This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by jellyfish configure 2.2.4, which was
generated by GNU Autoconf 2.68.  Invocation command line was

  $ ./configure 

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

hostname = venus
uname -m = x86_64
uname -r = 2.6.32-696.18.7.el6.x86_64
uname -s = Linux
uname -v = #1 SMP Thu Dec 28 20:15:47 EST 2017

/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: /home/psgendb/BIRCHDEV/local/script
PATH: /home/psgendb/BIRCHDEV/local/bin-linux-x86_64
PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /opt/thinlinc/bin
PATH: /usr/local/bin
PATH: /usr/bin/X11
PATH: /usr/dt/bin
PATH: /usr/openwin/bin
PATH: /sbin
PATH: /usr/sbin
PATH: /usr/local/sbin
PATH: /var/cfengine/bin
PATH: /home/psgendb/BIRCHDEV/script
PATH: /home/psgendb/BIRCHDEV/bin-linux-x86_64
PATH: /home/psgendb/BIRCHDEV/local/pkg/EMBOSS/linux-x86_64/bin
PATH: /home/psgendb/bin


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

configure:2507: checking build system type
configure:2521: result: x86_64-unknown-linux-gnu
configure:2541: checking host system type
configure:2554: result: x86_64-unknown-linux-gnu
configure:2591: checking for a BSD-compatible install
configure:2659: result: /usr/bin/install -c
configure:2670: checking whether build environment is sane
configure:2725: result: yes
configure:2876: checking for a thread-safe mkdir -p
configure:2915: result: /bin/mkdir -p
configure:2922: checking for gawk
configure:2938: found /bin/gawk
configure:2949: result: gawk
configure:2960: checking whether make sets $(MAKE)
configure:2982: result: yes
configure:3011: checking whether make supports nested variables
configure:3028: result: yes
configure:3165: checking whether make supports nested variables
configure:3182: result: yes
configure:3242: checking how to print strings
configure:3269: result: printf
configure:3302: checking for style of include used by make
configure:3330: result: GNU
configure:3401: checking for gcc
configure:3417: found /usr/bin/gcc
configure:3428: result: gcc
configure:3657: checking for C compiler version
configure:3666: gcc --version >&5
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:3677: $? = 0
configure:3666: gcc -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) 
configure:3677: $? = 0
configure:3666: gcc -V >&5
gcc: '-V' option must have argument
configure:3677: $? = 1
configure:3666: gcc -qversion >&5
gcc: unrecognized option '-qversion'
gcc: no input files
configure:3677: $? = 1
configure:3697: checking whether the C compiler works
configure:3719: gcc    conftest.c  >&5
configure:3723: $? = 0
configure:3771: result: yes
configure:3774: checking for C compiler default output file name
configure:3776: result: a.out
configure:3782: checking for suffix of executables
configure:3789: gcc -o conftest    conftest.c  >&5
configure:3793: $? = 0
configure:3815: result: 
configure:3837: checking whether we are cross compiling
configure:3845: gcc -o conftest    conftest.c  >&5
configure:3849: $? = 0
configure:3856: ./conftest
configure:3860: $? = 0
configure:3875: result: no
configure:3880: checking for suffix of object files
configure:3902: gcc -c   conftest.c >&5
configure:3906: $? = 0
configure:3927: result: o
configure:3931: checking whether we are using the GNU C compiler
configure:3950: gcc -c   conftest.c >&5
configure:3950: $? = 0
configure:3959: result: yes
configure:3968: checking whether gcc accepts -g
configure:3988: gcc -c -g  conftest.c >&5
configure:3988: $? = 0
configure:4029: result: yes
configure:4046: checking for gcc option to accept ISO C89
configure:4110: gcc  -c -g -O2  conftest.c >&5
configure:4110: $? = 0
configure:4123: result: none needed
configure:4148: checking whether gcc understands -c and -o together
configure:4170: gcc -c conftest.c -o conftest2.o
configure:4173: $? = 0
configure:4170: gcc -c conftest.c -o conftest2.o
configure:4173: $? = 0
configure:4185: result: yes
configure:4204: checking dependency style of gcc
configure:4315: result: gcc3
configure:4330: checking for a sed that does not truncate output
configure:4394: result: /bin/sed
configure:4412: checking for grep that handles long lines and -e
configure:4470: result: /bin/grep
configure:4475: checking for egrep
configure:4537: result: /bin/grep -E
configure:4542: checking for fgrep
configure:4604: result: /bin/grep -F
configure:4639: checking for ld used by gcc
configure:4706: result: /usr/bin/ld
configure:4713: checking if the linker (/usr/bin/ld) is GNU ld
configure:4728: result: yes
configure:4740: checking for BSD- or MS-compatible name lister (nm)
