/
config.log
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/
config.log
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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 1.1.4, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --program-prefix=jsj_ CXX=g++44 CC=gcc44 --prefix=/cluster/home/jstjohn
## --------- ##
## Platform. ##
## --------- ##
hostname = kolossus
uname -m = x86_64
uname -r = 2.6.18-194.3.1.el5
uname -s = Linux
uname -v = #1 SMP Thu May 13 13:08:30 EDT 2010
/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: /cluster/home/jstjohn/src/cactus_packages/assemblaScripts/bin
PATH: /cluster/home/jstjohn/src/cactus_packages/referenceScripts/bin
PATH: /cluster/home/jstjohn/src/cactus_packages/cactusTools/bin
PATH: /cluster/home/jstjohn/src/cactus_packages/cactus/bin
PATH: /cluster/home/jstjohn/src/cactus_packages/jobTree/bin
PATH: /cluster/home/jstjohn/src/cactus_packages/sonLib/bin
PATH: .
PATH: /hive/groups/genomeAssem/bin/454/bin
PATH: /hive/groups/genomeAssem/src/scala/bin
PATH: /hive/groups/genomeAssem/src/MUMmer
PATH: /hive/groups/genomeAssem/bin/bowtie2
PATH: /hive/groups/genomeAssem/bin/tophat
PATH: /hive/groups/genomeAssem/src/genometools/bin
PATH: /hive/groups/genomeAssem/src/velvet
PATH: /hive/groups/genomeAssem/src/oases
PATH: /hive/groups/genomeAssem/bin/cufflinks
PATH: /hive/groups/genomeAssem/bin/bowtie
PATH: /hive/groups/genomeAssem/src/wise/src/bin
PATH: /hive/groups/genomeAssem/bin
PATH: /hive/groups/genomeAssem/scripts
PATH: /hive/groups/genomeAssem/src/seqclean-x86_64
PATH: /hive/groups/genomeAssem/src/trinity
PATH: /hive/groups/genomeAssem/src/ncbi-blast/bin
PATH: /hive/groups/genomeAssem/src/wgs/Linux-amd64/bin
PATH: /hive/groups/genomeAssem/src/Price
PATH: /hive/groups/genomeAssem/src/SHRiMP/bin
PATH: /hive/groups/genomeAssem/lib64/R/bin
PATH: /hive/groups/genomeAssem/src/mia/scripts
PATH: /hive/groups/genomeAssem/src/velvet
PATH: /hive/groups/genomeAssem/bin/tophat
PATH: /hive/groups/genomeAssem/src/stampy
PATH: /hive/groups/genomeAssem/src/tabix
PATH: /hive/groups/genomeAssem/src/SOAPdenovo-V1.05/bin
PATH: /hive/groups/genomeAssem/src/bwa
PATH: /hive/groups/genomeAssem/src/bamtools/bin
PATH: /hive/groups/genomeAssem/src/Quake/bin
PATH: /hive/groups/genomeAssem/src/samtools_svn
PATH: /hive/groups/genomeAssem/src/sga/src/bin
PATH: /hive/groups/genomeAssem/src/samtools_svn/misc
PATH: /hive/groups/genomeAssem/src/samtools_svn/bcftools
PATH: /hive/groups/genomeAssem/src/vcftools/cpp
PATH: /hive/groups/genomeAssem/src/vcftools/bin
PATH: /hive/groups/genomeAssem/src/vcftools/perl
PATH: /data/home/common/bin
PATH: /parasol/bin
PATH: /hive/groups/recon/local/bin
PATH: /hive/groups/recon/local/bin/x86_64
PATH: /cluster/bin/x86_64
PATH: /cluster/bin/scripts
PATH: /scratch/data/RepeatMasker
PATH: /cluster/bin/penn/i386
PATH: /usr/bin
PATH: /bin
PATH: /usr/local/bin
PATH: .
