Created
October 20, 2012 16:27
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tmap-3.2.0 config log, OSX 10.8.2 with --enable-perftools
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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 tmap configure 3.2.0, which was | |
| generated by GNU Autoconf 2.69. Invocation command line was | |
| $ ./configure --disable-dependency-tracking --prefix=/usr/local/Cellar/tmap/3.2.0 --enable-perftools | |
| ## --------- ## | |
| ## Platform. ## | |
| ## --------- ## | |
| hostname = iBlub.local | |
| uname -m = x86_64 | |
| uname -r = 12.2.0 | |
| uname -s = Darwin | |
| uname -v = Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 | |
| /usr/bin/uname -p = i386 | |
| /bin/uname -X = unknown | |
| /bin/arch = unknown | |
| /usr/bin/arch -k = unknown | |
| /usr/convex/getsysinfo = unknown | |
| /usr/bin/hostinfo = Mach kernel version: | |
| Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 | |
| Kernel configured for up to 4 processors. | |
| 4 processors are physically available. | |
| 4 processors are logically available. | |
| Processor type: i486 (Intel 80486) | |
| Processors active: 0 1 2 3 | |
| Primary memory available: 8.00 gigabytes | |
| Default processor set: 115 tasks, 559 threads, 4 processors | |
| Load average: 1.54, Mach factor: 2.47 | |
| /bin/machine = unknown | |
| /usr/bin/oslevel = unknown | |
| /bin/universe = unknown | |
| PATH: /usr/local/bin | |
| PATH: /usr/local/sbin | |
| PATH: /usr/local/share/python | |
| PATH: /usr/bin | |
| PATH: /bin | |
| PATH: /usr/sbin | |
| PATH: /sbin | |
| PATH: /opt/X11/bin | |
| PATH: /usr/local/texlive/2012/bin/x86_64-darwin | |
| PATH: /usr/local/Library/Contributions/cmds | |
| ## ----------- ## | |
| ## Core tests. ## | |
| ## ----------- ## | |
| configure:2628: checking for a BSD-compatible install | |
| configure:2696: result: /usr/bin/install -c | |
| configure:2707: checking whether build environment is sane | |
| configure:2762: result: yes | |
| configure:2913: checking for a thread-safe mkdir -p | |
| configure:2952: result: config/install-sh -c -d | |
| configure:2959: checking for gawk | |
| configure:2989: result: no | |
| configure:2959: checking for mawk | |
| configure:2989: result: no | |
| configure:2959: checking for nawk | |
| configure:2989: result: no | |
| configure:2959: checking for awk | |
| configure:2975: found /usr/bin/awk | |
| configure:2986: result: awk | |
| configure:2997: checking whether make sets $(MAKE) | |
| configure:3019: result: yes | |
| configure:3114: checking build system type | |
| configure:3128: result: x86_64-apple-darwin12.2.0 | |
| configure:3200: checking for gcc | |
| configure:3227: result: /usr/bin/llvm-gcc | |
| configure:3456: checking for C compiler version | |
| configure:3465: /usr/bin/llvm-gcc --version >&5 | |
| i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00) | |
| Copyright (C) 2007 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:3476: $? = 0 | |
| configure:3465: /usr/bin/llvm-gcc -v >&5 | |
| Using built-in specs. | |
| Target: i686-apple-darwin11 | |
| Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2336.11~67/src/configure --disable-checking --enable-werror --prefix=/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2336.11~67/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1 | |
| Thread model: posix | |
| gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00) | |
| configure:3476: $? = 0 | |
| configure:3465: /usr/bin/llvm-gcc -V >&5 | |
| llvm-gcc-4.2: argument to `-V' is missing | |
| configure:3476: $? = 1 | |
| configure:3465: /usr/bin/llvm-gcc -qversion >&5 | |
| i686-apple-darwin11-llvm-gcc-4.2: no input files | |
| configure:3476: $? = 1 | |
| configure:3496: checking whether the C compiler works | |
| configure:3518: /usr/bin/llvm-gcc -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -L/usr/local/lib conftest.c >&5 | |
| configure:3522: $? = 0 | |
| configure:3570: result: yes | |
| configure:3573: checking for C compiler default output file name | |
| configure:3575: result: a.out | |
| configure:3581: checking for suffix of executables | |
| configure:3588: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -L/usr/local/lib conftest.c >&5 | |
| configure:3592: $? = 0 | |
| configure:3614: result: | |
| configure:3636: checking whether we are cross compiling | |
| configure:3644: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -L/usr/local/lib conftest.c >&5 | |
| configure:3648: $? = 0 | |
| configure:3655: ./conftest | |
| configure:3659: $? = 0 | |
| configure:3674: result: no | |
| configure:3679: checking for suffix of object files | |
| configure:3701: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:3705: $? = 0 | |
| configure:3726: result: o | |
| configure:3730: checking whether we are using the GNU C compiler | |
| configure:3749: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:3749: $? = 0 | |
| configure:3758: result: yes | |
| configure:3767: checking whether /usr/bin/llvm-gcc accepts -g | |
| configure:3787: /usr/bin/llvm-gcc -c -g conftest.c >&5 | |
| configure:3787: $? = 0 | |
| configure:3828: result: yes | |
| configure:3845: checking for /usr/bin/llvm-gcc option to accept ISO C89 | |
| configure:3908: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:3908: $? = 0 | |
| configure:3921: result: none needed | |
| configure:3952: checking for style of include used by make | |
| configure:3980: result: GNU | |
| configure:4006: checking dependency style of /usr/bin/llvm-gcc | |
| configure:4117: result: none | |
| configure:4133: checking whether /usr/bin/llvm-gcc and cc understand -c and -o together | |
| configure:4164: /usr/bin/llvm-gcc -c conftest.c -o conftest2.o >&5 | |
| configure:4168: $? = 0 | |
| configure:4174: /usr/bin/llvm-gcc -c conftest.c -o conftest2.o >&5 | |
| configure:4178: $? = 0 | |
