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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 BamDeal configure 0.22, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure LDFLAGS=-L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ CXXFLAGS=-I/ifshk4/BC_PUB/biosoft/newblc/01.Usr/include/ CFLAGS=-I/include/
## --------- ##
## Platform. ##
## --------- ##
hostname = hk-login-38-2.hk.hpc
uname -m = x86_64
uname -r = 2.6.32-696.el6.x86_64
uname -s = Linux
uname -v = #1 SMP Tue Mar 21 19:29:05 UTC 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: /ifshk4/BC_PUB/biosoft/newblc/04.UsrHgcc/bin
PATH: /ifshk4/BC_PUB/biosoft/newblc/01.Usr/bin
PATH: /ifshk7/BC_PAP/PROJECT/F13HPCAPKF0126_LEGvaoR/bin/RAD_NPGT/bin/
PATH: /opt/openmpi/bin
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: /opt/bio/ncbi/bin
PATH: /opt/bio/mpiblast/bin
PATH: /opt/bio/EMBOSS/bin
PATH: /opt/bio/clustalw/bin
PATH: /opt/bio/tcoffee/bin
PATH: /opt/bio/hmmer/bin
PATH: /opt/bio/phylip/exe
PATH: /opt/bio/mrbayes
PATH: /opt/bio/fasta
PATH: /opt/bio/glimmer/bin
PATH: /opt/bio/glimmer/scripts
PATH: /opt/bio/gromacs/bin
PATH: /opt/bio/gmap/bin
PATH: /opt/bio/tigr/bin
PATH: /opt/bio/autodocksuite/bin
PATH: /opt/bio/wgs/bin
PATH: /opt/ganglia/bin
PATH: /opt/ganglia/sbin
PATH: /usr/java/latest/bin
PATH: /opt/pdsh/bin
PATH: /opt/rocks/bin
PATH: /opt/rocks/sbin
PATH: /opt/condor/bin
PATH: /opt/condor/sbin
PATH: /opt/gridengine/bin/linux-x64
PATH: /home/heweiming/bin
PATH: /ifshk7/BC_PAP/PROJECT/F13HPCAPKF0126_LEGvaoR/bin/RAD_NPGT/bin/
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2413: checking for a BSD-compatible install
configure:2481: result: /usr/bin/install -c
configure:2492: checking whether build environment is sane
configure:2542: result: yes
configure:2683: checking for a thread-safe mkdir -p
configure:2722: result: /bin/mkdir -p
configure:2735: checking for gawk
configure:2751: found /bin/gawk
configure:2762: result: gawk
configure:2773: checking whether make sets $(MAKE)
configure:2795: result: yes
configure:2883: checking for gawk
configure:2910: result: gawk
configure:2979: checking for g++
configure:2995: found /ifshk4/BC_PUB/biosoft/newblc/04.UsrHgcc/bin/g++
configure:3006: result: g++
configure:3033: checking for C++ compiler version
configure:3042: g++ --version >&5
g++ (GCC) 6.4.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3053: $? = 0
configure:3042: g++ -v >&5
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/ifshk4/BC_PUB/biosoft/newblc/04.UsrHgcc/libexec/gcc/x86_64-pc-linux-gnu/6.4.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ./configure --prefix=/ifshk4/BC_PUB/biosoft/newblc/04.UsrHgcc --with-gmp=/ifshk4/BC_PUB/biosoft/newblc/01.Usr --with-mpc=/ifshk4/BC_PUB/biosoft/newblc/01.Usr --with-mpfr=/ifshk4/BC_PUB/biosoft/newblc/01.Usr -enable-checking=release -enable-languages=c,c++,fortran,go,objc,obj-c++,java -disable-multilib
Thread model: posix
gcc version 6.4.0 (GCC)
configure:3053: $? = 0
configure:3042: g++ -V >&5
g++: error: unrecognized command line option '-V'
g++: fatal error: no input files
compilation terminated.
configure:3053: $? = 1
configure:3042: g++ -qversion >&5
g++: error: unrecognized command line option '-qversion'; did you mean '--version'?
g++: fatal error: no input files
compilation terminated.
