefs.h. */
| int foo(void);
| int
| main ()
| {
| foo()
| ;
| return 0;
| }
configure:7081: result: no
configure:7147: checking for the pthreads library -lpthreads
configure:7185: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c -lpthreads >&5
/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
configure:7185: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #define MAX_HASHES 32
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void *a) { a = 0; }
| static void *start_routine(void *a) { return a; }
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_create(&th, 0, start_routine, 0);
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_cleanup_pop(0) /* ; */
| ;
| return 0;
| }
configure:7194: result: no
configure:7092: checking whether pthreads work without any flags
configure:7185: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c >&5
/tmp/cc56vAU5.o: In function `main':
/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/conftest.c:64: undefined reference to `pthread_create'
/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/conftest.c:65: undefined reference to `pthread_join'
/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/conftest.c:67: undefined reference to `__pthread_register_cancel'
/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/conftest.c:68: undefined reference to `__pthread_unregister_cancel'
collect2: error: ld returned 1 exit status
configure:7185: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #define MAX_HASHES 32
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void *a) { a = 0; }
| static void *start_routine(void *a) { return a; }
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_create(&th, 0, start_routine, 0);
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_cleanup_pop(0) /* ; */
| ;
| return 0;
| }
configure:7194: result: no
configure:7097: checking whether pthreads work with -Kthread
configure:7185: gcc -o conftest -g -O2 -Kthread -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c >&5
gcc: error: unrecognized command line option '-Kthread'; did you mean '-pthread'?
configure:7185: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #define MAX_HASHES 32
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void *a) { a = 0; }
| static void *start_routine(void *a) { return a; }
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_create(&th, 0, start_routine, 0);
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_cleanup_pop(0) /* ; */
| ;
| return 0;
| }
configure:7194: result: no
configure:7097: checking whether pthreads work with -kthread
configure:7185: gcc -o conftest -g -O2 -kthread -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c >&5
gcc: error: unrecognized command line option '-kthread'; did you mean '-pthread'?
configure:7185: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #define MAX_HASHES 32
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void *a) { a = 0; }
| static void *start_routine(void *a) { return a; }
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_create(&th, 0, start_routine, 0);
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_cleanup_pop(0) /* ; */
| ;
| return 0;
| }
configure:7194: result: no
configure:7147: checking for the pthreads library -llthread
configure:7185: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c -llthread >&5
/bin/ld: cannot find -llthread
collect2: error: ld returned 1 exit status
configure:7185: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #define MAX_HASHES 32
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void *a) { a = 0; }
| static void *start_routine(void *a) { return a; }
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_create(&th, 0, start_routine, 0);
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_cleanup_pop(0) /* ; */
| ;
| return 0;
| }
configure:7194: result: no
configure:7097: checking whether pthreads work with -pthread
configure:7185: gcc -o conftest -g -O2 -pthread -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c >&5
configure:7185: $? = 0
configure:7194: result: yes
configure:7213: checking for joinable pthread attribute
configure:7228: gcc -o conftest -g -O2 -pthread -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c >&5
configure:7228: $? = 0
configure:7234: result: PTHREAD_CREATE_JOINABLE
configure:7244: checking if more special flags are required for pthreads
configure:7259: result: no
configure:7265: checking for PTHREAD_PRIO_INHERIT
configure:7282: gcc -o conftest -g -O2 -pthread -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c >&5
configure:7282: $? = 0
configure:7291: result: yes
configure:7407: checking mpi.h usability
configure:7407: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.c >&5
conftest.c:93:10: fatal error: mpi.h: No such file or directory
#include <mpi.h>
^~~~~~~
compilation terminated.
configure:7407: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #define MAX_HASHES 32
| #define HAVE_PTHREAD_PRIO_INHERIT 1
| #define MPICH_SKIP_MPICXX 1
| #define OMPI_SKIP_MPICXX 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| #include <mpi.h>
configure:7407: result: no
configure:7407: checking mpi.h presence
configure:7407: gcc -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.c
conftest.c:60:10: fatal error: mpi.h: No such file or directory
#include <mpi.h>
^~~~~~~
compilation terminated.