| configure:4189: cc -c conftest.c >&5 | |
| configure:4193: $? = 0 | |
| configure:4201: cc -c conftest.c -o conftest2.o >&5 | |
| configure:4205: $? = 0 | |
| configure:4211: cc -c conftest.c -o conftest2.o >&5 | |
| configure:4215: $? = 0 | |
| configure:4233: result: yes | |
| configure:4370: checking for C++ compiler version | |
| configure:4379: /usr/bin/llvm-g++ --version >&5 | |
| i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00) | |
| Copyright (C) 2007 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:4390: $? = 0 | |
| configure:4379: /usr/bin/llvm-g++ -v >&5 | |
| Using built-in specs. | |
| Target: i686-apple-darwin11 | |
| Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2336.11~67/src/configure --disable-checking --enable-werror --prefix=/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2336.11~67/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1 | |
| Thread model: posix | |
| gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00) | |
| configure:4390: $? = 0 | |
| configure:4379: /usr/bin/llvm-g++ -V >&5 | |
| llvm-g++-4.2: argument to `-V' is missing | |
| configure:4390: $? = 1 | |
| configure:4379: /usr/bin/llvm-g++ -qversion >&5 | |
| i686-apple-darwin11-llvm-g++-4.2: no input files | |
| configure:4390: $? = 1 | |
| configure:4394: checking whether we are using the GNU C++ compiler | |
| configure:4413: /usr/bin/llvm-g++ -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.cpp >&5 | |
| configure:4413: $? = 0 | |
| configure:4422: result: yes | |
| configure:4431: checking whether /usr/bin/llvm-g++ accepts -g | |
| configure:4451: /usr/bin/llvm-g++ -c -g conftest.cpp >&5 | |
| configure:4451: $? = 0 | |
| configure:4492: result: yes | |
| configure:4517: checking dependency style of /usr/bin/llvm-g++ | |
| configure:4628: result: none | |
| configure:4648: checking whether /usr/bin/llvm-g++ understands -c and -o together | |
| configure:4672: /usr/bin/llvm-g++ -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -c conftest.cpp -o conftest2.o >&5 | |
| configure:4676: $? = 0 | |
| configure:4683: /usr/bin/llvm-g++ -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -c conftest.cpp -o conftest2.o >&5 | |
| configure:4687: $? = 0 | |
| configure:4695: result: yes | |
| configure:4718: checking how to run the C preprocessor | |
| configure:4749: /usr/bin/llvm-gcc -E conftest.c | |
| configure:4749: $? = 0 | |
| configure:4763: /usr/bin/llvm-gcc -E conftest.c | |
| conftest.c:11:28: error: ac_nonexistent.h: No such file or directory | |
| configure:4763: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | /* end confdefs.h. */ | |
| | #include <ac_nonexistent.h> | |
| configure:4788: result: /usr/bin/llvm-gcc -E | |
| configure:4808: /usr/bin/llvm-gcc -E conftest.c | |
| configure:4808: $? = 0 | |
| configure:4822: /usr/bin/llvm-gcc -E conftest.c | |
| conftest.c:11:28: error: ac_nonexistent.h: No such file or directory | |
| configure:4822: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | /* end confdefs.h. */ | |
| | #include <ac_nonexistent.h> | |
| configure:4851: checking for grep that handles long lines and -e | |
| configure:4909: result: /usr/bin/grep | |
| configure:4914: checking for egrep | |
| configure:4976: result: /usr/bin/grep -E | |
| configure:4981: checking for ANSI C header files | |
| configure:5001: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5001: $? = 0 | |
| configure:5074: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -L/usr/local/lib conftest.c >&5 | |
| configure:5074: $? = 0 | |
| configure:5074: ./conftest | |
| configure:5074: $? = 0 | |
| configure:5085: result: yes | |
| configure:5098: checking for sys/types.h | |
| configure:5098: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5098: $? = 0 | |
| configure:5098: result: yes | |
| configure:5098: checking for sys/stat.h | |
| configure:5098: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5098: $? = 0 | |
| configure:5098: result: yes | |
| configure:5098: checking for stdlib.h | |
| configure:5098: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5098: $? = 0 | |
| configure:5098: result: yes | |
| configure:5098: checking for string.h | |
| configure:5098: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5098: $? = 0 | |
| configure:5098: result: yes | |
| configure:5098: checking for memory.h | |
| configure:5098: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5098: $? = 0 | |
| configure:5098: result: yes | |
| configure:5098: checking for strings.h | |
| configure:5098: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5098: $? = 0 | |
| configure:5098: result: yes | |
| configure:5098: checking for inttypes.h | |
| configure:5098: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5098: $? = 0 | |
| configure:5098: result: yes | |
| configure:5098: checking for stdint.h | |
| configure:5098: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5098: $? = 0 | |
| configure:5098: result: yes | |
| configure:5098: checking for unistd.h | |
| configure:5098: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5098: $? = 0 | |
| configure:5098: result: yes | |
| configure:5111: checking minix/config.h usability | |
| configure:5111: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| conftest.c:54:26: error: minix/config.h: No such file or directory | |
| configure:5111: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | #include <minix/config.h> | |
| configure:5111: result: no | |
| configure:5111: checking minix/config.h presence | |
| configure:5111: /usr/bin/llvm-gcc -E conftest.c | |
| conftest.c:21:26: error: minix/config.h: No such file or directory | |
| configure:5111: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | /* end confdefs.h. */ | |
| | #include <minix/config.h> | |
| configure:5111: result: no | |
| configure:5111: checking for minix/config.h | |