configure:3053: $? = 1
configure:3073: checking whether the C++ compiler works
configure:3095: g++ -I/ifshk4/BC_PUB/biosoft/newblc/01.Usr/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.cpp >&5
configure:3099: $? = 0
configure:3147: result: yes
configure:3150: checking for C++ compiler default output file name
configure:3152: result: a.out
configure:3158: checking for suffix of executables
configure:3165: g++ -o conftest -I/ifshk4/BC_PUB/biosoft/newblc/01.Usr/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.cpp >&5
configure:3169: $? = 0
configure:3191: result:
configure:3213: checking whether we are cross compiling
configure:3221: g++ -o conftest -I/ifshk4/BC_PUB/biosoft/newblc/01.Usr/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.cpp >&5
configure:3225: $? = 0
configure:3232: ./conftest
configure:3236: $? = 0
configure:3251: result: no
configure:3256: checking for suffix of object files
configure:3278: g++ -c -I/ifshk4/BC_PUB/biosoft/newblc/01.Usr/include/ conftest.cpp >&5
configure:3282: $? = 0
configure:3303: result: o
configure:3307: checking whether we are using the GNU C++ compiler
configure:3326: g++ -c -I/ifshk4/BC_PUB/biosoft/newblc/01.Usr/include/ conftest.cpp >&5
configure:3326: $? = 0
configure:3335: result: yes
configure:3344: checking whether g++ accepts -g
configure:3364: g++ -c -g conftest.cpp >&5
configure:3364: $? = 0
configure:3405: result: yes
configure:3439: checking for style of include used by make
configure:3467: result: GNU
configure:3492: checking dependency style of g++
configure:3602: result: gcc3
configure:3671: checking for gcc
configure:3687: found /ifshk4/BC_PUB/biosoft/newblc/04.UsrHgcc/bin/gcc
configure:3698: result: gcc
configure:3729: checking for C compiler version
configure:3738: gcc --version >&5
gcc (GCC) 6.4.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3749: $? = 0
configure:3738: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/ifshk4/BC_PUB/biosoft/newblc/04.UsrHgcc/libexec/gcc/x86_64-pc-linux-gnu/6.4.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ./configure --prefix=/ifshk4/BC_PUB/biosoft/newblc/04.UsrHgcc --with-gmp=/ifshk4/BC_PUB/biosoft/newblc/01.Usr --with-mpc=/ifshk4/BC_PUB/biosoft/newblc/01.Usr --with-mpfr=/ifshk4/BC_PUB/biosoft/newblc/01.Usr -enable-checking=release -enable-languages=c,c++,fortran,go,objc,obj-c++,java -disable-multilib
Thread model: posix
gcc version 6.4.0 (GCC)
configure:3749: $? = 0
configure:3738: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3749: $? = 1
configure:3738: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'; did you mean '--version'?
gcc: fatal error: no input files
compilation terminated.
configure:3749: $? = 1
configure:3753: checking whether we are using the GNU C compiler
configure:3772: gcc -c -I/include/ conftest.c >&5
configure:3772: $? = 0
configure:3781: result: yes
configure:3790: checking whether gcc accepts -g
configure:3810: gcc -c -g conftest.c >&5
configure:3810: $? = 0
configure:3851: result: yes
configure:3868: checking for gcc option to accept ISO C89
configure:3931: gcc -c -I/include/ conftest.c >&5
configure:3931: $? = 0
configure:3944: result: none needed
configure:3966: checking dependency style of gcc
configure:4076: result: gcc3
configure:4096: checking how to run the C preprocessor
configure:4127: gcc -E conftest.c
configure:4127: $? = 0
configure:4141: gcc -E conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^
compilation terminated.
configure:4141: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BamDeal"
| #define PACKAGE_TARNAME "bamdeal"
| #define PACKAGE_VERSION "0.22"
| #define PACKAGE_STRING "BamDeal 0.22"
| #define PACKAGE_BUGREPORT "hewm2008@qq.com"
| #define PACKAGE_URL ""
| #define PACKAGE "BamDeal"
| #define VERSION "0.22"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4166: result: gcc -E
configure:4186: gcc -E conftest.c
configure:4186: $? = 0
configure:4200: gcc -E conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^
compilation terminated.
