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 sga configure 0.10.12, which was
generated by GNU Autoconf 2.63.  Invocation command line was

  $ ./configure --prefix=/home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/SGA --with-bamtools=/home/yuhan/bin/bamtools-master

## --------- ##
## Platform. ##
## --------- ##

hostname = bip7
uname -m = x86_64
uname -r = 2.6.32-431.20.3.el6.x86_64
uname -s = Linux
uname -v = #1 SMP Thu Jun 19 21:14:45 UTC 2014

/usr/bin/uname -p = unknown
/bin/uname -X     = unknown

/bin/arch              = x86_64
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /sbin
PATH: /home/yide102/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:1901: checking for a BSD-compatible install
configure:1969: result: /usr/bin/install -c
configure:1980: checking whether build environment is sane
configure:2040: result: yes
configure:2181: checking for a thread-safe mkdir -p
configure:2220: result: /bin/mkdir -p
configure:2233: checking for gawk
configure:2249: found /bin/gawk
configure:2260: result: gawk
configure:2271: checking whether make sets $(MAKE)
configure:2293: result: yes
configure:2508: checking for g++
configure:2524: found /usr/local/bin/g++
configure:2535: result: g++
configure:2562: checking for C++ compiler version
configure:2570: g++ --version >&5
g++ (GCC) 4.9.2
Copyright (C) 2014 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:2574: $? = 0
configure:2581: g++ -v >&5
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.9.2/configure --enable-checking=release --enable-languages=c,c++ --disable-multilib
Thread model: posix
gcc version 4.9.2 (GCC) 
configure:2585: $? = 0
configure:2592: g++ -V >&5
g++: error: unrecognized command line option '-V'
g++: fatal error: no input files
compilation terminated.
configure:2596: $? = 1
configure:2619: checking for C++ compiler default output file name
configure:2641: g++    conftest.cpp  >&5
configure:2645: $? = 0
configure:2683: result: a.out
configure:2702: checking whether the C++ compiler works
configure:2712: ./a.out
configure:2716: $? = 0
configure:2735: result: yes
configure:2742: checking whether we are cross compiling
configure:2744: result: no
configure:2747: checking for suffix of executables
configure:2754: g++ -o conftest    conftest.cpp  >&5
configure:2758: $? = 0
configure:2784: result: 
configure:2790: checking for suffix of object files
configure:2816: g++ -c   conftest.cpp >&5
configure:2820: $? = 0
configure:2845: result: o
configure:2849: checking whether we are using the GNU C++ compiler
configure:2878: g++ -c   conftest.cpp >&5
configure:2885: $? = 0
configure:2902: result: yes
configure:2911: checking whether g++ accepts -g
configure:2941: g++ -c -g  conftest.cpp >&5
configure:2948: $? = 0
configure:3049: result: yes
configure:3083: checking for style of include used by make
configure:3111: result: GNU
configure:3136: checking dependency style of g++
configure:3246: result: gcc3
configure:3309: checking for gcc
configure:3325: found /usr/local/bin/gcc
configure:3336: result: gcc
configure:3568: checking for C compiler version
configure:3576: gcc --version >&5
gcc (GCC) 4.9.2
Copyright (C) 2014 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:3580: $? = 0
configure:3587: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.9.2/configure --enable-checking=release --enable-languages=c,c++ --disable-multilib
Thread model: posix
gcc version 4.9.2 (GCC) 
configure:3591: $? = 0
configure:3598: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3602: $? = 1
configure:3605: checking whether we are using the GNU C compiler
configure:3634: gcc -c   conftest.c >&5
configure:3641: $? = 0
configure:3658: result: yes
configure:3667: checking whether gcc accepts -g
configure:3697: gcc -c -g  conftest.c >&5
configure:3704: $? = 0
configure:3805: result: yes
configure:3822: checking for gcc option to accept ISO C89
configure:3896: gcc  -c -g -O2  conftest.c >&5
configure:3903: $? = 0
configure:3926: result: none needed
configure:3946: checking dependency style of gcc
configure:4056: result: gcc3
configure:4114: checking for ranlib
configure:4130: found /usr/bin/ranlib
configure:4141: result: ranlib
configure:4177: checking how to run the C++ preprocessor
configure:4213: g++ -E  conftest.cpp
configure:4220: $? = 0
configure:4251: g++ -E  conftest.cpp