PATH: /cluster/home/jstjohn/src/cscripts/bin
PATH: /cluster/home/jstjohn/bin
PATH: /hive/users/jstjohn/src/RepeatModeler
PATH: /cluster/home/jstjohn/src/rmblast/bin
PATH: /cluster/home/jstjohn/bin/jars
PATH: /cluster/home/jstjohn/bin/x86_64
PATH: /cluster/home/jstjohn/bin/scripts
PATH: /cluster/home/jstjohn/src/ant/bin
PATH: /bin
PATH: /cluster/home/jstjohn/src/ncbi-blast-2.2.23+/bin
PATH: /data/home/common/bin
PATH: /hive/data/outside/samtools/samtools/x86_64
PATH: /hive/data/outside/samtools/samtools/x86_64/misc
PATH: /cluster/home/jstjohn/src/2009-09-16/bin
PATH: /parasol/bin
PATH: /hive/groups/recon/local/bin
PATH: /hive/groups/recon/local/bin/x86_64
PATH: /cluster/bin/x86_64
PATH: /cluster/bin/scripts
PATH: /scratch/data/RepeatMasker
PATH: /cluster/bin/penn/i386
PATH: /usr/kerberos/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /usr/lpp/mmfs/bin/
PATH: /opt/dell/srvadmin/bin
PATH: /usr/bin
PATH: /bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2614: checking build system type
configure:2628: result: x86_64-unknown-linux-gnu
configure:2648: checking host system type
configure:2661: result: x86_64-unknown-linux-gnu
configure:2698: checking for a BSD-compatible install
configure:2766: result: /usr/bin/install -c
configure:2777: checking whether build environment is sane
configure:2827: result: yes
configure:2968: checking for a thread-safe mkdir -p
configure:3007: result: /bin/mkdir -p
configure:3020: checking for gawk
configure:3036: found /usr/bin/gawk
configure:3047: result: gawk
configure:3058: checking whether make sets $(MAKE)
configure:3080: result: yes
configure:3171: checking whether make supports nested variables
configure:3188: result: yes
configure:3313: checking for C++ compiler version
configure:3322: g++44 --version >&5
g++44 (GCC) 4.4.0 20090514 (Red Hat 4.4.0-6)
Copyright (C) 2009 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:3333: $? = 0
configure:3322: g++44 -v >&5
Using built-in specs.
Target: x86_64-redhat-linux6E
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-languages=c,c++,fortran --disable-libgcj --with-mpfr=/builddir/build/BUILD/gcc-4.4.0-20090514/obj-x86_64-redhat-linux6E/mpfr-install/ --with-ppl=/builddir/build/BUILD/gcc-4.4.0-20090514/obj-x86_64-redhat-linux6E/ppl-install --with-cloog=/builddir/build/BUILD/gcc-4.4.0-20090514/obj-x86_64-redhat-linux6E/cloog-install --with-tune=generic --with-arch_32=i586 --build=x86_64-redhat-linux6E
Thread model: posix
gcc version 4.4.0 20090514 (Red Hat 4.4.0-6) (GCC)
configure:3333: $? = 0
configure:3322: g++44 -V >&5
g++44: '-V' option must have argument
configure:3333: $? = 1
configure:3322: g++44 -qversion >&5
g++44: unrecognized option '-qversion'
g++44: no input files
configure:3333: $? = 1
configure:3353: checking whether the C++ compiler works
configure:3375: g++44 conftest.cpp >&5
configure:3379: $? = 0
configure:3427: result: yes
configure:3430: checking for C++ compiler default output file name
configure:3432: result: a.out
configure:3438: checking for suffix of executables
configure:3445: g++44 -o conftest conftest.cpp >&5
configure:3449: $? = 0
configure:3471: result:
configure:3493: checking whether we are cross compiling
configure:3501: g++44 -o conftest conftest.cpp >&5
configure:3505: $? = 0
configure:3512: ./conftest
configure:3516: $? = 0
configure:3531: result: no
configure:3536: checking for suffix of object files
configure:3558: g++44 -c conftest.cpp >&5
configure:3562: $? = 0
configure:3583: result: o
configure:3587: checking whether we are using the GNU C++ compiler
configure:3606: g++44 -c conftest.cpp >&5
configure:3606: $? = 0
configure:3615: result: yes
configure:3624: checking whether g++44 accepts -g
configure:3644: g++44 -c -g conftest.cpp >&5
configure:3644: $? = 0
configure:3685: result: yes
configure:3719: checking for style of include used by make
configure:3747: result: GNU
configure:3773: checking dependency style of g++44
configure:3884: result: gcc3
configure:3912: checking for md5sum
configure:3928: found /usr/bin/md5sum
configure:3939: result: md5sum
configure:4068: checking for gcc
configure:4095: result: gcc44
configure:4324: checking for C compiler version
configure:4333: gcc44 --version >&5
gcc44 (GCC) 4.4.0 20090514 (Red Hat 4.4.0-6)
Copyright (C) 2009 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:4344: $? = 0
configure:4333: gcc44 -v >&5
Using built-in specs.