configure:4200: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BamDeal"
| #define PACKAGE_TARNAME "bamdeal"
| #define PACKAGE_VERSION "0.22"
| #define PACKAGE_STRING "BamDeal 0.22"
| #define PACKAGE_BUGREPORT "hewm2008@qq.com"
| #define PACKAGE_URL ""
| #define PACKAGE "BamDeal"
| #define VERSION "0.22"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4228: checking whether ln -s works
configure:4232: result: yes
configure:4239: checking whether make sets $(MAKE)
configure:4261: result: yes
configure:4313: checking for ranlib
configure:4329: found /usr/bin/ranlib
configure:4340: result: ranlib
configure:4366: checking for main in -lz
configure:4385: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lz >&5
configure:4385: $? = 0
configure:4394: result: yes
configure:4409: checking for main in -lhts
configure:4428: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
configure:4428: $? = 0
configure:4437: result: yes
configure:4455: checking for grep that handles long lines and -e
configure:4513: result: /bin/grep
configure:4518: checking for egrep
configure:4580: result: /bin/grep -E
configure:4585: checking for ANSI C header files
configure:4605: gcc -c -I/include/ conftest.c >&5
configure:4605: $? = 0
configure:4678: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
configure:4678: $? = 0
configure:4678: ./conftest
configure:4678: $? = 0
configure:4689: result: yes
configure:4702: checking for sys/types.h
configure:4702: gcc -c -I/include/ conftest.c >&5
configure:4702: $? = 0
configure:4702: result: yes
configure:4702: checking for sys/stat.h
configure:4702: gcc -c -I/include/ conftest.c >&5
configure:4702: $? = 0
configure:4702: result: yes
configure:4702: checking for stdlib.h
configure:4702: gcc -c -I/include/ conftest.c >&5
configure:4702: $? = 0
configure:4702: result: yes
configure:4702: checking for string.h
configure:4702: gcc -c -I/include/ conftest.c >&5
configure:4702: $? = 0
configure:4702: result: yes
configure:4702: checking for memory.h
configure:4702: gcc -c -I/include/ conftest.c >&5
configure:4702: $? = 0
configure:4702: result: yes
configure:4702: checking for strings.h
configure:4702: gcc -c -I/include/ conftest.c >&5
configure:4702: $? = 0
configure:4702: result: yes
configure:4702: checking for inttypes.h
configure:4702: gcc -c -I/include/ conftest.c >&5
configure:4702: $? = 0
configure:4702: result: yes
configure:4702: checking for stdint.h
configure:4702: gcc -c -I/include/ conftest.c >&5
configure:4702: $? = 0
configure:4702: result: yes
configure:4702: checking for unistd.h
configure:4702: gcc -c -I/include/ conftest.c >&5
configure:4702: $? = 0
configure:4702: result: yes
configure:4716: checking zlib.h usability
configure:4716: gcc -c -I/include/ conftest.c >&5
configure:4716: $? = 0
configure:4716: result: yes
configure:4716: checking zlib.h presence
configure:4716: gcc -E conftest.c
configure:4716: $? = 0
configure:4716: result: yes
configure:4716: checking for zlib.h
configure:4716: result: yes
configure:4731: checking htslib/sam.h usability
configure:4731: gcc -c -I/include/ conftest.c >&5
configure:4731: $? = 0
configure:4731: result: yes
configure:4731: checking htslib/sam.h presence
configure:4731: gcc -E conftest.c
configure:4731: $? = 0
configure:4731: result: yes
configure:4731: checking for htslib/sam.h
configure:4731: result: yes
configure:4731: checking htslib/kseq.h usability
configure:4731: gcc -c -I/include/ conftest.c >&5
configure:4731: $? = 0
configure:4731: result: yes
configure:4731: checking htslib/kseq.h presence
configure:4731: gcc -E conftest.c
configure:4731: $? = 0
configure:4731: result: yes
configure:4731: checking for htslib/kseq.h
configure:4731: result: yes