conftest.cpp:10:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:4258: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "sga"
| #define PACKAGE_TARNAME "sga"
| #define PACKAGE_VERSION "0.10.12"
| #define PACKAGE_STRING "sga 0.10.12"
| #define PACKAGE_BUGREPORT "js18@sanger.ac.uk"
| #define PACKAGE "sga"
| #define VERSION "0.10.12"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:4291: result: g++ -E
configure:4320: g++ -E  conftest.cpp
configure:4327: $? = 0
configure:4358: g++ -E  conftest.cpp
conftest.cpp:10:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:4365: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "sga"
| #define PACKAGE_TARNAME "sga"
| #define PACKAGE_VERSION "0.10.12"
| #define PACKAGE_STRING "sga 0.10.12"
| #define PACKAGE_BUGREPORT "js18@sanger.ac.uk"
| #define PACKAGE "sga"
| #define VERSION "0.10.12"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:4405: checking for grep that handles long lines and -e
configure:4465: result: /bin/grep
configure:4470: checking for egrep
configure:4534: result: /bin/grep -E
configure:4539: checking for ANSI C header files
configure:4569: g++ -c -g -O2  conftest.cpp >&5
configure:4576: $? = 0
configure:4675: g++ -o conftest -g -O2   conftest.cpp  >&5
configure:4679: $? = 0
configure:4685: ./conftest
configure:4689: $? = 0
configure:4707: result: yes
configure:4731: checking for sys/types.h
configure:4752: g++ -c -g -O2  conftest.cpp >&5
configure:4759: $? = 0
configure:4776: result: yes
configure:4731: checking for sys/stat.h
configure:4752: g++ -c -g -O2  conftest.cpp >&5
configure:4759: $? = 0
configure:4776: result: yes
configure:4731: checking for stdlib.h
configure:4752: g++ -c -g -O2  conftest.cpp >&5
configure:4759: $? = 0
configure:4776: result: yes
configure:4731: checking for string.h
configure:4752: g++ -c -g -O2  conftest.cpp >&5
configure:4759: $? = 0
configure:4776: result: yes
configure:4731: checking for memory.h
configure:4752: g++ -c -g -O2  conftest.cpp >&5
configure:4759: $? = 0
configure:4776: result: yes
configure:4731: checking for strings.h
configure:4752: g++ -c -g -O2  conftest.cpp >&5
configure:4759: $? = 0
configure:4776: result: yes
configure:4731: checking for inttypes.h
configure:4752: g++ -c -g -O2  conftest.cpp >&5
configure:4759: $? = 0
configure:4776: result: yes
configure:4731: checking for stdint.h
configure:4752: g++ -c -g -O2  conftest.cpp >&5
configure:4759: $? = 0
configure:4776: result: yes
configure:4731: checking for unistd.h
configure:4752: g++ -c -g -O2  conftest.cpp >&5
configure:4759: $? = 0
configure:4776: result: yes
configure:4800: checking zlib.h usability
configure:4817: g++ -c -g -O2  conftest.cpp >&5
configure:4824: $? = 0
configure:4838: result: yes
configure:4842: checking zlib.h presence
configure:4857: g++ -E  conftest.cpp
configure:4864: $? = 0
configure:4878: result: yes
configure:4911: checking for zlib.h
configure:4918: result: yes
configure:4926: checking for library containing gzopen
configure:4967: g++ -o conftest -g -O2   conftest.cpp  >&5
/tmp/cctOAwZZ.o: In function `main':
/home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/conftest.cpp:31: undefined reference to `gzopen'
collect2: error: ld returned 1 exit status
configure:4974: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "sga"
| #define PACKAGE_TARNAME "sga"
| #define PACKAGE_VERSION "0.10.12"
| #define PACKAGE_STRING "sga 0.10.12"
| #define PACKAGE_BUGREPORT "js18@sanger.ac.uk"
| #define PACKAGE "sga"
| #define VERSION "0.10.12"
| #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
| /* 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 gzopen ();
| int
| main ()
| {
| return gzopen ();
|   ;
|   return 0;
| }
configure:4967: g++ -o conftest -g -O2   conftest.cpp -lz   >&5
configure:4974: $? = 0
configure:5005: result: -lz
configure:5017: checking for library containing clock_gettime
configure:5058: g++ -o conftest -g -O2   conftest.cpp -lz  >&5
/tmp/ccOThoA1.o: In function `main':
/home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/conftest.cpp:31: undefined reference to `clock_gettime'
collect2: error: ld returned 1 exit status
configure:5065: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "sga"
| #define PACKAGE_TARNAME "sga"
| #define PACKAGE_VERSION "0.10.12"
| #define PACKAGE_STRING "sga 0.10.12"