| configure:5111: result: no | |
| configure:5132: checking whether it is safe to define __EXTENSIONS__ | |
| configure:5150: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 conftest.c >&5 | |
| configure:5150: $? = 0 | |
| configure:5157: result: yes | |
| configure:5188: checking whether the git revision is available | |
| configure:5207: result: no | |
| configure:5222: checking for BZ2_bzRead in -lbz2 | |
| configure:5247: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -L/usr/local/lib conftest.c -lbz2 >&5 | |
| configure:5247: $? = 0 | |
| configure:5256: result: yes | |
| configure:5281: checking for malloc in -ltcmalloc | |
| configure:5306: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -L/usr/local/lib conftest.c -ltcmalloc -lbz2 >&5 | |
| configure:5306: $? = 0 | |
| configure:5315: result: yes | |
| configure:5341: WARNING: "Using 64-bit SA intervals; Genome sizes greater than 4Gb are supported" | |
| configure:5365: checking for an ANSI C-conforming const | |
| configure:5431: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:5431: $? = 0 | |
| configure:5438: result: yes | |
| configure:5446: checking for working volatile | |
| configure:5465: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:5465: $? = 0 | |
| configure:5472: result: yes | |
| configure:5480: checking for inline | |
| configure:5496: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:5496: $? = 0 | |
| configure:5504: result: inline | |
| configure:5525: checking for stdlib.h | |
| configure:5525: result: yes | |
| configure:5535: checking for GNU libc compatible malloc | |
| configure:5559: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:5559: $? = 0 | |
| configure:5559: ./conftest | |
| ./configure: line 1702: 46013 Segmentation fault: 11 ./conftest$ac_exeext | |
| configure:5559: $? = 139 | |
| configure: program exited with status 139 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | /* end confdefs.h. */ | |
| | #if defined STDC_HEADERS || defined HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | #else | |
| | char *malloc (); | |
| | #endif | |
| | | |
| | int | |
| | main () | |
| | { | |
| | return ! malloc (0); | |
| | ; | |
| | return 0; | |
| | } | |
| configure:5569: result: no | |
| configure:5592: checking for stdlib.h | |
| configure:5592: result: yes | |
| configure:5602: checking for GNU libc compatible realloc | |
| configure:5626: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:5626: $? = 0 | |
| configure:5626: ./conftest | |
| ./configure: line 1702: 46028 Segmentation fault: 11 ./conftest$ac_exeext | |
| configure:5626: $? = 139 | |
| configure: program exited with status 139 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | /* end confdefs.h. */ | |
| | #if defined STDC_HEADERS || defined HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | #else | |
| | char *realloc (); | |
| | #endif | |
| | | |
| | int | |
| | main () | |
| | { | |
| | return ! realloc (0, 0); | |
| | ; | |
| | return 0; | |
| | } | |
| configure:5636: result: no | |
| configure:5657: checking for size_t | |
| configure:5657: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:5657: $? = 0 | |
| configure:5657: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:70: error: expected expression before ')' token | |
| configure:5657: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | /* 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:5657: result: yes | |
| configure:5670: checking for working alloca.h | |
| configure:5687: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:5687: $? = 0 | |
| configure:5695: result: yes | |
| configure:5703: checking for alloca | |
| configure:5740: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:5740: $? = 0 | |
| configure:5748: result: yes | |
| configure:5854: checking for error_at_line | |
| configure:5870: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| conftest.c:36:19: error: error.h: No such file or directory | |
| configure:5870: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | /* end confdefs.h. */ | |
| | #include <error.h> | |
| | int | |
| | main () | |
| | { | |
| | error_at_line (0, 0, "", 0, "an error occurred"); | |
| | ; | |
| | return 0; | |
| | } | |
| configure:5878: result: no | |
| configure:5889: checking for _LARGEFILE_SOURCE value needed for large files | |
| configure:5908: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:5908: $? = 0 | |
| configure:5936: result: no | |
| configure:5957: checking for working memcmp | |
| configure:6000: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6000: $? = 0 | |
| configure:6000: ./conftest | |
| ./configure: line 1702: 46114 Segmentation fault: 11 ./conftest$ac_exeext | |
| configure:6000: $? = 139 | |
| configure: program exited with status 139 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 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 () | |
| | { | |
| | | |
| | /* Some versions of memcmp are not 8-bit clean. */ | |
| | char c0 = '\100', c1 = '\200', c2 = '\201'; | |
| | if (memcmp(&c0, &c2, 1) >= 0 || memcmp(&c1, &c2, 1) >= 0) | |
| | return 1; | |
| | | |
| | /* The Next x86 OpenStep bug shows up only when comparing 16 bytes | |
| | or more and with at least one buffer not starting on a 4-byte boundary. | |
| | William Lewis provided this test program. */ | |
| | { | |
| | char foo[21]; | |
| | char bar[21]; | |
| | int i; | |
| | for (i = 0; i < 4; i++) | |
| | { | |
| | char *a = foo + i; | |
| | char *b = bar + i; | |
| | strcpy (a, "--------01111111"); | |
| | strcpy (b, "--------10000000"); | |
| | if (memcmp (a, b, 16) >= 0) | |
| | return 1; | |
| | } | |
| | return 0; | |
| | } | |
| | | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6010: result: no | |
| configure:6022: checking sys/select.h usability | |
| configure:6022: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6022: $? = 0 | |