configure:4789: result: /usr/bin/nm -B
configure:4919: checking the name lister (/usr/bin/nm -B) interface
configure:4926: gcc -c -g -O2  conftest.c >&5
configure:4929: /usr/bin/nm -B "conftest.o"
configure:4932: output
0000000000000000 B some_variable
configure:4939: result: BSD nm
configure:4942: checking whether ln -s works
configure:4946: result: yes
configure:4954: checking the maximum length of command line arguments
configure:5084: result: 1966080
configure:5101: checking whether the shell understands some XSI constructs
configure:5111: result: yes
configure:5115: checking whether the shell understands "+="
configure:5121: result: yes
configure:5156: checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format
configure:5196: result: func_convert_file_noop
configure:5203: checking how to convert x86_64-unknown-linux-gnu file names to toolchain format
configure:5223: result: func_convert_file_noop
configure:5230: checking for /usr/bin/ld option to reload object files
configure:5237: result: -r
configure:5311: checking for objdump
configure:5327: found /usr/bin/objdump
configure:5338: result: objdump
configure:5370: checking how to recognize dependent libraries
configure:5572: result: pass_all
configure:5657: checking for dlltool
configure:5687: result: no
configure:5717: checking how to associate runtime and link libraries
configure:5744: result: printf %s\n
configure:5805: checking for ar
configure:5821: found /usr/bin/ar
configure:5832: result: ar
configure:5869: checking for archiver @FILE support
configure:5886: gcc -c -g -O2  conftest.c >&5
configure:5886: $? = 0
configure:5889: ar cru libconftest.a @conftest.lst >&5
configure:5892: $? = 0
configure:5897: ar cru libconftest.a @conftest.lst >&5
ar: conftest.o: No such file or directory
configure:5900: $? = 1
configure:5912: result: @
configure:5970: checking for strip
configure:5986: found /usr/bin/strip
configure:5997: result: strip
configure:6069: checking for ranlib
configure:6085: found /usr/bin/ranlib
configure:6096: result: ranlib
configure:6198: checking command to parse /usr/bin/nm -B output from gcc object
configure:6318: gcc -c -g -O2  conftest.c >&5
configure:6321: $? = 0
configure:6325: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' | sed '/ __gnu_lto/d' \> conftest.nm
configure:6328: $? = 0
configure:6394: gcc -o conftest -g -O2   conftest.c conftstm.o >&5
configure:6397: $? = 0
configure:6435: result: ok
configure:6472: checking for sysroot
configure:6502: result: no
configure:6579: gcc -c -g -O2  conftest.c >&5
configure:6582: $? = 0
configure:6758: checking for mt
configure:6788: result: no
configure:6808: checking if : is a manifest tool
configure:6814: : '-?'
configure:6822: result: no
configure:7464: checking how to run the C preprocessor
configure:7495: gcc -E  conftest.c
configure:7495: $? = 0
configure:7509: gcc -E  conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:7509: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "2.2.4"
| #define PACKAGE_STRING "jellyfish 2.2.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "2.2.4"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:7534: result: gcc -E
configure:7554: gcc -E  conftest.c
configure:7554: $? = 0
configure:7568: gcc -E  conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:7568: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "2.2.4"
| #define PACKAGE_STRING "jellyfish 2.2.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "2.2.4"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:7597: checking for ANSI C header files
configure:7617: gcc -c -g -O2  conftest.c >&5
configure:7617: $? = 0
configure:7690: gcc -o conftest -g -O2   conftest.c  >&5
configure:7690: $? = 0
configure:7690: ./conftest
configure:7690: $? = 0
configure:7701: result: yes
configure:7714: checking for sys/types.h
configure:7714: gcc -c -g -O2  conftest.c >&5
configure:7714: $? = 0
configure:7714: result: yes
configure:7714: checking for sys/stat.h
configure:7714: gcc -c -g -O2  conftest.c >&5
configure:7714: $? = 0
configure:7714: result: yes
configure:7714: checking for stdlib.h
configure:7714: gcc -c -g -O2  conftest.c >&5
configure:7714: $? = 0
configure:7714: result: yes
configure:7714: checking for string.h
configure:7714: gcc -c -g -O2  conftest.c >&5
configure:7714: $? = 0
configure:7714: result: yes
configure:7714: checking for memory.h
configure:7714: gcc -c -g -O2  conftest.c >&5
configure:7714: $? = 0
configure:7714: result: yes
configure:7714: checking for strings.h
configure:7714: gcc -c -g -O2  conftest.c >&5