| #define PACKAGE_BUGREPORT "js18@sanger.ac.uk"
| #define PACKAGE "sga"
| #define VERSION "0.10.12"
| #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
| /* 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 clock_gettime ();
| int
| main ()
| {
| return clock_gettime ();
|   ;
|   return 0;
| }
configure:5058: g++ -o conftest -g -O2   conftest.cpp -lrt  -lz  >&5
configure:5065: $? = 0
configure:5096: result: -lrt
configure:5112: checking for OpenMP flag of C++ compiler
configure:5162: g++ -o conftest -g -O2 -fopenmp   conftest.cpp -lrt -lz  >&5
configure:5169: $? = 0
configure:5192: result: -fopenmp
configure:5280: checking for host type
configure:5287: result: you are not using osx so multi-threading should work.
configure:5560: checking google/sparse_hash_set usability
configure:5577: g++ -c -O3  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp >&5
configure:5584: $? = 0
configure:5598: result: yes
configure:5602: checking google/sparse_hash_set presence
configure:5617: g++ -E  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp
configure:5624: $? = 0
configure:5638: result: yes
configure:5671: checking for google/sparse_hash_set
configure:5680: result: yes
configure:5717: checking for google/sparse_hash_set
configure:5724: result: yes
configure:5728: checking google/sparse_hash_map usability
configure:5745: g++ -c -O3  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp >&5
configure:5752: $? = 0
configure:5766: result: yes
configure:5770: checking google/sparse_hash_map presence
configure:5785: g++ -E  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp
configure:5792: $? = 0
configure:5806: result: yes
configure:5839: checking for google/sparse_hash_map
configure:5848: result: yes
configure:5728: checking unordered_map usability
configure:5745: g++ -c -O3  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp >&5
In file included from /usr/local/include/c++/4.9.2/unordered_map:35:0,
                 from conftest.cpp:58:
/usr/local/include/c++/4.9.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \
  ^
configure:5752: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "sga"
| #define PACKAGE_TARNAME "sga"
| #define PACKAGE_VERSION "0.10.12"
| #define PACKAGE_STRING "sga 0.10.12"
| #define PACKAGE_BUGREPORT "js18@sanger.ac.uk"
| #define PACKAGE "sga"
| #define VERSION "0.10.12"
| #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_CLOCK_GETTIME 1
| #define HAVE_OPENMP 1
| #define HAVE_GOOGLE_SPARSE_HASH_SET 1
| #define HAVE_GOOGLE_SPARSE_HASH_SET 1
| #define HAVE_GOOGLE_SPARSE_HASH_MAP 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 <unordered_map>
configure:5766: result: no
configure:5770: checking unordered_map presence
configure:5785: g++ -E  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp
In file included from /usr/local/include/c++/4.9.2/unordered_map:35:0,
                 from conftest.cpp:25:
/usr/local/include/c++/4.9.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \
  ^
configure:5792: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "sga"
| #define PACKAGE_TARNAME "sga"
| #define PACKAGE_VERSION "0.10.12"
| #define PACKAGE_STRING "sga 0.10.12"
| #define PACKAGE_BUGREPORT "js18@sanger.ac.uk"
| #define PACKAGE "sga"
| #define VERSION "0.10.12"
| #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_CLOCK_GETTIME 1
| #define HAVE_OPENMP 1
| #define HAVE_GOOGLE_SPARSE_HASH_SET 1
| #define HAVE_GOOGLE_SPARSE_HASH_SET 1
| #define HAVE_GOOGLE_SPARSE_HASH_MAP 1
| /* end confdefs.h.  */
| #include <unordered_map>
configure:5806: result: no
configure:5839: checking for unordered_map
configure:5848: result: no
configure:5728: checking tr1/unordered_map usability
configure:5745: g++ -c -O3  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp >&5
configure:5752: $? = 0
configure:5766: result: yes
configure:5770: checking tr1/unordered_map presence
configure:5785: g++ -E  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp
configure:5792: $? = 0
configure:5806: result: yes
configure:5839: checking for tr1/unordered_map
configure:5848: result: yes
configure:5728: checking ext/hash_map usability
configure:5745: g++ -c -O3  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp >&5
In file included from /usr/local/include/c++/4.9.2/ext/hash_map:60:0,
                 from conftest.cpp:59:
/usr/local/include/c++/4.9.2/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^
configure:5752: $? = 0
configure:5766: result: yes
configure:5770: checking ext/hash_map presence
configure:5785: g++ -E  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp
In file included from /usr/local/include/c++/4.9.2/ext/hash_map:60:0,
                 from conftest.cpp:26:
/usr/local/include/c++/4.9.2/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^
configure:5792: $? = 0
configure:5806: result: yes
configure:5839: checking for ext/hash_map
configure:5848: result: yes
configure:5728: checking unordered_set usability
configure:5745: g++ -c -O3  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp >&5
In file included from /usr/local/include/c++/4.9.2/unordered_set:35:0,
                 from conftest.cpp:60:
/usr/local/include/c++/4.9.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \
  ^
configure:5752: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "sga"
| #define PACKAGE_TARNAME "sga"
| #define PACKAGE_VERSION "0.10.12"
| #define PACKAGE_STRING "sga 0.10.12"
| #define PACKAGE_BUGREPORT "js18@sanger.ac.uk"
| #define PACKAGE "sga"
| #define VERSION "0.10.12"
| #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_CLOCK_GETTIME 1
| #define HAVE_OPENMP 1
| #define HAVE_GOOGLE_SPARSE_HASH_SET 1
| #define HAVE_GOOGLE_SPARSE_HASH_SET 1
| #define HAVE_GOOGLE_SPARSE_HASH_MAP 1
| #define HAVE_TR1_UNORDERED_MAP 1
| #define HAVE_EXT_HASH_MAP 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 <unordered_set>
configure:5766: result: no
configure:5770: checking unordered_set presence
configure:5785: g++ -E  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp
In file included from /usr/local/include/c++/4.9.2/unordered_set:35:0,
                 from conftest.cpp:27:
/usr/local/include/c++/4.9.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \
  ^
configure:5792: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "sga"
| #define PACKAGE_TARNAME "sga"
| #define PACKAGE_VERSION "0.10.12"
| #define PACKAGE_STRING "sga 0.10.12"
| #define PACKAGE_BUGREPORT "js18@sanger.ac.uk"
| #define PACKAGE "sga"
| #define VERSION "0.10.12"
| #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_CLOCK_GETTIME 1
| #define HAVE_OPENMP 1
| #define HAVE_GOOGLE_SPARSE_HASH_SET 1
| #define HAVE_GOOGLE_SPARSE_HASH_SET 1
| #define HAVE_GOOGLE_SPARSE_HASH_MAP 1
| #define HAVE_TR1_UNORDERED_MAP 1
| #define HAVE_EXT_HASH_MAP 1
| /* end confdefs.h.  */
| #include <unordered_set>
configure:5806: result: no
configure:5839: checking for unordered_set
configure:5848: result: no
configure:5728: checking tr1/unordered_set usability
configure:5745: g++ -c -O3  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp >&5
configure:5752: $? = 0
configure:5766: result: yes
configure:5770: checking tr1/unordered_set presence
configure:5785: g++ -E  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp
configure:5792: $? = 0
configure:5806: result: yes
configure:5839: checking for tr1/unordered_set
configure:5848: result: yes
configure:5728: checking ext/hash_set usability
configure:5745: g++ -c -O3  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp >&5
In file included from /usr/local/include/c++/4.9.2/ext/hash_set:60:0,
                 from conftest.cpp:61:
/usr/local/include/c++/4.9.2/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^
configure:5752: $? = 0
configure:5766: result: yes
configure:5770: checking ext/hash_set presence
configure:5785: g++ -E  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp
In file included from /usr/local/include/c++/4.9.2/ext/hash_set:60:0,
                 from conftest.cpp:28:
/usr/local/include/c++/4.9.2/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^
configure:5792: $? = 0
configure:5806: result: yes
configure:5839: checking for ext/hash_set
configure:5848: result: yes
configure:5881: checking api/BamReader.h usability
configure:5898: g++ -c -O3  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp >&5
configure:5905: $? = 0
configure:5919: result: yes
configure:5923: checking api/BamReader.h presence
configure:5938: g++ -E  -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools conftest.cpp
configure:5945: $? = 0
configure:5959: result: yes
configure:5992: checking for api/BamReader.h
configure:6001: result: yes
configure:6155: creating ./config.status