configure:7407: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #define MAX_HASHES 32
| #define HAVE_PTHREAD_PRIO_INHERIT 1
| #define MPICH_SKIP_MPICXX 1
| #define OMPI_SKIP_MPICXX 1
| /* end confdefs.h. */
| #include <mpi.h>
configure:7407: result: no
configure:7407: checking for mpi.h
configure:7407: result: no
configure:7787: checking for MPI_Init in -lmpi
configure:7812: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c -lmpi >&5
/bin/ld: cannot find -lmpi
collect2: error: ld returned 1 exit status
configure:7812: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #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:7821: result: no
configure:7846: checking for sqrt in -lm
configure:7871: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c -lm >&5
conftest.c:67:6: warning: conflicting types for built-in function 'sqrt' [-Wbuiltin-declaration-mismatch]
char sqrt ();
^~~~
configure:7871: $? = 0
configure:7880: result: yes
configure:7894: checking for pow
configure:7894: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c -lm >&5
conftest.c:84:6: warning: conflicting types for built-in function 'pow' [-Wbuiltin-declaration-mismatch]
char pow ();
^~~
configure:7894: $? = 0
configure:7894: result: yes
configure:7894: checking for sqrt
configure:7894: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c -lm >&5
conftest.c:85:6: warning: conflicting types for built-in function 'sqrt' [-Wbuiltin-declaration-mismatch]
char sqrt ();
^~~~
configure:7894: $? = 0
configure:7894: result: yes
configure:7903: checking for ceilf
configure:7903: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c -lm >&5
conftest.c:86:6: warning: conflicting types for built-in function 'ceilf' [-Wbuiltin-declaration-mismatch]
char ceilf ();
^~~~~
configure:7903: $? = 0
configure:7903: result: yes
configure:7914: checking for dlsym in -ldl
configure:7939: gcc -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.c -ldl -lm >&5
configure:7939: $? = 0
configure:7948: result: yes
configure:7973: gcc -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.c >&5
conftest.c:64:20: warning: extra tokens at end of #include directive
#include <stdint.h>,
^
configure:7973: $? = 0
configure:7996: checking how to run the C++ preprocessor
configure:8023: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8023: $? = 0
configure:8037: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
conftest.cpp:65:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:8037: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #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 <ac_nonexistent.h>
configure:8062: result: g++ -E
configure:8082: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8082: $? = 0
configure:8096: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
conftest.cpp:65:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:8096: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #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 <ac_nonexistent.h>
configure:8137: checking functional usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking functional presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for functional
configure:8137: result: yes
configure:8137: checking tr1/functional usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking tr1/functional presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for tr1/functional
configure:8137: result: yes
configure:8137: checking boost/functional/hash.hpp usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking boost/functional/hash.hpp presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for boost/functional/hash.hpp
configure:8137: result: yes
configure:8137: checking boost/property_map/property_map.hpp usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking boost/property_map/property_map.hpp presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for boost/property_map/property_map.hpp
configure:8137: result: yes
configure:8137: checking google/sparse_hash_map usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking google/sparse_hash_map presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for google/sparse_hash_map
configure:8137: result: yes
configure:8137: checking unordered_map usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking unordered_map presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for unordered_map