Target: x86_64-redhat-linux6E
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-languages=c,c++,fortran --disable-libgcj --with-mpfr=/builddir/build/BUILD/gcc-4.4.0-20090514/obj-x86_64-redhat-linux6E/mpfr-install/ --with-ppl=/builddir/build/BUILD/gcc-4.4.0-20090514/obj-x86_64-redhat-linux6E/ppl-install --with-cloog=/builddir/build/BUILD/gcc-4.4.0-20090514/obj-x86_64-redhat-linux6E/cloog-install --with-tune=generic --with-arch_32=i586 --build=x86_64-redhat-linux6E
Thread model: posix
gcc version 4.4.0 20090514 (Red Hat 4.4.0-6) (GCC)
configure:4344: $? = 0
configure:4333: gcc44 -V >&5
gcc44: '-V' option must have argument
configure:4344: $? = 1
configure:4333: gcc44 -qversion >&5
gcc44: unrecognized option '-qversion'
gcc44: no input files
configure:4344: $? = 1
configure:4348: checking whether we are using the GNU C compiler
configure:4367: gcc44 -c conftest.c >&5
configure:4367: $? = 0
configure:4376: result: yes
configure:4385: checking whether gcc44 accepts -g
configure:4405: gcc44 -c -g conftest.c >&5
configure:4405: $? = 0
configure:4446: result: yes
configure:4463: checking for gcc44 option to accept ISO C89
configure:4526: gcc44 -c -g -O2 conftest.c >&5
configure:4526: $? = 0
configure:4539: result: none needed
configure:4561: checking dependency style of gcc44
configure:4672: result: gcc3
configure:4693: checking how to run the C preprocessor
configure:4724: gcc44 -E conftest.c
configure:4724: $? = 0
configure:4738: gcc44 -E conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:4738: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "1.1.4"
| #define PACKAGE_STRING "jellyfish 1.1.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "1.1.4"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4763: result: gcc44 -E
configure:4783: gcc44 -E conftest.c
configure:4783: $? = 0
configure:4797: gcc44 -E conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:4797: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "1.1.4"
| #define PACKAGE_STRING "jellyfish 1.1.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "1.1.4"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4826: checking for grep that handles long lines and -e
configure:4884: result: /bin/grep
configure:4889: checking for egrep
configure:4951: result: /bin/grep -E
configure:4956: checking for ANSI C header files
configure:4976: gcc44 -c -g -O2 conftest.c >&5
configure:4976: $? = 0
configure:5049: gcc44 -o conftest -g -O2 conftest.c >&5
configure:5049: $? = 0
configure:5049: ./conftest
configure:5049: $? = 0
configure:5060: result: yes
configure:5073: checking for sys/types.h
configure:5073: gcc44 -c -g -O2 conftest.c >&5
configure:5073: $? = 0
configure:5073: result: yes
configure:5073: checking for sys/stat.h
configure:5073: gcc44 -c -g -O2 conftest.c >&5
configure:5073: $? = 0
configure:5073: result: yes
configure:5073: checking for stdlib.h
configure:5073: gcc44 -c -g -O2 conftest.c >&5
configure:5073: $? = 0
configure:5073: result: yes
configure:5073: checking for string.h
configure:5073: gcc44 -c -g -O2 conftest.c >&5
configure:5073: $? = 0
configure:5073: result: yes
configure:5073: checking for memory.h
configure:5073: gcc44 -c -g -O2 conftest.c >&5
configure:5073: $? = 0
configure:5073: result: yes
configure:5073: checking for strings.h
configure:5073: gcc44 -c -g -O2 conftest.c >&5
configure:5073: $? = 0
configure:5073: result: yes
configure:5073: checking for inttypes.h
configure:5073: gcc44 -c -g -O2 conftest.c >&5
configure:5073: $? = 0
configure:5073: result: yes
configure:5073: checking for stdint.h
configure:5073: gcc44 -c -g -O2 conftest.c >&5
configure:5073: $? = 0
configure:5073: result: yes
configure:5073: checking for unistd.h
configure:5073: gcc44 -c -g -O2 conftest.c >&5
configure:5073: $? = 0
configure:5073: result: yes
configure:5085: checking whether strerror_r is declared
configure:5085: gcc44 -c -g -O2 conftest.c >&5
configure:5085: $? = 0
configure:5085: result: yes