| configure:6022: result: yes | |
| configure:6022: checking sys/select.h presence | |
| configure:6022: /usr/bin/llvm-gcc -E conftest.c | |
| configure:6022: $? = 0 | |
| configure:6022: result: yes | |
| configure:6022: checking for sys/select.h | |
| configure:6022: result: yes | |
| configure:6022: checking sys/socket.h usability | |
| configure:6022: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6022: $? = 0 | |
| configure:6022: result: yes | |
| configure:6022: checking sys/socket.h presence | |
| configure:6022: /usr/bin/llvm-gcc -E conftest.c | |
| configure:6022: $? = 0 | |
| configure:6022: result: yes | |
| configure:6022: checking for sys/socket.h | |
| configure:6022: result: yes | |
| configure:6032: checking types of arguments for select | |
| configure:6060: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6060: $? = 0 | |
| configure:6071: result: int,fd_set *,struct timeval * | |
| configure:6094: checking whether lstat correctly handles trailing slash | |
| configure:6120: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6120: $? = 0 | |
| configure:6120: ./conftest | |
| ./configure: line 1702: 46194 Segmentation fault: 11 ./conftest$ac_exeext | |
| configure:6120: $? = 139 | |
| configure: program exited with status 139 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | /* 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 () | |
| | { | |
| | struct stat sbuf; | |
| | /* Linux will dereference the symlink and fail, as required by POSIX. | |
| | That is better in the sense that it means we will not | |
| | have to compile and use the lstat wrapper. */ | |
| | return lstat ("conftest.sym/", &sbuf) == 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6137: result: no | |
| configure:6156: checking whether stat accepts an empty string | |
| configure:6176: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6176: $? = 0 | |
| configure:6176: ./conftest | |
| ./configure: line 1702: 46209 Segmentation fault: 11 ./conftest$ac_exeext | |
| configure:6176: $? = 139 | |
| configure: program exited with status 139 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | /* 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 () | |
| | { | |
| | struct stat sbuf; | |
| | return stat ("", &sbuf) == 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6186: result: yes | |
| configure:6202: checking for working strtod | |
| configure:6243: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6243: $? = 0 | |
| configure:6243: ./conftest | |
| ./configure: line 1702: 46224 Segmentation fault: 11 ./conftest$ac_exeext | |
| configure:6243: $? = 139 | |
| configure: program exited with status 139 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 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 | |
| | #ifndef strtod | |
| | double strtod (); | |
| | #endif | |
| | int | |
| | main() | |
| | { | |
| | { | |
| | /* Some versions of Linux strtod mis-parse strings with leading '+'. */ | |
| | char *string = " +69"; | |
| | char *term; | |
| | double value; | |
| | value = strtod (string, &term); | |
| | if (value != 69 || term != (string + 4)) | |
| | return 1; | |
| | } | |
| | | |
| | { | |
| | /* Under Solaris 2.4, strtod returns the wrong value for the | |
| | terminating character under some conditions. */ | |
| | char *string = "NaN"; | |
| | char *term; | |
| | strtod (string, &term); | |
| | if (term != string && *(term - 1) == 0) | |
| | return 1; | |
| | } | |
| | return 0; | |
| | } | |
| | | |
| configure:6253: result: no | |
| configure:6262: checking for pow | |
| configure:6262: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6262: $? = 0 | |
| configure:6262: result: yes | |
| configure:6317: checking for vprintf | |
| configure:6317: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6317: $? = 0 | |
| configure:6317: result: yes | |
| configure:6323: checking for _doprnt | |
| configure:6323: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -ltcmalloc -lbz2 -lprofiler >&5 | |
| Undefined symbols for architecture x86_64: | |
| "__doprnt", referenced from: | |
| _main in ccIhVU5B.o | |
| ld: symbol(s) not found for architecture x86_64 | |
| collect2: ld returned 1 exit status | |
| configure:6323: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 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:6323: result: no | |
| configure:6334: checking for gzread in -lz | |
| configure:6359: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6359: $? = 0 | |
| configure:6368: result: yes | |
| configure:6379: checking for pow in -lm | |
| configure:6404: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6404: $? = 0 | |
| configure:6413: result: yes | |
| configure:6424: checking for pthread_create in -lpthread | |
| configure:6449: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6449: $? = 0 | |
| configure:6458: result: yes | |
| configure:6473: checking for pow | |
| configure:6473: result: yes | |
| configure:6473: checking for strdup | |
| configure:6473: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6473: $? = 0 | |
| configure:6473: result: yes | |
| configure:6473: checking for memset | |
| configure:6473: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6473: $? = 0 | |
| configure:6473: result: yes | |
| configure:6473: checking for strchr | |
| configure:6473: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6473: $? = 0 | |
| configure:6473: result: yes | |
| configure:6473: checking for strdup | |
| configure:6473: result: yes | |
| configure:6473: checking for strstr | |
| configure:6473: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6473: $? = 0 | |
| configure:6473: result: yes | |
| configure:6473: checking for memmove | |
| configure:6473: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6473: $? = 0 | |
| configure:6473: result: yes | |
