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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 BatMeth configure 2.00(mmx), which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure
## --------- ##
## Platform. ##
## --------- ##
hostname = login
uname -m = x86_64
uname -r = 2.6.32-504.el6.x86_64
uname -s = Linux
uname -v = #1 SMP Wed Oct 15 04:27:16 UTC 2014
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /public/home/qwzhou/anaconda3/bin
PATH: /public/home/qwzhou/software_devp/git-lfs-pack
PATH: /public/home/qwzhou/software/pigz/
PATH: /public/home/qwzhou/scheng/test/software/gatk
PATH: /public/home/qwzhou/scheng/test/software/FastUniq/source
PATH: /public/home/qwzhou/software/bsalign
PATH: /public/home/qwzhou/software/ucsc_tools/
PATH: /public/home/qwzhou/software/qualimap_v2.2/
PATH: /public/home/qwzhou/software/hisat2-2.1.0/
PATH: /public/home/qwzhou/software/parallel-20190122/bin
PATH: /public/home/qwzhou/software/autoconf-2.69/bin
PATH: /public/home/qwzhou/software/axel/bin/
PATH: /public/home/qwzhou/software_devp/methyhaplo/bin
PATH: /public/home/qwzhou/software/fastp/
PATH: /public/home/qwzhou/localperlv5.8/bin
PATH: /public/home/qwzhou/software/emase/scripts
PATH: /public/home/qwzhou/software_devp/batmeth2-run/bin
PATH: /public/home/qwzhou/software/biscuit
PATH: /public/home/qwzhou/software/jdk1.8.0_172/bin
PATH: /public/home/qwzhou/software/hisat2-2.1.0
PATH: /public/home/qwzhou/software/CrossMap-0.2.9/public/home/qwzhou/anaconda/bin/
PATH: /public/home/qwzhou/software/SNPsplit_v0.3.2
PATH: /public/home/qwzhou/software/bedtools2/bin
PATH: /public/home/qwzhou/software/aseq-v1.1.11/
PATH: /public/home/qwzhou/software/bwa-meth-master
PATH: /public/home/qwzhou/software/R-3.4.3/bin
PATH: /public/home/qwzhou/software/HapCUT2/build
PATH: /public/home/qwzhou/software/R-3.4.3/bin
PATH: /public/home/qwzhou/software/packagesR
PATH: /public/home/qwzhou/software/packagesR/bin
PATH: /public/home/qwzhou/software/cgmaptools
PATH: /public/home/qwzhou/software/cgmaptools/bin
PATH: /public/home/qwzhou/software/vcftools_0.1.13/bin
PATH: /public/home/qwzhou/software/bwa-0.7.13
PATH: /public/home/qwzhou/software/bowtie-1.1.2
PATH: /public/home/qwzhou/software/bowtie2-2.3.3.1-linux-x86_64
PATH: /public/home/qwzhou/software/bcftools-1.2
PATH: /public/home/qwzhou/software/samtools-1.3.1
PATH: /public/home/qwzhou/software/bsmooth-align-0.8.1/bin
PATH: /public/home/qwzhou/software/bsmap-2.74
PATH: /public/home/qwzhou/software/Bismark_v0.19.0
PATH: /public/home/qwzhou/software/sratoolkit.2.9.2-ubuntu64/bin/
PATH: /public/home/qwzhou/.aspera/connect/bin
PATH: /public/home/qwzhou/software/FastQC
PATH: /public/home/qwzhou/software/HiC-Pro_2.9.0/bin
PATH: /public/home/qwzhou/mnliu/software/HiCPlotter-master
PATH: /usr/lib64/qt-3.3/bin
PATH: /public/software/mpi/openmpi/1.6.5/intel/bin
PATH: /public/software/mpi/openmpi/1.6.5/gnu/bin
PATH: /opt/gridview//pbs/dispatcher-sched/bin
PATH: /opt/gridview//pbs/dispatcher-sched/sbin
PATH: /opt/gridview//pbs/dispatcher/bin/lsf_cmd
PATH: /opt/gridview//pbs/dispatcher/bin
PATH: /opt/gridview//pbs/dispatcher/sbin
PATH: /public/software/compiler/intel/composer_xe_2013_sp1.0.080/bin/intel64
PATH: /opt/clusconf/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /sbin
PATH: /opt/ibutils/bin
PATH: /public/home/qwzhou/software/jdk1.8.0_172/bin
PATH: /public/home/qwzhou/software/jdk1.8.0_172/jre/bin
PATH: /public/home/zjwang/software/zjwang_tools
PATH: /public/home/qwzhou/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2281: checking for a BSD-compatible install
configure:2349: result: /usr/bin/install -c
configure:2360: checking whether build environment is sane
configure:2410: result: yes
configure:2551: checking for a thread-safe mkdir -p
configure:2590: result: /bin/mkdir -p
configure:2603: checking for gawk
configure:2619: found /bin/gawk
configure:2630: result: gawk
configure:2641: checking whether make sets $(MAKE)
configure:2663: result: yes
configure:2806: checking for g++
configure:2822: found /usr/bin/g++
configure:2833: result: g++
configure:2860: checking for C++ compiler version
configure:2869: g++ --version >&5
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
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:2880: $? = 0
configure:2869: 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 4.4.7-23) (GCC)
configure:2880: $? = 0
configure:2869: g++ -V >&5
g++: '-V' option must have argument
configure:2880: $? = 1
configure:2869: g++ -qversion >&5
g++: unrecognized option '-qversion'
g++: no input files
configure:2880: $? = 1
configure:2900: checking whether the C++ compiler works
configure:2922: g++ -L/public/home/qwzhou/software/packagesR/lib conftest.cpp >&5
configure:2926: $? = 0
configure:2974: result: yes
configure:2977: checking for C++ compiler default output file name
configure:2979: result: a.out
configure:2985: checking for suffix of executables
configure:2992: g++ -o conftest -L/public/home/qwzhou/software/packagesR/lib conftest.cpp >&5
configure:2996: $? = 0