configure:5098: checking for strerror_r
configure:5098: gcc44 -o conftest -g -O2 conftest.c >&5
configure:5098: $? = 0
configure:5098: result: yes
configure:5107: checking whether strerror_r returns char *
configure:5131: gcc44 -c -g -O2 conftest.c >&5
conftest.c: In function 'main':
conftest.c:61: error: invalid type argument of 'unary *' (have 'int')
conftest.c:62: warning: initialization makes pointer from integer without a cast
configure:5131: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "1.1.4"
| #define PACKAGE_STRING "jellyfish 1.1.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "1.1.4"
| #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_DECL_STRERROR_R 1
| #define HAVE_STRERROR_R 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 ()
| {
|
| char buf[100];
| char x = *strerror_r (0, buf, sizeof buf);
| char *p = strerror_r (0, buf, sizeof buf);
| return !p || x;
|
| ;
| return 0;
| }
configure:5169: result: no
configure:5180: checking execinfo.h usability
configure:5180: gcc44 -c -g -O2 conftest.c >&5
configure:5180: $? = 0
configure:5180: result: yes
configure:5180: checking execinfo.h presence
configure:5180: gcc44 -E conftest.c
configure:5180: $? = 0
configure:5180: result: yes
configure:5180: checking for execinfo.h
configure:5180: result: yes
configure:5191: checking for siginfo_t.si_int
configure:5191: gcc44 -c -g -O2 conftest.c >&5
configure:5191: $? = 0
configure:5191: result: yes
configure:5225: checking for a sed that does not truncate output
configure:5289: result: /bin/sed
configure:5307: checking for fgrep
configure:5369: result: /bin/grep -F
configure:5404: checking for ld used by gcc44
configure:5471: result: /usr/bin/ld
configure:5478: checking if the linker (/usr/bin/ld) is GNU ld
configure:5493: result: yes
configure:5505: checking for BSD- or MS-compatible name lister (nm)
configure:5554: result: /usr/bin/nm -B
configure:5672: checking the name lister (/usr/bin/nm -B) interface
configure:5679: gcc44 -c -g -O2 conftest.c >&5
configure:5682: /usr/bin/nm -B "conftest.o"
configure:5685: output
0000000000000000 B some_variable
configure:5692: result: BSD nm
configure:5695: checking whether ln -s works
configure:5699: result: yes
configure:5707: checking the maximum length of command line arguments
configure:5827: result: 98304
configure:5844: checking whether the shell understands some XSI constructs
configure:5854: result: yes
configure:5858: checking whether the shell understands "+="
configure:5864: result: yes
configure:5899: checking for /usr/bin/ld option to reload object files
configure:5906: result: -r
configure:5975: checking for objdump
configure:5991: found /usr/bin/objdump
configure:6002: result: objdump
configure:6034: checking how to recognize dependent libraries
configure:6230: result: pass_all
configure:6290: checking for ar
configure:6306: found /usr/bin/ar
configure:6317: result: ar
configure:6395: checking for strip
configure:6411: found /usr/bin/strip
configure:6422: result: strip
configure:6494: checking for ranlib
configure:6510: found /usr/bin/ranlib
configure:6521: result: ranlib
configure:6611: checking command to parse /usr/bin/nm -B output from gcc44 object
configure:6729: gcc44 -c -g -O2 conftest.c >&5
configure:6732: $? = 0
configure:6736: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
configure:6739: $? = 0
configure:6793: gcc44 -o conftest -g -O2 conftest.c conftstm.o >&5
configure:6796: $? = 0
configure:6834: result: ok
configure:6929: gcc44 -c -g -O2 conftest.c >&5
configure:6932: $? = 0
configure:7639: checking for dlfcn.h
configure:7639: gcc44 -c -g -O2 conftest.c >&5
configure:7639: $? = 0
configure:7639: result: yes
configure:7764: checking for C++ compiler version
configure:7773: g++44 --version >&5
g++44 (GCC) 4.4.0 20090514 (Red Hat 4.4.0-6)
Copyright (C) 2009 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:7784: $? = 0
configure:7773: g++44 -v >&5
Using built-in specs.