| configure:6473: checking for getopt_long | |
| configure:6473: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6473: $? = 0 | |
| configure:6473: result: yes | |
| configure:6473: checking for gettimeofday | |
| configure:6473: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6473: $? = 0 | |
| configure:6473: result: yes | |
| configure:6485: checking for gethostbyaddr | |
| configure:6485: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6485: $? = 0 | |
| configure:6485: result: yes | |
| configure:6485: checking for gethostbyname | |
| configure:6485: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6485: $? = 0 | |
| configure:6485: result: yes | |
| configure:6485: checking for memchr | |
| configure:6485: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6485: $? = 0 | |
| configure:6485: result: yes | |
| configure:6485: checking for select | |
| configure:6485: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6485: $? = 0 | |
| configure:6485: result: yes | |
| configure:6485: checking for socket | |
| configure:6485: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6485: $? = 0 | |
| configure:6485: result: yes | |
| configure:6485: checking for sqrt | |
| configure:6485: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6485: $? = 0 | |
| configure:6485: result: yes | |
| configure:6485: checking for strerror | |
| configure:6485: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6485: $? = 0 | |
| configure:6485: result: yes | |
| configure:6485: checking for strtol | |
| configure:6485: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6485: $? = 0 | |
| configure:6485: result: yes | |
| configure:6496: checking for int8_t | |
| configure:6496: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6496: $? = 0 | |
| configure:6496: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:102: error: size of array 'test_array' is negative | |
| configure:6496: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 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 = 8 / 2 - 1 }; | |
| | int | |
| | main () | |
| | { | |
| | static int test_array [1 - 2 * !((int8_t) (((((int8_t) 1 << N) << N) - 1) * 2 + 1) | |
| | < (int8_t) (((((int8_t) 1 << N) << N) - 1) * 2 + 2))]; | |
| | test_array [0] = 0; | |
| | return test_array [0]; | |
| | | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6496: result: yes | |
| configure:6507: checking for int16_t | |
| configure:6507: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6507: $? = 0 | |
| configure:6507: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:102: error: size of array 'test_array' is negative | |
| configure:6507: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 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 = 16 / 2 - 1 }; | |
| | int | |
| | main () | |
| | { | |
| | static int test_array [1 - 2 * !((int16_t) (((((int16_t) 1 << N) << N) - 1) * 2 + 1) | |
| | < (int16_t) (((((int16_t) 1 << N) << N) - 1) * 2 + 2))]; | |
| | test_array [0] = 0; | |
| | return test_array [0]; | |
| | | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6507: result: yes | |
| configure:6518: checking for int32_t | |
| configure:6518: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6518: $? = 0 | |
| configure:6518: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:102: error: size of array 'test_array' is negative | |
| configure:6518: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 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:6518: result: yes | |
| configure:6529: checking for int64_t | |
| configure:6529: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6529: $? = 0 | |
| configure:6529: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:102: error: size of array 'test_array' is negative | |
| configure:6529: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 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 = 64 / 2 - 1 }; | |
| | int | |
| | main () | |
| | { | |
| | static int test_array [1 - 2 * !((int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 1) | |
| | < (int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 2))]; | |
| | test_array [0] = 0; | |
| | return test_array [0]; | |
| | | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6529: result: yes | |
| configure:6540: checking for uint8_t | |
| configure:6540: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6540: $? = 0 | |
| configure:6540: result: yes | |
| configure:6554: checking for uint16_t | |
| configure:6554: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6554: $? = 0 | |
| configure:6554: result: yes | |
| configure:6566: checking for uint32_t | |
| configure:6566: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6566: $? = 0 | |
| configure:6566: result: yes | |
| configure:6580: checking for uint64_t | |
| configure:6580: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6580: $? = 0 | |
| configure:6580: result: yes | |
| configure:6594: checking for size_t | |
| configure:6594: result: yes | |
| configure:6605: checking for off_t | |
| configure:6605: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6605: $? = 0 | |
| configure:6605: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:100: error: expected expression before ')' token | |
| configure:6605: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 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 ((off_t))) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6605: result: yes | |
| configure:6616: checking return type of signal handlers | |
| configure:6634: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:70: error: void value not ignored as it ought to be | |
| configure:6634: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 1 | |
| | /* end confdefs.h. */ | |
| | #include <sys/types.h> | |
| | #include <signal.h> | |
| | | |
| | int | |
| | main () | |
| | { | |