configure:3018: result:
configure:3040: checking whether we are cross compiling
configure:3048: g++ -o conftest -L/public/home/qwzhou/software/packagesR/lib conftest.cpp >&5
configure:3052: $? = 0
configure:3059: ./conftest
configure:3063: $? = 0
configure:3078: result: no
configure:3083: checking for suffix of object files
configure:3105: g++ -c conftest.cpp >&5
configure:3109: $? = 0
configure:3130: result: o
configure:3134: checking whether we are using the GNU C++ compiler
configure:3153: g++ -c conftest.cpp >&5
configure:3153: $? = 0
configure:3162: result: yes
configure:3171: checking whether g++ accepts -g
configure:3191: g++ -c -g conftest.cpp >&5
configure:3191: $? = 0
configure:3232: result: yes
configure:3266: checking for style of include used by make
configure:3294: result: GNU
configure:3319: checking dependency style of g++
configure:3429: result: gcc3
configure:3492: checking for gcc
configure:3508: found /usr/bin/gcc
configure:3519: result: gcc
configure:3748: checking for C compiler version
configure:3757: gcc --version >&5
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
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:3768: $? = 0
configure:3757: 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 4.4.7-23) (GCC)
configure:3768: $? = 0
configure:3757: gcc -V >&5
gcc: '-V' option must have argument
configure:3768: $? = 1
configure:3757: gcc -qversion >&5
gcc: unrecognized option '-qversion'
gcc: no input files
configure:3768: $? = 1
configure:3772: checking whether we are using the GNU C compiler
configure:3791: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:3791: $? = 0
configure:3800: result: yes
configure:3809: checking whether gcc accepts -g
configure:3829: gcc -c -g conftest.c >&5
configure:3829: $? = 0
configure:3870: result: yes
configure:3887: checking for gcc option to accept ISO C89
configure:3950: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:3950: $? = 0
configure:3963: result: none needed
configure:3985: checking dependency style of gcc
configure:4095: result: gcc3
configure:4120: checking how to run the C preprocessor
configure:4151: gcc -E conftest.c
configure:4151: $? = 0
configure:4165: gcc -E conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:4165: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BatMeth"
| #define PACKAGE_TARNAME "batmeth"
| #define PACKAGE_VERSION "2.00(mmx)"
| #define PACKAGE_STRING "BatMeth 2.00(mmx)"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL ""
| #define PACKAGE "BatMeth"
| #define VERSION "2.00_mmx"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4190: result: gcc -E
configure:4210: gcc -E conftest.c
configure:4210: $? = 0
configure:4224: gcc -E conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:4224: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BatMeth"
| #define PACKAGE_TARNAME "batmeth"
| #define PACKAGE_VERSION "2.00(mmx)"
| #define PACKAGE_STRING "BatMeth 2.00(mmx)"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL ""
| #define PACKAGE "BatMeth"
| #define VERSION "2.00_mmx"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4253: checking for grep that handles long lines and -e
configure:4311: result: /bin/grep
configure:4316: checking for egrep
configure:4378: result: /bin/grep -E
configure:4383: checking for ANSI C header files
configure:4403: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4403: $? = 0
configure:4476: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
configure:4476: $? = 0
configure:4476: ./conftest
configure:4476: $? = 0
configure:4487: result: yes
configure:4500: checking for sys/types.h
configure:4500: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4500: $? = 0
configure:4500: result: yes
configure:4500: checking for sys/stat.h
configure:4500: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4500: $? = 0
configure:4500: result: yes
configure:4500: checking for stdlib.h
configure:4500: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4500: $? = 0
configure:4500: result: yes
configure:4500: checking for string.h
configure:4500: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4500: $? = 0
configure:4500: result: yes
configure:4500: checking for memory.h
configure:4500: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4500: $? = 0
configure:4500: result: yes
configure:4500: checking for strings.h
configure:4500: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4500: $? = 0
configure:4500: result: yes
configure:4500: checking for inttypes.h
configure:4500: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4500: $? = 0
configure:4500: result: yes
configure:4500: checking for stdint.h
configure:4500: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4500: $? = 0
configure:4500: result: yes
configure:4500: checking for unistd.h
configure:4500: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4500: $? = 0
configure:4500: result: yes
configure:4515: checking limits.h usability
configure:4515: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking limits.h presence