Target: x86_64-redhat-linux6E
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-languages=c,c++,fortran --disable-libgcj --with-mpfr=/builddir/build/BUILD/gcc-4.4.0-20090514/obj-x86_64-redhat-linux6E/mpfr-install/ --with-ppl=/builddir/build/BUILD/gcc-4.4.0-20090514/obj-x86_64-redhat-linux6E/ppl-install --with-cloog=/builddir/build/BUILD/gcc-4.4.0-20090514/obj-x86_64-redhat-linux6E/cloog-install --with-tune=generic --with-arch_32=i586 --build=x86_64-redhat-linux6E
Thread model: posix
gcc version 4.4.0 20090514 (Red Hat 4.4.0-6) (GCC)
configure:7784: $? = 0
configure:7773: g++44 -V >&5
g++44: '-V' option must have argument
configure:7784: $? = 1
configure:7773: g++44 -qversion >&5
g++44: unrecognized option '-qversion'
g++44: no input files
configure:7784: $? = 1
configure:7788: checking whether we are using the GNU C++ compiler
configure:7816: result: yes
configure:7825: checking whether g++44 accepts -g
configure:7886: result: yes
configure:7911: checking dependency style of g++44
configure:8022: result: gcc3
configure:8045: checking how to run the C++ preprocessor
configure:8072: g++44 -E conftest.cpp
configure:8072: $? = 0
configure:8086: g++44 -E conftest.cpp
conftest.cpp:26:28: error: ac_nonexistent.h: No such file or directory
configure:8086: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "1.1.4"
| #define PACKAGE_STRING "jellyfish 1.1.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "1.1.4"
| #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_DECL_STRERROR_R 1
| #define HAVE_STRERROR_R 1
| #define HAVE_EXECINFO_H 1
| #define HAVE_SI_INT 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:8111: result: g++44 -E
configure:8131: g++44 -E conftest.cpp
configure:8131: $? = 0
configure:8145: g++44 -E conftest.cpp
conftest.cpp:26:28: error: ac_nonexistent.h: No such file or directory
configure:8145: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "jellyfish"
| #define PACKAGE_TARNAME "jellyfish"
| #define PACKAGE_VERSION "1.1.4"
| #define PACKAGE_STRING "jellyfish 1.1.4"
| #define PACKAGE_BUGREPORT "gmarcais@umd.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "jellyfish"
| #define VERSION "1.1.4"
| #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_DECL_STRERROR_R 1
| #define HAVE_STRERROR_R 1
| #define HAVE_EXECINFO_H 1
| #define HAVE_SI_INT 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:8351: checking for objdir
configure:8366: result: .libs
configure:8662: checking if gcc44 supports -fno-rtti -fno-exceptions
configure:8680: gcc44 -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:8684: $? = 0
configure:8697: result: no
configure:8717: checking for gcc44 option to produce PIC
configure:8989: result: -fPIC -DPIC
configure:9001: checking if gcc44 PIC flag -fPIC -DPIC works
configure:9019: gcc44 -c -g -O2 -fPIC -DPIC -DPIC conftest.c >&5
configure:9023: $? = 0
configure:9036: result: yes
configure:9060: checking if gcc44 static flag -static works
configure:9088: result: yes
configure:9103: checking if gcc44 supports -c -o file.o
configure:9124: gcc44 -c -g -O2 -o out/conftest2.o conftest.c >&5
configure:9128: $? = 0
configure:9150: result: yes
configure:9158: checking if gcc44 supports -c -o file.o
configure:9205: result: yes
configure:9238: checking whether the gcc44 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:10224: result: yes
configure:10261: checking whether -lc should be explicitly linked in
configure:10266: gcc44 -c -g -O2 conftest.c >&5
configure:10269: $? = 0
configure:10284: gcc44 -shared conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /bin/grep -lc \>/dev/null 2\>\&1
configure:10287: $? = 0
configure:10299: result: no
configure:10463: checking dynamic linker characteristics
configure:10896: gcc44 -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.c >&5
configure:10896: $? = 0
configure:11117: result: GNU/Linux ld.so
configure:11219: checking how to hardcode library paths into programs
configure:11244: result: immediate
configure:11764: checking whether stripping libraries is possible
configure:11769: result: yes
configure:11804: checking if libtool supports shared libraries
configure:11806: result: yes
configure:11809: checking whether to build shared libraries
configure:11830: result: yes
configure:11833: checking whether to build static libraries
configure:11837: result: yes
configure:11987: checking for ld used by g++44
configure:12054: result: /usr/bin/ld -m elf_x86_64
configure:12061: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld
configure:12076: result: yes
configure:12131: checking whether the g++44 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:13044: result: yes
configure:13072: g++44 -c conftest.cpp >&5
configure:13075: $? = 0
configure:13257: checking for g++44 option to produce PIC
configure:13574: result: -fPIC -DPIC
configure:13583: checking if g++44 PIC flag -fPIC -DPIC works