configure:4731: checking for zlib.h
configure:4731: result: yes
configure:4731: checking htslib/kstring.h usability
configure:4731: gcc -c -I/include/ conftest.c >&5
configure:4731: $? = 0
configure:4731: result: yes
configure:4731: checking htslib/kstring.h presence
configure:4731: gcc -E conftest.c
configure:4731: $? = 0
configure:4731: result: yes
configure:4731: checking for htslib/kstring.h
configure:4731: result: yes
configure:4731: checking for stdlib.h
configure:4731: result: yes
configure:4731: checking for string.h
configure:4731: result: yes
configure:4731: checking for unistd.h
configure:4731: result: yes
configure:4743: checking for htslib/kseq.h
configure:4743: result: yes
configure:4757: checking for htslib/sam.h
configure:4757: result: yes
configure:4771: checking for htslib/kstring.h
configure:4771: result: yes
configure:4786: checking for stdbool.h that conforms to C99
configure:4853: gcc -c -I/include/ conftest.c >&5
configure:4853: $? = 0
configure:4860: result: yes
configure:4862: checking for _Bool
configure:4862: gcc -c -I/include/ conftest.c >&5
configure:4862: $? = 0
configure:4862: gcc -c -I/include/ conftest.c >&5
conftest.c: In function 'main':
conftest.c:70:20: error: expected expression before ')' token
if (sizeof ((_Bool)))
^
configure:4862: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BamDeal"
| #define PACKAGE_TARNAME "bamdeal"
| #define PACKAGE_VERSION "0.22"
| #define PACKAGE_STRING "BamDeal 0.22"
| #define PACKAGE_BUGREPORT "hewm2008@qq.com"
| #define PACKAGE_URL ""
| #define PACKAGE "BamDeal"
| #define VERSION "0.22"
| #define HAVE_LIBZ 1
| #define HAVE_LIBHTS 1
| #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_ZLIB_H 1
| #define HAVE_HTSLIB_SAM_H 1
| #define HAVE_HTSLIB_KSEQ_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_HTSLIB_KSTRING_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_HTSLIB_KSEQ_H 1
| #define HAVE_HTSLIB_SAM_H 1
| #define HAVE_HTSLIB_KSTRING_H 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((_Bool)))
| return 0;
| ;
| return 0;
| }
configure:4862: result: yes
configure:4873: checking for inline
configure:4889: gcc -c -I/include/ conftest.c >&5
configure:4889: $? = 0
configure:4897: result: inline
configure:4915: checking for int32_t
configure:4915: gcc -c -I/include/ conftest.c >&5
configure:4915: $? = 0
configure:4915: gcc -c -I/include/ conftest.c >&5
conftest.c: In function 'main':
conftest.c:73:53: warning: integer overflow in expression [-Woverflow]
< (int32_t) (((((int32_t) 1 << N) << N) - 1) * 2 + 2))];
^
conftest.c:72:12: error: storage size of 'test_array' isn't constant
static int test_array [1 - 2 * !((int32_t) (((((int32_t) 1 << N) << N) - 1) * 2 + 1)
^~~~~~~~~~
configure:4915: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BamDeal"
| #define PACKAGE_TARNAME "bamdeal"
| #define PACKAGE_VERSION "0.22"
| #define PACKAGE_STRING "BamDeal 0.22"
| #define PACKAGE_BUGREPORT "hewm2008@qq.com"
| #define PACKAGE_URL ""
| #define PACKAGE "BamDeal"
| #define VERSION "0.22"
| #define HAVE_LIBZ 1
| #define HAVE_LIBHTS 1
| #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_ZLIB_H 1
| #define HAVE_HTSLIB_SAM_H 1
| #define HAVE_HTSLIB_KSEQ_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_HTSLIB_KSTRING_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_HTSLIB_KSEQ_H 1
| #define HAVE_HTSLIB_SAM_H 1
| #define HAVE_HTSLIB_KSTRING_H 1
| #define HAVE__BOOL 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| enum { N = 32 / 2 - 1 };
| int
| main ()
| {
| static int test_array [1 - 2 * !((int32_t) (((((int32_t) 1 << N) << N) - 1) * 2 + 1)
| < (int32_t) (((((int32_t) 1 << N) << N) - 1) * 2 + 2))];
| test_array [0] = 0;
| return test_array [0];