| | return *(signal (0, 0)) (0) == 1; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6641: result: void | |
| configure:6649: checking for ssize_t | |
| configure:6649: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6649: $? = 0 | |
| configure:6649: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:101: error: expected expression before ')' token | |
| configure:6649: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 1 | |
| | #define RETSIGTYPE void | |
| | /* 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 ((ssize_t))) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6649: result: yes | |
| configure:6666: checking size of short int | |
| configure:6671: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6671: $? = 0 | |
| configure:6671: ./conftest | |
| ./configure: line 1702: 46833 Segmentation fault: 11 ./conftest$ac_exeext | |
| configure:6671: $? = 139 | |
| configure: program exited with status 139 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 1 | |
| | #define RETSIGTYPE void | |
| | /* 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 | |
| | static long int longval () { return (long int) (sizeof (short int)); } | |
| | static unsigned long int ulongval () { return (long int) (sizeof (short int)); } | |
| | #include <stdio.h> | |
| | #include <stdlib.h> | |
| | int | |
| | main () | |
| | { | |
| | | |
| | FILE *f = fopen ("conftest.val", "w"); | |
| | if (! f) | |
| | return 1; | |
| | if (((long int) (sizeof (short int))) < 0) | |
| | { | |
| | long int i = longval (); | |
| | if (i != ((long int) (sizeof (short int)))) | |
| | return 1; | |
| | fprintf (f, "%ld", i); | |
| | } | |
| | else | |
| | { | |
| | unsigned long int i = ulongval (); | |
| | if (i != ((long int) (sizeof (short int)))) | |
| | return 1; | |
| | fprintf (f, "%lu", i); | |
| | } | |
| | /* Do not output a trailing newline, as this causes \r\n confusion | |
| | on some platforms. */ | |
| | return ferror (f) || fclose (f) != 0; | |
| | | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6685: result: 0 | |
| configure:6699: checking size of int | |
| configure:6704: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6704: $? = 0 | |
| configure:6704: ./conftest | |
| ./configure: line 1702: 46849 Segmentation fault: 11 ./conftest$ac_exeext | |
| configure:6704: $? = 139 | |
| configure: program exited with status 139 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 1 | |
| | #define RETSIGTYPE void | |
| | #define SIZEOF_SHORT_INT 0 | |
| | /* 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 | |
| | static long int longval () { return (long int) (sizeof (int)); } | |
| | static unsigned long int ulongval () { return (long int) (sizeof (int)); } | |
| | #include <stdio.h> | |
| | #include <stdlib.h> | |
| | int | |
| | main () | |
| | { | |
| | | |
| | FILE *f = fopen ("conftest.val", "w"); | |
| | if (! f) | |
| | return 1; | |
| | if (((long int) (sizeof (int))) < 0) | |
| | { | |
| | long int i = longval (); | |
| | if (i != ((long int) (sizeof (int)))) | |
| | return 1; | |
| | fprintf (f, "%ld", i); | |
| | } | |
| | else | |
| | { | |
| | unsigned long int i = ulongval (); | |
| | if (i != ((long int) (sizeof (int)))) | |
| | return 1; | |
| | fprintf (f, "%lu", i); | |
| | } | |
| | /* Do not output a trailing newline, as this causes \r\n confusion | |
| | on some platforms. */ | |
| | return ferror (f) || fclose (f) != 0; | |
| | | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6718: result: 0 | |
| configure:6732: checking size of long int | |
| configure:6737: /usr/bin/llvm-gcc -o conftest -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -L/usr/local/lib conftest.c -lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler >&5 | |
| configure:6737: $? = 0 | |
| configure:6737: ./conftest | |
| ./configure: line 1702: 46865 Segmentation fault: 11 ./conftest$ac_exeext | |
| configure:6737: $? = 139 | |
| configure: program exited with status 139 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 1 | |
| | #define RETSIGTYPE void | |
| | #define SIZEOF_SHORT_INT 0 | |
| | #define SIZEOF_INT 0 | |
| | /* 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 | |
| | static long int longval () { return (long int) (sizeof (long int)); } | |
| | static unsigned long int ulongval () { return (long int) (sizeof (long int)); } | |
| | #include <stdio.h> | |
| | #include <stdlib.h> | |
| | int | |
| | main () | |
| | { | |
| | | |
| | FILE *f = fopen ("conftest.val", "w"); | |
| | if (! f) | |
| | return 1; | |
| | if (((long int) (sizeof (long int))) < 0) | |
| | { | |
| | long int i = longval (); | |
| | if (i != ((long int) (sizeof (long int)))) | |
| | return 1; | |
| | fprintf (f, "%ld", i); | |
| | } | |
| | else | |
| | { | |
| | unsigned long int i = ulongval (); | |
| | if (i != ((long int) (sizeof (long int)))) | |
| | return 1; | |
| | fprintf (f, "%lu", i); | |
| | } | |
| | /* Do not output a trailing newline, as this causes \r\n confusion | |
| | on some platforms. */ | |
| | return ferror (f) || fclose (f) != 0; | |
| | | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6751: result: 0 | |
| configure:6763: checking for ANSI C header files | |
| configure:6867: result: yes | |
| configure:6875: checking for stdbool.h that conforms to C99 | |
| configure:6942: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6942: $? = 0 | |
| configure:6949: result: yes | |
| configure:6951: checking for _Bool | |
| configure:6951: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6951: $? = 0 | |
| configure:6951: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:105: error: expected expression before ')' token | |
| configure:6951: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 1 | |
| | #define RETSIGTYPE void | |
| | #define SIZEOF_SHORT_INT 0 | |
| | #define SIZEOF_INT 0 | |
| | #define SIZEOF_LONG_INT 0 | |