configure:13601: g++44 -c -fPIC -DPIC -DPIC conftest.cpp >&5
configure:13605: $? = 0
configure:13618: result: yes
configure:13639: checking if g++44 static flag -static works
configure:13667: result: yes
configure:13679: checking if g++44 supports -c -o file.o
configure:13700: g++44 -c -o out/conftest2.o conftest.cpp >&5
configure:13704: $? = 0
configure:13726: result: yes
configure:13731: checking if g++44 supports -c -o file.o
configure:13778: result: yes
configure:13808: checking whether the g++44 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:13834: result: yes
configure:13971: checking dynamic linker characteristics
configure:14352: g++44 -o conftest -Wl,-rpath -Wl,/foo conftest.cpp >&5
configure:14352: $? = 0
configure:14573: result: GNU/Linux ld.so
configure:14624: checking how to hardcode library paths into programs
configure:14649: result: immediate
configure:14845: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by jellyfish config.status 1.1.4, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on kolossus
config.status:1133: creating Makefile
config.status:1133: creating tests/compat.sh
config.status:1133: creating jellyfish-1.1.pc
config.status:1133: creating config.h
config.status:1314: config.h is unchanged
config.status:1362: executing depfiles commands
config.status:1362: 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=set
ac_cv_env_CC_value=gcc44
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=set
ac_cv_env_CXX_value=g++44
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_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_strerror_r=yes
ac_cv_func_strerror_r_char_p=no
ac_cv_have_decl_strerror_r=yes
ac_cv_header_dlfcn_h=yes
ac_cv_header_execinfo_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_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='gcc44 -E'
ac_cv_prog_CXXCPP='g++44 -E'
ac_cv_prog_MD5=md5sum
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_CC=gcc44
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
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
am_cv_make_support_nested_variables=yes
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_prog_compiler_c_o=yes
lt_cv_prog_compiler_c_o_CXX=yes
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_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'''
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]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_max_cmd_len=98304
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /cluster/home/jstjohn/src/jsj_Jellyfish/missing --run aclocal-1.11'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='0'
AM_V='$(V)'
AR='ar'
AUTOCONF='${SHELL} /cluster/home/jstjohn/src/jsj_Jellyfish/missing --run autoconf'
AUTOHEADER='${SHELL} /cluster/home/jstjohn/src/jsj_Jellyfish/missing --run autoheader'
AUTOMAKE='${SHELL} /cluster/home/jstjohn/src/jsj_Jellyfish/missing --run automake-1.11'
AWK='gawk'
CC='gcc44'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc44 -E'
CPPFLAGS=''
CXX='g++44'
CXXCPP='g++44 -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS=''
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
DSYMUTIL=''
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
FGREP='/bin/grep -F'
GREP='/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LD='/usr/bin/ld -m elf_x86_64'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LIPO=''
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /cluster/home/jstjohn/src/jsj_Jellyfish/missing --run makeinfo'
MD5='md5sum'
MKDIR_P='/bin/mkdir -p'
NM='/usr/bin/nm -B'
NMEDIT=''
OBJDUMP='objdump'
OBJEXT='o'
OTOOL64=''
OTOOL=''
PACKAGE='jellyfish'
PACKAGE_BUGREPORT='gmarcais@umd.edu'
PACKAGE_NAME='jellyfish'
PACKAGE_STRING='jellyfish 1.1.4'
PACKAGE_TARNAME='jellyfish'
PACKAGE_URL=''
PACKAGE_VERSION='1.1.4'
PATH_SEPARATOR=':'
RANLIB='ranlib'
SED='/bin/sed'
SET_MAKE=''
SHELL='/bin/sh'
STRIP='strip'
VERSION='1.1.4'
ac_ct_CC='gcc44'
ac_ct_CXX=''
ac_ct_DUMPBIN=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep='_no'
am__quote=''
am__tar='$${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='${SHELL} /cluster/home/jstjohn/src/jsj_Jellyfish/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
lt_ECHO='echo'
mandir='${datarootdir}/man'
mkdir_p='/bin/mkdir -p'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/cluster/home/jstjohn'
program_transform_name='s&^&jsj_&'
psdir='${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 "1.1.4"
#define PACKAGE_STRING "jellyfish 1.1.4"
#define PACKAGE_BUGREPORT "gmarcais@umd.edu"
#define PACKAGE_URL ""
#define PACKAGE "jellyfish"
#define VERSION "1.1.4"
#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_DECL_STRERROR_R 1
#define HAVE_STRERROR_R 1
#define HAVE_EXECINFO_H 1
#define HAVE_SI_INT 1
#define HAVE_DLFCN_H 1
#define LT_OBJDIR ".libs/"
configure: exit 0