configure:7714: $? = 0
configure:7714: result: yes
configure:7714: checking for inttypes.h
configure:7714: gcc -c -g -O2  conftest.c >&5
configure:7714: $? = 0
configure:7714: result: yes
configure:7714: checking for stdint.h
configure:7714: gcc -c -g -O2  conftest.c >&5
configure:7714: $? = 0
configure:7714: result: yes
configure:7714: checking for unistd.h
configure:7714: gcc -c -g -O2  conftest.c >&5
configure:7714: $? = 0
configure:7714: result: yes
configure:7728: checking for dlfcn.h
configure:7728: gcc -c -g -O2  conftest.c >&5
configure:7728: $? = 0
configure:7728: result: yes
configure:7934: checking for objdir
configure:7949: result: .libs
configure:8220: checking if gcc supports -fno-rtti -fno-exceptions
configure:8238: gcc -c -g -O2  -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C
configure:8242: $? = 0
configure:8255: result: no
configure:8582: checking for gcc option to produce PIC
configure:8589: result: -fPIC -DPIC
configure:8597: checking if gcc PIC flag -fPIC -DPIC works
configure:8615: gcc -c -g -O2  -fPIC -DPIC -DPIC conftest.c >&5
configure:8619: $? = 0
configure:8632: result: yes
configure:8661: checking if gcc static flag -static works
configure:8689: result: yes
configure:8704: checking if gcc supports -c -o file.o
configure:8725: gcc -c -g -O2  -o out/conftest2.o conftest.c >&5
configure:8729: $? = 0
configure:8751: result: yes
configure:8759: checking if gcc supports -c -o file.o
configure:8806: result: yes
configure:8839: checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:9992: result: yes
configure:10029: checking whether -lc should be explicitly linked in
configure:10037: gcc -c -g -O2  conftest.c >&5
configure:10040: $? = 0
configure:10055: gcc -shared  -fPIC -DPIC conftest.o  -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /bin/grep  -lc  \>/dev/null 2\>\&1
configure:10058: $? = 0
configure:10072: result: no
configure:10232: checking dynamic linker characteristics
configure:10743: gcc -o conftest -g -O2   -Wl,-rpath -Wl,/foo conftest.c  >&5
configure:10743: $? = 0
configure:10969: result: GNU/Linux ld.so
configure:11076: checking how to hardcode library paths into programs
configure:11101: result: immediate
configure:11641: checking whether stripping libraries is possible
configure:11646: result: yes
configure:11681: checking if libtool supports shared libraries
configure:11683: result: yes
configure:11686: checking whether to build shared libraries
configure:11707: result: yes
configure:11710: checking whether to build static libraries
configure:11714: result: yes
configure:11820: checking for g++
configure:11836: found /usr/bin/g++
configure:11847: result: g++
configure:11874: checking for C++ compiler version
configure:11883: g++ --version >&5
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:11894: $? = 0
configure:11883: g++ -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) 
configure:11894: $? = 0
configure:11883: g++ -V >&5
g++: '-V' option must have argument
configure:11894: $? = 1
configure:11883: g++ -qversion >&5
g++: unrecognized option '-qversion'
g++: no input files
configure:11894: $? = 1
configure:11898: checking whether we are using the GNU C++ compiler
configure:11917: g++ -c -std=c++0x   conftest.cpp >&5
configure:11917: $? = 0
configure:11926: result: yes
configure:11935: checking whether g++ accepts -g
configure:11955: g++ -c -g  conftest.cpp >&5
configure:11955: $? = 0
configure:11996: result: yes
configure:12021: checking dependency style of g++
configure:12132: result: gcc3
configure:12165: checking how to run the C++ preprocessor
configure:12192: g++ -E  conftest.cpp
configure:12192: $? = 0
configure:12206: g++ -E  conftest.cpp
conftest.cpp:23:28: error: ac_nonexistent.h: No such file or directory
configure:12206: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "2.2.4"
| #define PACKAGE_STRING "jellyfish 2.2.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "2.2.4"
| #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 LT_OBJDIR ".libs/"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:12231: result: g++ -E
configure:12251: g++ -E  conftest.cpp
configure:12251: $? = 0
configure:12265: g++ -E  conftest.cpp
conftest.cpp:23:28: error: ac_nonexistent.h: No such file or directory
configure:12265: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "2.2.4"
| #define PACKAGE_STRING "jellyfish 2.2.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "2.2.4"
| #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 LT_OBJDIR ".libs/"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:12434: checking for ld used by g++