configure:4515: gcc -E conftest.c
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking for limits.h
configure:4515: result: yes
configure:4515: checking malloc.h usability
configure:4515: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking malloc.h presence
configure:4515: gcc -E conftest.c
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking for malloc.h
configure:4515: result: yes
configure:4515: checking stddef.h usability
configure:4515: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking stddef.h presence
configure:4515: gcc -E conftest.c
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking for stddef.h
configure:4515: result: yes
configure:4515: checking for stdint.h
configure:4515: result: yes
configure:4515: checking for stdlib.h
configure:4515: result: yes
configure:4515: checking for string.h
configure:4515: result: yes
configure:4515: checking sys/socket.h usability
configure:4515: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking sys/socket.h presence
configure:4515: gcc -E conftest.c
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking for sys/socket.h
configure:4515: result: yes
configure:4515: checking sys/time.h usability
configure:4515: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking sys/time.h presence
configure:4515: gcc -E conftest.c
configure:4515: $? = 0
configure:4515: result: yes
configure:4515: checking for sys/time.h
configure:4515: result: yes
configure:4515: checking for unistd.h
configure:4515: result: yes
configure:4527: checking for an ANSI C-conforming const
configure:4593: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4593: $? = 0
configure:4600: result: yes
configure:4608: checking for size_t
configure:4608: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4608: $? = 0
configure:4608: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:66: error: expected expression before ')' token
configure:4608: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BatMeth"
| #define PACKAGE_TARNAME "batmeth"
| #define PACKAGE_VERSION "2.00(mmx)"
| #define PACKAGE_STRING "BatMeth 2.00(mmx)"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL ""
| #define PACKAGE "BatMeth"
| #define VERSION "2.00_mmx"
| #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_LIMITS_H 1
| #define HAVE_MALLOC_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_SYS_SOCKET_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_UNISTD_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 ((size_t)))
| return 0;
| ;
| return 0;
| }
configure:4608: result: yes
configure:4619: checking whether time.h and sys/time.h may both be included
configure:4639: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4639: $? = 0
configure:4646: result: yes
configure:4654: checking for working volatile
configure:4673: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4673: $? = 0
configure:4680: result: yes
configure:4688: checking for ptrdiff_t
configure:4688: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
configure:4688: $? = 0
configure:4688: gcc -c -I/public/home/qwzhou/software/packagesR/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:67: error: expected expression before ')' token
configure:4688: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BatMeth"
| #define PACKAGE_TARNAME "batmeth"
| #define PACKAGE_VERSION "2.00(mmx)"
| #define PACKAGE_STRING "BatMeth 2.00(mmx)"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL ""
| #define PACKAGE "BatMeth"
| #define VERSION "2.00_mmx"
| #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_LIMITS_H 1
| #define HAVE_MALLOC_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_SYS_SOCKET_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_UNISTD_H 1
| #define TIME_WITH_SYS_TIME 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((ptrdiff_t)))
| return 0;
| ;
| return 0;
| }
configure:4688: result: yes
configure:4702: checking for stdlib.h
configure:4702: result: yes
configure:4712: checking for GNU libc compatible malloc
configure:4736: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
configure:4736: $? = 0
configure:4736: ./conftest
configure:4736: $? = 0
configure:4746: result: yes
configure:4769: checking for stdlib.h
configure:4769: result: yes
configure:4779: checking for GNU libc compatible realloc
configure:4803: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
configure:4803: $? = 0
configure:4803: ./conftest
configure:4803: $? = 0
configure:4813: result: yes
configure:4843: checking for vprintf
configure:4843: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
conftest.c:59: warning: conflicting types for built-in function 'vprintf'
configure:4843: $? = 0
configure:4843: result: yes
configure:4849: checking for _doprnt
configure:4849: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
/tmp/ccUAjvk5.o: In function `main':
conftest.c:(.text+0xa): undefined reference to `_doprnt'
collect2: ld returned 1 exit status
configure:4849: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BatMeth"