configure:8137: result: yes
configure:8137: checking tr1/unordered_map usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking tr1/unordered_map presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for tr1/unordered_map
configure:8137: result: yes
configure:8137: checking unordered_set usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking unordered_set presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for unordered_set
configure:8137: result: yes
configure:8137: checking tr1/unordered_set usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking tr1/unordered_set presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for tr1/unordered_set
configure:8137: result: yes
configure:8137: checking boost/unordered_set.hpp usability
configure:8137: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking boost/unordered_set.hpp presence
configure:8137: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8137: $? = 0
configure:8137: result: yes
configure:8137: checking for boost/unordered_set.hpp
configure:8137: result: yes
configure:8165: checking sqlite3.h usability
configure:8165: g++ -c -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp >&5
configure:8165: $? = 0
configure:8165: result: yes
configure:8165: checking sqlite3.h presence
configure:8165: g++ -E -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 conftest.cpp
configure:8165: $? = 0
configure:8165: result: yes
configure:8165: checking for sqlite3.h
configure:8165: result: yes
configure:8175: checking for main in -lsqlite3
configure:8194: g++ -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.cpp -lsqlite3 -ldl -lm >&5
configure:8194: $? = 0
configure:8203: result: yes
configure:8241: checking for g++ option to support OpenMP
configure:8256: g++ -o conftest -g -O2 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.cpp -ldl -lm >&5
conftest.cpp:80:2: error: 'choke' does not name a type
choke me
^~~~~
In file included from conftest.cpp:82:0:
/usr/lib/gcc/x86_64-redhat-linux/7/include/omp.h:39:3: error: 'omp_lock_t' does not name a type
} omp_lock_t;
^~~~~~~~~~
/usr/lib/gcc/x86_64-redhat-linux/7/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/7/include/omp.h:95:28: error: 'omp_lock_t' was not declared in this scope
/usr/lib/gcc/x86_64-redhat-linux/7/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/7/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/7/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/7/include/omp.h:96:38: error: 'omp_lock_t' was not declared in this scope
/usr/lib/gcc/x86_64-redhat-linux/7/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/7/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/7/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/7/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/7/include/omp.h:98:31: error: 'omp_lock_t' was not declared in this scope
/usr/lib/gcc/x86_64-redhat-linux/7/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/7/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/7/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/7/include/omp.h:99:27: error: 'omp_lock_t' was not declared in this scope
/usr/lib/gcc/x86_64-redhat-linux/7/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/7/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/7/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/7/include/omp.h:100:29: error: 'omp_lock_t' was not declared in this scope
/usr/lib/gcc/x86_64-redhat-linux/7/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/7/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/7/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/7/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/7/include/omp.h:101:39: error: expected primary-expression before ')' token
extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW;
^
configure:8256: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABySS"
| #define PACKAGE_TARNAME "abyss"
| #define PACKAGE_VERSION "2.1.4"
| #define PACKAGE_STRING "ABySS 2.1.4"
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
| #define PACKAGE "abyss"