configure:12501: result: /usr/bin/ld -m elf_x86_64
configure:12508: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld
configure:12523: result: yes
configure:12578: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:13583: result: yes
configure:13619: g++ -c -std=c++0x   conftest.cpp >&5
configure:13622: $? = 0
configure:14142: checking for g++ option to produce PIC
configure:14149: result: -fPIC -DPIC
configure:14157: checking if g++ PIC flag -fPIC -DPIC works
configure:14175: g++ -c -std=c++0x   -fPIC -DPIC -DPIC conftest.cpp >&5
configure:14179: $? = 0
configure:14192: result: yes
configure:14215: checking if g++ static flag -static works
configure:14243: result: yes
configure:14255: checking if g++ supports -c -o file.o
configure:14276: g++ -c -std=c++0x   -o out/conftest2.o conftest.cpp >&5
configure:14280: $? = 0
configure:14302: result: yes
configure:14307: checking if g++ supports -c -o file.o
configure:14354: result: yes
configure:14384: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:14420: result: yes
configure:14561: checking dynamic linker characteristics
configure:15232: result: GNU/Linux ld.so
configure:15285: checking how to hardcode library paths into programs
configure:15310: result: immediate
configure:15360: checking for md5sum
configure:15376: found /usr/bin/md5sum
configure:15387: result: md5sum
configure:15444: checking for yaggo
configure:15475: result: false
configure:15563: checking for pkg-config
configure:15581: found /usr/bin/pkg-config
configure:15593: result: /usr/bin/pkg-config
configure:15618: checking pkg-config is at least version 0.9.0
configure:15621: result: yes
configure:15737: checking for __int128
configure:15737: g++ -c -std=c++0x   conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:60: error: '__int128' was not declared in this scope
configure:15737: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "2.2.4"
| #define PACKAGE_STRING "jellyfish 2.2.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "2.2.4"
| #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 LT_OBJDIR ".libs/"
| #define HAVE_SSE 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 (__int128))
| 	 return 0;
|   ;
|   return 0;
| }
configure:15737: result: no
configure:15744: checking for std::numeric_limits<__int128>
configure:15758: g++ -c -std=c++0x   conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:29: error: '__int128' was not declared in this scope
conftest.cpp:29: error: template argument 1 is invalid
conftest.cpp:29: error: template argument 1 is invalid
conftest.cpp:29: error: invalid type in declaration before ';' token
configure:15758: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "2.2.4"
| #define PACKAGE_STRING "jellyfish 2.2.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "2.2.4"
| #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 LT_OBJDIR ".libs/"
| #define HAVE_SSE 1
| /* end confdefs.h.  */
| #include <limits>
|                                             template<bool> struct StaticAssert; template<> struct StaticAssert<true> { static void assert() { } };
| int
| main ()
| {
| StaticAssert<std::numeric_limits<__int128>::is_specialized>::assert();
|   ;
|   return 0;
| }
configure:15765: result: no
configure:15772: checking for _NSGetExecutablePath
configure:15785: g++ -o conftest -std=c++0x    conftest.cpp  >&5
conftest.cpp:24:25: error: mach-o/dyld.h: No such file or directory
conftest.cpp: In function 'int main()':
conftest.cpp:28: error: '_NSGetExecutablePath' was not declared in this scope
configure:15785: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "2.2.4"
| #define PACKAGE_STRING "jellyfish 2.2.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "2.2.4"
| #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 LT_OBJDIR ".libs/"
| #define HAVE_SSE 1
| /* end confdefs.h.  */
| #include <mach-o/dyld.h>
| int
| main ()
| {
| _NSGetExecutablePath(0, 0);
|   ;
|   return 0;
| }
configure:15792: result: no
configure:15805: checking for execinfo.h
configure:15805: g++ -c -std=c++0x   conftest.cpp >&5
configure:15805: $? = 0
configure:15805: result: yes
configure:15805: checking for ext/stdio_filebuf.h
configure:15805: g++ -c -std=c++0x   conftest.cpp >&5
configure:15805: $? = 0
configure:15805: result: yes
configure:15821: checking for siginfo_t.si_int
configure:15821: g++ -c -std=c++0x   conftest.cpp >&5
configure:15821: $? = 0
configure:15821: result: yes
configure:16767: checking that generated files are newer than configure
configure:16773: result: done
configure:16816: creating ./config.status