| | #define STDC_HEADERS 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:6951: result: yes | |
| configure:6968: checking whether time.h and sys/time.h may both be included | |
| configure:6988: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:6988: $? = 0 | |
| configure:6995: result: yes | |
| configure:7006: checking for stdlib.h | |
| configure:7006: result: yes | |
| configure:7006: checking stdio.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking stdio.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for stdio.h | |
| configure:7006: result: yes | |
| configure:7006: checking for stdint.h | |
| configure:7006: result: yes | |
| configure:7006: checking for string.h | |
| configure:7006: result: yes | |
| configure:7006: checking sys/time.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking sys/time.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for sys/time.h | |
| configure:7006: result: yes | |
| configure:7006: checking for unistd.h | |
| configure:7006: result: yes | |
| configure:7006: checking float.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking float.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for float.h | |
| configure:7006: result: yes | |
| configure:7006: checking zlib.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking zlib.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for zlib.h | |
| configure:7006: result: yes | |
| configure:7006: checking bzlib.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking bzlib.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for bzlib.h | |
| configure:7006: result: yes | |
| configure:7006: checking pthread.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking pthread.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for pthread.h | |
| configure:7006: result: yes | |
| configure:7006: checking limits.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking limits.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for limits.h | |
| configure:7006: result: yes | |
| configure:7006: checking netinet/in.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking netinet/in.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for netinet/in.h | |
| configure:7006: result: yes | |
| configure:7006: checking emmintrin.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking emmintrin.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for emmintrin.h | |
| configure:7006: result: yes | |
| configure:7006: checking getopt.h usability | |
| configure:7006: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking getopt.h presence | |
| configure:7006: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7006: $? = 0 | |
| configure:7006: result: yes | |
| configure:7006: checking for getopt.h | |
| configure:7006: result: yes | |
| configure:7019: checking arpa/inet.h usability | |
| configure:7019: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking arpa/inet.h presence | |
| configure:7019: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking for arpa/inet.h | |
| configure:7019: result: yes | |
| configure:7019: checking fcntl.h usability | |
| configure:7019: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking fcntl.h presence | |
| configure:7019: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking for fcntl.h | |
| configure:7019: result: yes | |
| configure:7019: checking netdb.h usability | |
| configure:7019: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking netdb.h presence | |
| configure:7019: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking for netdb.h | |
| configure:7019: result: yes | |
| configure:7019: checking stddef.h usability | |
| configure:7019: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking stddef.h presence | |
| configure:7019: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking for stddef.h | |
| configure:7019: result: yes | |
| configure:7019: checking for sys/socket.h | |
| configure:7019: result: yes | |
| configure:7019: checking wchar.h usability | |
| configure:7019: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking wchar.h presence | |
| configure:7019: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking for wchar.h | |
| configure:7019: result: yes | |
| configure:7019: checking curses.h usability | |
| configure:7019: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking curses.h presence | |
| configure:7019: /usr/bin/llvm-gcc -E conftest.c | |
| configure:7019: $? = 0 | |
| configure:7019: result: yes | |
| configure:7019: checking for curses.h | |
| configure:7019: result: yes | |
| configure:7019: checking xcurses.h usability | |
| configure:7019: /usr/bin/llvm-gcc -c -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN conftest.c >&5 | |
| conftest.c:126:21: error: xcurses.h: No such file or directory | |
| configure:7019: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 1 | |
| | #define RETSIGTYPE void | |
| | #define SIZEOF_SHORT_INT 0 | |
| | #define SIZEOF_INT 0 | |
| | #define SIZEOF_LONG_INT 0 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define TIME_WITH_SYS_TIME 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STDIO_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_SYS_TIME_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_ZLIB_H 1 | |
| | #define HAVE_BZLIB_H 1 | |
| | #define HAVE_PTHREAD_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_NETINET_IN_H 1 | |
| | #define HAVE_EMMINTRIN_H 1 | |
| | #define HAVE_GETOPT_H 1 | |
| | #define HAVE_ARPA_INET_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_NETDB_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define HAVE_WCHAR_H 1 | |
| | #define HAVE_CURSES_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 | |
| | #include <xcurses.h> | |
| configure:7019: result: no | |
| configure:7019: checking xcurses.h presence | |