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by sga config.status 0.10.12, which was
generated by GNU Autoconf 2.63.  Invocation command line was

  CONFIG_FILES    = 
  CONFIG_HEADERS  = 
  CONFIG_LINKS    = 
  CONFIG_COMMANDS = 
  $ ./config.status 

on bip7

config.status:802: creating Makefile
config.status:802: creating bin/Makefile
config.status:802: creating Thirdparty/Makefile
config.status:802: creating Util/Makefile
config.status:802: creating SQG/Makefile
config.status:802: creating Bigraph/Makefile
config.status:802: creating Algorithm/Makefile
config.status:802: creating StringGraph/Makefile
config.status:802: creating Concurrency/Makefile
config.status:802: creating SuffixTools/Makefile
config.status:802: creating GraphDiff/Makefile
config.status:802: creating Scaffold/Makefile
config.status:802: creating SGA/Makefile
config.status:802: creating config.h
config.status:1076: executing depfiles commands

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_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_header_api_BamReader_h=yes
ac_cv_header_ext_hash_map=yes
ac_cv_header_ext_hash_set=yes
ac_cv_header_google_sparse_hash_map=yes
ac_cv_header_google_sparse_hash_set=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_tr1_unordered_map=yes
ac_cv_header_tr1_unordered_set=yes
ac_cv_header_unistd_h=yes
ac_cv_header_unordered_map=no
ac_cv_header_unordered_set=no
ac_cv_header_zlib_h=yes
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CXXCPP='g++ -E'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_search_clock_gettime=-lrt
ac_cv_search_gzopen=-lz
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
ax_cv_cxx_openmp=-fopenmp

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/missing --run aclocal-1.11'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/missing --run tar'
AM_CXXFLAGS='-Wall -Wextra -Wno-unknown-pragmas'
AUTOCONF='${SHELL} /home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/missing --run autoconf'
AUTOHEADER='${SHELL} /home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/missing --run autoheader'
AUTOMAKE='${SHELL} /home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/missing --run automake-1.11'
AWK='gawk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-O3'
CPPFLAGS=' -fopenmp  -I/home/yuhan/bin/bamtools-master/include -I/home/yuhan/bin/bamtools-master/include/bamtools'
CXX='g++'
CXXCPP='g++ -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-O3'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS='-fopenmp  -Wl,-rpath,/home/yuhan/bin/bamtools-master/lib -L/home/yuhan/bin/bamtools-master/lib -Wl,-rpath,/home/yuhan/bin/bamtools-master/lib/bamtools -L/home/yuhan/bin/bamtools-master/lib/bamtools '
LIBOBJS=''
LIBS='-lrt -lz  -lbamtools'
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/missing --run makeinfo'
MKDIR_P='/bin/mkdir -p'
OBJEXT='o'
PACKAGE='sga'
PACKAGE_BUGREPORT='js18@sanger.ac.uk'
PACKAGE_NAME='sga'
PACKAGE_STRING='sga 0.10.12'
PACKAGE_TARNAME='sga'
PACKAGE_VERSION='0.10.12'
PATH_SEPARATOR=':'
RANLIB='ranlib'
SET_MAKE=''
SHELL='/bin/sh'
STRIP=''
VERSION='0.10.12'
ac_ct_CC='gcc'
ac_ct_CXX='g++'
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='/bin/mkdir -p'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/home/yide102/Yi_De_102/SGAPacBioCorrection/src20150611/SGA'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

#define PACKAGE_NAME "sga"
#define PACKAGE_TARNAME "sga"
#define PACKAGE_VERSION "0.10.12"
#define PACKAGE_STRING "sga 0.10.12"
#define PACKAGE_BUGREPORT "js18@sanger.ac.uk"
#define PACKAGE "sga"
#define VERSION "0.10.12"
#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_CLOCK_GETTIME 1
#define HAVE_OPENMP 1
#define HAVE_GOOGLE_SPARSE_HASH_SET 1
#define HAVE_GOOGLE_SPARSE_HASH_SET 1
#define HAVE_GOOGLE_SPARSE_HASH_MAP 1
#define HAVE_TR1_UNORDERED_MAP 1
#define HAVE_EXT_HASH_MAP 1
#define HAVE_TR1_UNORDERED_SET 1
#define HAVE_EXT_HASH_SET 1
#define HAVE_API_BAMREADER_H 1

configure: exit 0