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

This file was extended by jellyfish config.status 2.2.4, which was
generated by GNU Autoconf 2.68.  Invocation command line was

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

on venus

config.status:1200: creating Makefile
config.status:1200: creating tests/compat.sh
config.status:1200: creating jellyfish-2.0.pc
config.status:1200: creating config.h
config.status:1429: executing depfiles commands
config.status:1429: executing libtool commands

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

ac_cv_build=x86_64-unknown-linux-gnu
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_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_MD5_set=
ac_cv_env_MD5_value=
ac_cv_env_PERL_EXT_CPPFLAGS_set=
ac_cv_env_PERL_EXT_CPPFLAGS_value=
ac_cv_env_PERL_EXT_INC_set=
ac_cv_env_PERL_EXT_INC_value=
ac_cv_env_PERL_EXT_LDFLAGS_set=
ac_cv_env_PERL_EXT_LDFLAGS_value=
ac_cv_env_PERL_EXT_LIB_set=
ac_cv_env_PERL_EXT_LIB_value=
ac_cv_env_PERL_EXT_PREFIX_set=
ac_cv_env_PERL_EXT_PREFIX_value=
ac_cv_env_PKG_CONFIG_LIBDIR_set=
ac_cv_env_PKG_CONFIG_LIBDIR_value=
ac_cv_env_PKG_CONFIG_PATH_set=
ac_cv_env_PKG_CONFIG_PATH_value=
ac_cv_env_PKG_CONFIG_set=
ac_cv_env_PKG_CONFIG_value=
ac_cv_env_PYTHON_VERSION_set=
ac_cv_env_PYTHON_VERSION_value=
ac_cv_env_RUBY_set=
ac_cv_env_RUBY_value=
ac_cv_env_VALGRIND_CFLAGS_set=
ac_cv_env_VALGRIND_CFLAGS_value=
ac_cv_env_VALGRIND_LIBS_set=
ac_cv_env_VALGRIND_LIBS_value=
ac_cv_env_YAGGO_set=
ac_cv_env_YAGGO_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_dlfcn_h=yes
ac_cv_header_execinfo_h=yes
ac_cv_header_ext_stdio_filebuf_h=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_unistd_h=yes
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_member_siginfo_t_si_int=yes
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_FGREP='/bin/grep -F'
ac_cv_path_GREP=/bin/grep
ac_cv_path_SED=/bin/sed
ac_cv_path_YAGGO=false
ac_cv_path_ac_pt_PKG_CONFIG=/usr/bin/pkg-config
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_CXXCPP='g++ -E'
ac_cv_prog_MD5=md5sum
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_ac_ct_OBJDUMP=objdump
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
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_type___int128=no
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
lt_cv_ar_at_file=@
lt_cv_archive_cmds_need_lc=no
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_nm_interface='BSD nm'
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/bin/ld
lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64'
lt_cv_path_NM='/usr/bin/nm -B'
lt_cv_path_mainfest_tool=no
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_c_o_CXX=yes
lt_cv_prog_compiler_pic='-fPIC -DPIC'
lt_cv_prog_compiler_pic_CXX='-fPIC -DPIC'
lt_cv_prog_compiler_pic_works=yes
lt_cv_prog_compiler_pic_works_CXX=yes
lt_cv_prog_compiler_rtti_exceptions=no
lt_cv_prog_compiler_static_works=yes
lt_cv_prog_compiler_static_works_CXX=yes
lt_cv_prog_gnu_ld=yes
lt_cv_prog_gnu_ldcxx=yes
lt_cv_sharedlib_from_linklib_cmd='printf %s\n'
lt_cv_shlibpath_overrides_runpath=no
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[	 ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[	 ][	 ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'' | sed '\''/ __gnu_lto/d'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/  {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/  {"\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/  {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/  {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/  {"lib\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_max_cmd_len=1966080
lt_cv_to_host_file_cmd=func_convert_file_noop
lt_cv_to_tool_file_cmd=func_convert_file_noop