|
| ;
| return 0;
| }
configure:4915: result: yes
configure:4926: checking for size_t
configure:4926: gcc -c -I/include/ conftest.c >&5
configure:4926: $? = 0
configure:4926: gcc -c -I/include/ conftest.c >&5
conftest.c: In function 'main':
conftest.c:71:21: error: expected expression before ')' token
if (sizeof ((size_t)))
^
configure:4926: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BamDeal"
| #define PACKAGE_TARNAME "bamdeal"
| #define PACKAGE_VERSION "0.22"
| #define PACKAGE_STRING "BamDeal 0.22"
| #define PACKAGE_BUGREPORT "hewm2008@qq.com"
| #define PACKAGE_URL ""
| #define PACKAGE "BamDeal"
| #define VERSION "0.22"
| #define HAVE_LIBZ 1
| #define HAVE_LIBHTS 1
| #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_ZLIB_H 1
| #define HAVE_HTSLIB_SAM_H 1
| #define HAVE_HTSLIB_KSEQ_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_HTSLIB_KSTRING_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_HTSLIB_KSEQ_H 1
| #define HAVE_HTSLIB_SAM_H 1
| #define HAVE_HTSLIB_KSTRING_H 1
| #define HAVE__BOOL 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((size_t)))
| return 0;
| ;
| return 0;
| }
configure:4926: result: yes
configure:4937: checking for uint32_t
configure:4937: gcc -c -I/include/ conftest.c >&5
configure:4937: $? = 0
configure:4937: result: yes
configure:4951: checking for uint8_t
configure:4951: gcc -c -I/include/ conftest.c >&5
configure:4951: $? = 0
configure:4951: result: yes
configure:4971: checking for stdlib.h
configure:4971: result: yes
configure:4981: checking for GNU libc compatible malloc
configure:5005: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
configure:5005: $? = 0
configure:5005: ./conftest
configure:5005: $? = 0
configure:5015: result: yes
configure:5038: checking for stdlib.h
configure:5038: result: yes
configure:5048: checking for GNU libc compatible realloc
configure:5072: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
configure:5072: $? = 0
configure:5072: ./conftest
configure:5072: $? = 0
configure:5082: result: yes
configure:5106: checking for memset
configure:5106: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
conftest.c:62:6: warning: conflicting types for built-in function 'memset'
char memset ();
^~~~~~
configure:5106: $? = 0
configure:5106: result: yes
configure:5106: checking for regcomp
configure:5106: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
configure:5106: $? = 0
configure:5106: result: yes
configure:5106: checking for sqrt
configure:5106: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
conftest.c:64:6: warning: conflicting types for built-in function 'sqrt'
char sqrt ();
^~~~
configure:5106: $? = 0
configure:5106: result: yes
configure:5106: checking for strdup
configure:5106: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
conftest.c:65:6: warning: conflicting types for built-in function 'strdup'
char strdup ();
^~~~~~
configure:5106: $? = 0
configure:5106: result: yes
configure:5106: checking for strncasecmp
configure:5106: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
conftest.c:66:6: warning: conflicting types for built-in function 'strncasecmp'
char strncasecmp ();
^~~~~~~~~~~
configure:5106: $? = 0
configure:5106: result: yes
configure:5106: checking for strtol
configure:5106: gcc -o conftest -I/include/ -L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/ conftest.c -lhts -lz >&5
configure:5106: $? = 0
configure:5106: result: yes
configure:5255: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by BamDeal config.status 0.22, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on hk-login-38-2.hk.hpc
config.status:879: creating Makefile
config.status:879: creating config.h