| #define VERSION "2.1.4"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FLOAT_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define STDC_HEADERS 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STD_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 128
| #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_GOOGLE_SPARSE_HASH_MAP 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
| #define HAVE_SQLITE3_H 1
| #define HAVE_LIBSQLITE3 1
| #define _SQL 1
| /* end confdefs.h. */
|
| #ifndef _OPENMP
| choke me
| #endif
| #include <omp.h>
| int main () { return omp_get_num_threads (); }
|
configure:8274: g++ -o conftest -g -O2 -fopenmp -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib conftest.cpp -ldl -lm >&5
configure:8274: $? = 0
configure:8288: result: -fopenmp
configure:8460: checking that generated files are newer than configure
configure:8466: result: done
configure:8522: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by ABySS config.status 2.1.4, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on oak
config.status:991: creating Makefile
config.status:991: creating ABYSS/Makefile
config.status:991: creating Align/Makefile
config.status:991: creating Assembly/Makefile
config.status:991: creating Common/Makefile
config.status:991: creating DataLayer/Makefile
config.status:991: creating FMIndex/Makefile
config.status:991: creating Graph/Makefile
config.status:991: creating Parallel/Makefile
config.status:991: creating bin/Makefile
config.status:991: creating doc/Makefile
config.status:991: creating dialign/Makefile
config.status:991: creating kmerprint/Makefile
config.status:991: creating AdjList/Makefile
config.status:991: creating Konnector/Makefile
config.status:991: creating DAssembler/Makefile
config.status:991: creating DistanceEst/Makefile
config.status:991: creating Layout/Makefile
config.status:991: creating Map/Makefile
config.status:991: creating Misc/Makefile
config.status:991: creating Overlap/Makefile
config.status:991: creating PopBubbles/Makefile
config.status:991: creating Scaffold/Makefile
config.status:991: creating SimpleGraph/Makefile
config.status:991: creating MergePaths/Makefile
config.status:991: creating KAligner/Makefile
config.status:991: creating PairedDBG/Makefile
config.status:991: creating ParseAligns/Makefile
config.status:991: creating PathOverlap/Makefile
config.status:991: creating Consensus/Makefile
config.status:991: creating FilterGraph/Makefile
config.status:991: creating GapFiller/Makefile
config.status:991: creating Sealer/Makefile
config.status:991: creating lib/gtest-1.7.0/Makefile
config.status:991: creating Unittest/Makefile
config.status:991: creating LogKmerCount/Makefile
config.status:991: creating Bloom/Makefile
config.status:991: creating BloomDBG/Makefile
config.status:991: creating DataBase/Makefile
config.status:991: creating lib/bloomfilter/Makefile
config.status:991: creating lib/nthash/Makefile
config.status:991: creating config.h
config.status:1172: config.h is unchanged
config.status:1220: executing depfiles commands
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-pc-linux-gnu
ac_cv_c_bigendian=no
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_c_inline=inline
ac_cv_c_int64_t=yes
ac_cv_c_uint16_t=yes
ac_cv_c_uint32_t=yes
ac_cv_c_uint64_t=yes
ac_cv_c_uint8_t=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=-I/s/chopin/a/grad/asharifi/usr/bin/include
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_func__doprnt=no
ac_cv_func_ceilf=yes
ac_cv_func_dup2=yes
ac_cv_func_fork=yes
ac_cv_func_fork_works=yes
ac_cv_func_gethostname=yes
ac_cv_func_getopt_long=yes
ac_cv_func_getpagesize=yes
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_memcmp_working=yes
ac_cv_func_memset=yes
ac_cv_func_pow=yes
ac_cv_func_realloc_0_nonnull=yes
ac_cv_func_setvbuf_reversed=no
ac_cv_func_sqrt=yes
ac_cv_func_strdup=yes
ac_cv_func_strerror=yes
ac_cv_func_strtoul=yes
ac_cv_func_vfork=yes
ac_cv_func_vfork_works=yes
ac_cv_func_vprintf=yes
ac_cv_have_decl_HOST_NAME_MAX=yes
ac_cv_header_boost_functional_hash_hpp=yes
ac_cv_header_boost_property_map_property_map_hpp=yes
ac_cv_header_boost_unordered_set_hpp=yes
ac_cv_header_dlfcn_h=yes
ac_cv_header_fcntl_h=yes
ac_cv_header_float_h=yes
ac_cv_header_functional=yes
ac_cv_header_google_sparse_hash_map=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_limits_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_mpi_h=no