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

ACLOCAL='${SHELL} /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish/missing aclocal-1.15'
ALL_CXXFLAGS='-std=c++0x'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='0'
AM_V='$(V)'
AR='ar'
AUTOCONF='${SHELL} /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish/missing autoconf'
AUTOHEADER='${SHELL} /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish/missing autoheader'
AUTOMAKE='${SHELL} /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish/missing automake-1.15'
AWK='gawk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=''
CXX='g++'
CXXCPP='g++ -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-std=c++0x '
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
DLLTOOL='false'
DSYMUTIL=''
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
FGREP='/bin/grep -F'
GREP='/bin/grep'
HAVE_SWIG_FALSE=''
HAVE_SWIG_TRUE='#'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LD='/usr/bin/ld -m elf_x86_64'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LIPO=''
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish/missing makeinfo'
MANIFEST_TOOL=':'
MD5='md5sum'
MKDIR_P='/bin/mkdir -p'
NM='/usr/bin/nm -B'
NMEDIT=''
OBJDUMP='objdump'
OBJEXT='o'
OTOOL64=''
OTOOL=''
PACKAGE='jellyfish'
PACKAGE_BUGREPORT='gmarcais@umd.edu'
PACKAGE_LIB='2.0'
PACKAGE_NAME='jellyfish'
PACKAGE_STRING='jellyfish 2.2.4'
PACKAGE_TARNAME='jellyfish'
PACKAGE_URL=''
PACKAGE_VERSION='2.2.4'
PATH_SEPARATOR=':'
PERL=''
PERL_BINDING_FALSE=''
PERL_BINDING_TRUE='#'
PERL_EXT_CPPFLAGS=''
PERL_EXT_INC=''
PERL_EXT_LDFLAGS=''
PERL_EXT_LIB=''
PERL_EXT_PREFIX=''
PKG_CONFIG='/usr/bin/pkg-config'
PKG_CONFIG_LIBDIR=''
PKG_CONFIG_PATH=''
PYTHON=''
PYTHON_BINDING_FALSE=''
PYTHON_BINDING_TRUE='#'
PYTHON_CPPFLAGS=''
PYTHON_EXTRA_LDFLAGS=''
PYTHON_EXTRA_LIBS=''
PYTHON_LDFLAGS=''
PYTHON_SITE_PKG=''
PYTHON_VERSION=''
RANLIB='ranlib'
RUBY=''
RUBY_BINDING_FALSE=''
RUBY_BINDING_TRUE='#'
RUBY_EXT_CFLAGS=''
RUBY_EXT_LDFLAGS=''
RUBY_EXT_LIB=''
RUBY_EXT_LIBS=''
RUBY_VERSION=''
SED='/bin/sed'
SET_MAKE=''
SHELL='/bin/sh'
STATIC_FLAGS=''
STRIP='strip'
SWIG=''
SWIG_LIB=''
VALGRIND_CFLAGS=''
VALGRIND_LIBS=''
VERSION='2.2.4'
YAGGO='false'
ac_ct_AR='ar'
ac_ct_CC='gcc'
ac_ct_CXX='g++'
ac_ct_DUMPBIN=''
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 -'
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish/install-sh'
libdir='${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='/usr/local'
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 "jellyfish"
#define PACKAGE_TARNAME "jellyfish"
#define PACKAGE_VERSION "2.2.4"
#define PACKAGE_STRING "jellyfish 2.2.4"
#define PACKAGE_BUGREPORT "gmarcais@umd.edu"
#define PACKAGE_URL ""
#define PACKAGE "jellyfish"
#define VERSION "2.2.4"
#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 LT_OBJDIR ".libs/"
#define HAVE_SSE 1
#define HAVE_EXECINFO_H 1
#define HAVE_EXT_STDIO_FILEBUF_H 1
#define HAVE_SI_INT 1

configure: exit 0