config.status:1108: executing depfiles commands
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_c_compiler_gnu=yes
ac_cv_c_inline=inline
ac_cv_c_int32_t=yes
ac_cv_c_uint32_t=yes
ac_cv_c_uint8_t=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value=-I/include/
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXFLAGS_set=set
ac_cv_env_CXXFLAGS_value=-I/ifshk4/BC_PUB/biosoft/newblc/01.Usr/include/
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value=-L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_memset=yes
ac_cv_func_realloc_0_nonnull=yes
ac_cv_func_regcomp=yes
ac_cv_func_sqrt=yes
ac_cv_func_strdup=yes
ac_cv_func_strncasecmp=yes
ac_cv_func_strtol=yes
ac_cv_header_htslib_kseq_h=yes
ac_cv_header_htslib_kstring_h=yes
ac_cv_header_htslib_sam_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdbool_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_header_zlib_h=yes
ac_cv_lib_hts_main=yes
ac_cv_lib_z_main=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_CPP='gcc -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_type__Bool=yes
ac_cv_type_size_t=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /ifshk7/BC_PS/heweiming/06.Delelop/BamDeal-0.21/missing --run aclocal-1.11'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /ifshk7/BC_PS/heweiming/06.Delelop/BamDeal-0.21/missing --run tar'
AUTOCONF='${SHELL} /ifshk7/BC_PS/heweiming/06.Delelop/BamDeal-0.21/missing --run autoconf'
AUTOHEADER='${SHELL} /ifshk7/BC_PS/heweiming/06.Delelop/BamDeal-0.21/missing --run autoheader'
AUTOMAKE='${SHELL} /ifshk7/BC_PS/heweiming/06.Delelop/BamDeal-0.21/missing --run automake-1.11'
AWK='gawk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-I/include/'
CPP='gcc -E'
CPPFLAGS=''
CXX='g++'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-I/ifshk4/BC_PUB/biosoft/newblc/01.Usr/include/'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS='-L/ifshk4/BC_PUB/biosoft/newblc/01.Usr/lib/'
LIBOBJS=''
LIBS='-lhts -lz '
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /ifshk7/BC_PS/heweiming/06.Delelop/BamDeal-0.21/missing --run makeinfo'
MKDIR_P='/bin/mkdir -p'
OBJEXT='o'
PACKAGE='BamDeal'
PACKAGE_BUGREPORT='hewm2008@qq.com'
PACKAGE_NAME='BamDeal'
PACKAGE_STRING='BamDeal 0.22'
PACKAGE_TARNAME='bamdeal'
PACKAGE_URL=''
PACKAGE_VERSION='0.22'
PATH_SEPARATOR=':'
RANLIB='ranlib'
SET_MAKE=''
SHELL='/bin/sh'
STRIP=''
VERSION='0.22'
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} /ifshk7/BC_PS/heweiming/06.Delelop/BamDeal-0.21/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='/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 "BamDeal"
#define PACKAGE_TARNAME "bamdeal"
#define PACKAGE_VERSION "0.22"
#define PACKAGE_STRING "BamDeal 0.22"
#define PACKAGE_BUGREPORT "hewm2008@qq.com"
#define PACKAGE_URL ""
#define PACKAGE "BamDeal"
#define VERSION "0.22"
#define HAVE_LIBZ 1
#define HAVE_LIBHTS 1
#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_ZLIB_H 1
#define HAVE_HTSLIB_SAM_H 1
#define HAVE_HTSLIB_KSEQ_H 1
#define HAVE_ZLIB_H 1
#define HAVE_HTSLIB_KSTRING_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_UNISTD_H 1
#define HAVE_HTSLIB_KSEQ_H 1
#define HAVE_HTSLIB_SAM_H 1
#define HAVE_HTSLIB_KSTRING_H 1
#define HAVE__BOOL 1
#define HAVE_STDLIB_H 1
#define HAVE_MALLOC 1
#define HAVE_STDLIB_H 1
#define HAVE_REALLOC 1
#define HAVE_MEMSET 1
#define HAVE_REGCOMP 1
#define HAVE_SQRT 1
#define HAVE_STRDUP 1
#define HAVE_STRNCASECMP 1
#define HAVE_STRTOL 1
configure: exit 0
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by BamDeal config.status 0.22, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status config.h
on hk-login-38-2.hk.hpc
config.status:879: creating config.h
config.status:1060: config.h is unchanged