| #define PACKAGE_TARNAME "batmeth"
| #define PACKAGE_VERSION "2.00(mmx)"
| #define PACKAGE_STRING "BatMeth 2.00(mmx)"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL ""
| #define PACKAGE "BatMeth"
| #define VERSION "2.00_mmx"
| #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_LIMITS_H 1
| #define HAVE_MALLOC_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_SYS_SOCKET_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_UNISTD_H 1
| #define TIME_WITH_SYS_TIME 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| /* end confdefs.h. */
| /* Define _doprnt to an innocuous variant, in case <limits.h> declares _doprnt.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define _doprnt innocuous__doprnt
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char _doprnt (); below.
| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
| <limits.h> exists even on freestanding compilers. */
|
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|
| #undef _doprnt
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char _doprnt ();
| /* The GNU C library defines this for functions which it implements
| to always fail with ENOSYS. Some functions are actually named
| something starting with __ and the normal name is an alias. */
| #if defined __stub__doprnt || defined __stub____doprnt
| choke me
| #endif
|
| int
| main ()
| {
| return _doprnt ();
| ;
| return 0;
| }
configure:4849: result: no
configure:4863: checking for floor
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
conftest.c:60: warning: conflicting types for built-in function 'floor'
/tmp/cckbCcpi.o: In function `main':
conftest.c:(.text+0xa): undefined reference to `floor'
collect2: ld returned 1 exit status
configure:4863: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BatMeth"
| #define PACKAGE_TARNAME "batmeth"
| #define PACKAGE_VERSION "2.00(mmx)"
| #define PACKAGE_STRING "BatMeth 2.00(mmx)"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL ""
| #define PACKAGE "BatMeth"
| #define VERSION "2.00_mmx"
| #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_LIMITS_H 1
| #define HAVE_MALLOC_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_SYS_SOCKET_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_UNISTD_H 1
| #define TIME_WITH_SYS_TIME 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| /* end confdefs.h. */
| /* Define floor to an innocuous variant, in case <limits.h> declares floor.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define floor innocuous_floor
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char floor (); below.
| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
| <limits.h> exists even on freestanding compilers. */
|
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|
| #undef floor
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char floor ();
| /* The GNU C library defines this for functions which it implements
| to always fail with ENOSYS. Some functions are actually named
| something starting with __ and the normal name is an alias. */
| #if defined __stub_floor || defined __stub___floor
| choke me
| #endif
|
| int
| main ()
| {
| return floor ();
| ;
| return 0;
| }
configure:4863: result: no
configure:4863: checking for gettimeofday
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
configure:4863: $? = 0
configure:4863: result: yes
configure:4863: checking for memmove
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
conftest.c:61: warning: conflicting types for built-in function 'memmove'
configure:4863: $? = 0
configure:4863: result: yes
configure:4863: checking for memset
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
conftest.c:62: warning: conflicting types for built-in function 'memset'
configure:4863: $? = 0
configure:4863: result: yes
configure:4863: checking for pow
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
conftest.c:63: warning: conflicting types for built-in function 'pow'
/tmp/ccIhWmH2.o: In function `main':
conftest.c:(.text+0xa): undefined reference to `pow'
collect2: ld returned 1 exit status
configure:4863: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BatMeth"
| #define PACKAGE_TARNAME "batmeth"
| #define PACKAGE_VERSION "2.00(mmx)"
| #define PACKAGE_STRING "BatMeth 2.00(mmx)"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL ""
| #define PACKAGE "BatMeth"
| #define VERSION "2.00_mmx"
| #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_LIMITS_H 1
| #define HAVE_MALLOC_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_SYS_SOCKET_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_UNISTD_H 1
| #define TIME_WITH_SYS_TIME 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| #define HAVE_GETTIMEOFDAY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| /* end confdefs.h. */
| /* Define pow to an innocuous variant, in case <limits.h> declares pow.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define pow innocuous_pow
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char pow (); below.
| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
| <limits.h> exists even on freestanding compilers. */
|
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|
| #undef pow
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char pow ();
| /* The GNU C library defines this for functions which it implements
| to always fail with ENOSYS. Some functions are actually named
| something starting with __ and the normal name is an alias. */
| #if defined __stub_pow || defined __stub___pow
| choke me
| #endif
|
| int
| main ()
| {
| return pow ();
| ;
| return 0;
| }
configure:4863: result: no
configure:4863: checking for socket
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
configure:4863: $? = 0
configure:4863: result: yes
configure:4863: checking for sqrt
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
conftest.c:64: warning: conflicting types for built-in function 'sqrt'
/tmp/ccVpwP5d.o: In function `main':
conftest.c:(.text+0xa): undefined reference to `sqrt'
collect2: ld returned 1 exit status
configure:4863: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "BatMeth"
| #define PACKAGE_TARNAME "batmeth"
| #define PACKAGE_VERSION "2.00(mmx)"
| #define PACKAGE_STRING "BatMeth 2.00(mmx)"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL ""
| #define PACKAGE "BatMeth"
| #define VERSION "2.00_mmx"
| #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_LIMITS_H 1
| #define HAVE_MALLOC_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_SYS_SOCKET_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_UNISTD_H 1
| #define TIME_WITH_SYS_TIME 1
| #define HAVE_PTRDIFF_T 1
| #define HAVE_STDLIB_H 1
| #define HAVE_MALLOC 1
| #define HAVE_STDLIB_H 1
| #define HAVE_REALLOC 1
| #define HAVE_VPRINTF 1
| #define HAVE_GETTIMEOFDAY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_SOCKET 1
| /* end confdefs.h. */
| /* Define sqrt to an innocuous variant, in case <limits.h> declares sqrt.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define sqrt innocuous_sqrt
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char sqrt (); below.
| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
| <limits.h> exists even on freestanding compilers. */
|
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|
| #undef sqrt
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char sqrt ();
| /* The GNU C library defines this for functions which it implements
| to always fail with ENOSYS. Some functions are actually named
| something starting with __ and the normal name is an alias. */
| #if defined __stub_sqrt || defined __stub___sqrt
| choke me
| #endif
|
| int
| main ()
| {
| return sqrt ();
| ;
| return 0;
| }
configure:4863: result: no
configure:4863: checking for strchr
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
conftest.c:64: warning: conflicting types for built-in function 'strchr'
configure:4863: $? = 0
configure:4863: result: yes
configure:4863: checking for strdup
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
conftest.c:65: warning: conflicting types for built-in function 'strdup'
configure:4863: $? = 0
configure:4863: result: yes
configure:4863: checking for strtoul
configure:4863: gcc -o conftest -I/public/home/qwzhou/software/packagesR/include -L/public/home/qwzhou/software/packagesR/lib conftest.c >&5
configure:4863: $? = 0
configure:4863: result: yes
configure:4872: checking Checking for SIMD support and for a gcc bug...
configure:4887: gcc -c -I/public/home/qwzhou/software/packagesR/include -msse2 conftest.c >&5
conftest.c:44:23: warning: extra tokens at end of #include directive
configure:4887: $? = 0
configure:4888: result: OK...
configure:5036: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by BatMeth config.status 2.00(mmx), which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on login
config.status:878: creating Makefile
config.status:878: creating scripts/Makefile
config.status:878: creating config.h
config.status:1059: config.h is unchanged
config.status:1107: executing depfiles commands
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_c_volatile=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/public/home/qwzhou/software/packagesR/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=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value=-L/public/home/qwzhou/software/packagesR/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__doprnt=no
ac_cv_func_floor=no
ac_cv_func_gettimeofday=yes
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_memmove=yes
ac_cv_func_memset=yes
ac_cv_func_pow=no
ac_cv_func_realloc_0_nonnull=yes
ac_cv_func_setvbuf_reversed=no
ac_cv_func_socket=yes
ac_cv_func_sqrt=no
ac_cv_func_strchr=yes
ac_cv_func_strdup=yes
ac_cv_func_strtoul=yes
ac_cv_func_vprintf=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_limits_h=yes
ac_cv_header_malloc_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stddef_h=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_socket_h=yes
ac_cv_header_sys_stat_h=yes