ac_cv_header_sqlite3_h=yes
ac_cv_header_stdbool_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stddef_h=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_param_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_tr1_functional=yes
ac_cv_header_tr1_unordered_map=yes
ac_cv_header_tr1_unordered_set=yes
ac_cv_header_unistd_h=yes
ac_cv_header_unordered_map=yes
ac_cv_header_unordered_set=yes
ac_cv_header_vfork_h=no
ac_cv_host=x86_64-pc-linux-gnu
ac_cv_lib_dl_dlsym=yes
ac_cv_lib_m_sqrt=yes
ac_cv_lib_mpi_MPI_Init=no
ac_cv_lib_sqlite3_main=yes
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_path_install='/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_CXXCPP='g++ -E'
ac_cv_prog_PANDOC=yes
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_ac_ct_GHC=ghc
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_make_support_nested_variables=yes
am_cv_prog_cc_c_o=yes
ax_cv_PTHREAD_PRIO_INHERIT=yes
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /s/chopin/a/grad/asharifi/mostafa/Applications/abyss/missing aclocal-1.15'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_CXXFLAGS='-Wall -Wextra'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AUTOCONF='${SHELL} /s/chopin/a/grad/asharifi/mostafa/Applications/abyss/missing autoconf'
AUTOHEADER='${SHELL} /s/chopin/a/grad/asharifi/mostafa/Applications/abyss/missing autoheader'
AUTOMAKE='${SHELL} /s/chopin/a/grad/asharifi/mostafa/Applications/abyss/missing automake-1.15'
AWK='gawk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS='-I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0'
CXX='g++'
CXXCPP='g++ -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-g -O2'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GHC='ghc'
GREP='/bin/grep'
HAVE_GHC_FALSE='#'
HAVE_GHC_TRUE=''
HAVE_LIBMPI_FALSE=''
HAVE_LIBMPI_TRUE='#'
HAVE_PANDOC_FALSE='#'
HAVE_PANDOC_TRUE=''
HAVE_PTHREAD_FALSE='#'
HAVE_PTHREAD_TRUE=''
HAVE_SQLITE3_FALSE='#'
HAVE_SQLITE3_TRUE=''
HAVE_TR1_TUPLE_FALSE='#'
HAVE_TR1_TUPLE_TRUE=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS='-L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib '
LIBOBJS=''
LIBS='-ldl -lm '
LTLIBOBJS=''
MAKEINFO='${SHELL} /s/chopin/a/grad/asharifi/mostafa/Applications/abyss/missing makeinfo'
MKDIR_P='/bin/mkdir -p'
MPI_LIBS=''
OBJEXT='o'
OPENMP_CXXFLAGS='-fopenmp'
PACKAGE='abyss'
PACKAGE_BUGREPORT='abyss-users@bcgsc.ca'
PACKAGE_NAME='ABySS'
PACKAGE_STRING='ABySS 2.1.4'
PACKAGE_TARNAME='abyss'
PACKAGE_URL='http://www.bcgsc.ca/platform/bioinfo/software/abyss'
PACKAGE_VERSION='2.1.4'
PAIRED_DBG_FALSE='#'
PAIRED_DBG_TRUE=''
PANDOC='yes'
PATH_SEPARATOR=':'
PTHREAD_CC='gcc'
PTHREAD_CFLAGS='-pthread'
PTHREAD_LIBS=''
RANLIB='ranlib'
SET_MAKE=''
SHELL='/bin/sh'
SQLITE_LIBS='-lsqlite3 -ldl -lm '
STRIP=''
VERSION='2.1.4'
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-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
ax_pthread_config=''
bindir='${exec_prefix}/bin'
build='x86_64-pc-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='pc'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-pc-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='pc'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /s/chopin/a/grad/asharifi/mostafa/Applications/abyss/install-sh'
libdir='${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='/s/chopin/a/grad/asharifi/usr/bin'
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 "2.1.4"
#define PACKAGE_STRING "ABySS 2.1.4"
#define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca"
#define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
#define PACKAGE "abyss"
#define VERSION "2.1.4"
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_DLFCN_H 1
#define HAVE_FCNTL_H 1
#define HAVE_FLOAT_H 1
#define HAVE_LIMITS_H 1
#define HAVE_STDDEF_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_SYS_PARAM_H 1
#define HAVE__BOOL 1
#define HAVE_STDBOOL_H 1
#define STDC_HEADERS 1
#define HAVE_PTRDIFF_T 1
#define HAVE_STD_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 128
#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_GOOGLE_SPARSE_HASH_MAP 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
#define HAVE_SQLITE3_H 1
#define HAVE_LIBSQLITE3 1
#define _SQL 1
configure: exit 0
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