| configure:7019: /usr/bin/llvm-gcc -E conftest.c | |
| conftest.c:93:21: error: xcurses.h: No such file or directory | |
| configure:7019: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "tmap" | |
| | #define PACKAGE_TARNAME "tmap" | |
| | #define PACKAGE_VERSION "3.2.0" | |
| | #define PACKAGE_STRING "tmap 3.2.0" | |
| | #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| | #define PACKAGE_URL "" | |
| | #define PACKAGE "tmap" | |
| | #define VERSION "3.2.0" | |
| | #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 __EXTENSIONS__ 1 | |
| | #define _ALL_SOURCE 1 | |
| | #define _GNU_SOURCE 1 | |
| | #define _POSIX_PTHREAD_SEMANTICS 1 | |
| | #define _TANDEM_SOURCE 1 | |
| | #define HAVE_LIBBZ2 1 | |
| | #define HAVE_LIBTCMALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 0 | |
| | #define malloc rpl_malloc | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 0 | |
| | #define realloc rpl_realloc | |
| | #define HAVE_ALLOCA_H 1 | |
| | #define HAVE_ALLOCA 1 | |
| | #define HAVE_FSEEKO 1 | |
| | #define HAVE_SYS_SELECT_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define SELECT_TYPE_ARG1 int | |
| | #define SELECT_TYPE_ARG234 (fd_set *) | |
| | #define SELECT_TYPE_ARG5 (struct timeval *) | |
| | #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define HAVE_LIBZ 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_LIBPTHREAD 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRCHR 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRSTR 1 | |
| | #define HAVE_MEMMOVE 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETTIMEOFDAY 1 | |
| | #define HAVE_GETHOSTBYADDR 1 | |
| | #define HAVE_GETHOSTBYNAME 1 | |
| | #define HAVE_MEMCHR 1 | |
| | #define HAVE_SELECT 1 | |
| | #define HAVE_SOCKET 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOL 1 | |
| | #define RETSIGTYPE void | |
| | #define SIZEOF_SHORT_INT 0 | |
| | #define SIZEOF_INT 0 | |
| | #define SIZEOF_LONG_INT 0 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define TIME_WITH_SYS_TIME 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STDIO_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_SYS_TIME_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_ZLIB_H 1 | |
| | #define HAVE_BZLIB_H 1 | |
| | #define HAVE_PTHREAD_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_NETINET_IN_H 1 | |
| | #define HAVE_EMMINTRIN_H 1 | |
| | #define HAVE_GETOPT_H 1 | |
| | #define HAVE_ARPA_INET_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_NETDB_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_SYS_SOCKET_H 1 | |
| | #define HAVE_WCHAR_H 1 | |
| | #define HAVE_CURSES_H 1 | |
| | /* end confdefs.h. */ | |
| | #include <xcurses.h> | |
| configure:7019: result: no | |
| configure:7019: checking for xcurses.h | |
| configure:7019: result: no | |
| configure:7142: checking that generated files are newer than configure | |
| configure:7148: result: done | |
| configure:7175: creating ./config.status | |
| ## ---------------------- ## | |
| ## Running config.status. ## | |
| ## ---------------------- ## | |
| This file was extended by tmap config.status 3.2.0, which was | |
| generated by GNU Autoconf 2.69. Invocation command line was | |
| CONFIG_FILES = | |
| CONFIG_HEADERS = | |
| CONFIG_LINKS = | |
| CONFIG_COMMANDS = | |
| $ ./config.status | |
| on iBlub.local | |
| config.status:934: creating Makefile | |
| config.status:934: creating config.h | |
| config.status:1163: executing depfiles commands | |
| ## ---------------- ## | |
| ## Cache variables. ## | |
| ## ---------------- ## | |
| ac_cv_build=x86_64-apple-darwin12.2.0 | |
| ac_cv_c_compiler_gnu=yes | |
| ac_cv_c_const=yes | |
| ac_cv_c_inline=inline | |
| ac_cv_c_int16_t=yes | |
| ac_cv_c_int32_t=yes | |
| ac_cv_c_int64_t=yes | |
| ac_cv_c_int8_t=yes | |
| ac_cv_c_uint16_t=yes | |
| ac_cv_c_uint32_t=yes | |
| ac_cv_c_uint64_t=yes | |
| ac_cv_c_uint8_t=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=set | |
| ac_cv_env_CC_value=/usr/bin/llvm-gcc | |
| ac_cv_env_CFLAGS_set=set | |
| ac_cv_env_CFLAGS_value='-Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4' | |
| 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='-Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4' | |
| ac_cv_env_CXX_set=set | |
| ac_cv_env_CXX_value=/usr/bin/llvm-g++ | |
| ac_cv_env_LDFLAGS_set=set | |
| ac_cv_env_LDFLAGS_value=-L/usr/local/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_alloca_works=yes | |
| ac_cv_func_gethostbyaddr=yes | |
| ac_cv_func_gethostbyname=yes | |
| ac_cv_func_getopt_long=yes | |
| ac_cv_func_gettimeofday=yes | |
| ac_cv_func_lstat_dereferences_slashed_symlink=no | |
| ac_cv_func_malloc_0_nonnull=no | |
| ac_cv_func_memchr=yes | |
| ac_cv_func_memcmp_working=no | |
| ac_cv_func_memmove=yes | |
| ac_cv_func_memset=yes | |
| ac_cv_func_pow=yes | |
| ac_cv_func_realloc_0_nonnull=no | |
| ac_cv_func_select=yes | |
| ac_cv_func_select_args='int,fd_set *,struct timeval *' | |
| ac_cv_func_socket=yes | |
| ac_cv_func_sqrt=yes | |
| ac_cv_func_stat_empty_string_bug=yes | |
| ac_cv_func_strchr=yes | |
| ac_cv_func_strdup=yes | |
| ac_cv_func_strerror=yes | |
| ac_cv_func_strstr=yes | |
| ac_cv_func_strtod=no | |
| ac_cv_func_strtol=yes | |
| ac_cv_func_vprintf=yes | |
| ac_cv_header_arpa_inet_h=yes | |
| ac_cv_header_bzlib_h=yes | |
| ac_cv_header_curses_h=yes | |
| ac_cv_header_emmintrin_h=yes | |
| ac_cv_header_fcntl_h=yes | |
| ac_cv_header_float_h=yes | |
| ac_cv_header_getopt_h=yes | |
| ac_cv_header_inttypes_h=yes | |
| ac_cv_header_limits_h=yes | |
| ac_cv_header_memory_h=yes | |
| ac_cv_header_minix_config_h=no | |
| ac_cv_header_netdb_h=yes | |
| ac_cv_header_netinet_in_h=yes | |
| ac_cv_header_pthread_h=yes | |
| ac_cv_header_stdbool_h=yes | |
| ac_cv_header_stdc=yes | |
| ac_cv_header_stddef_h=yes | |
| ac_cv_header_stdint_h=yes | |
| ac_cv_header_stdio_h=yes | |
| ac_cv_header_stdlib_h=yes | |
| ac_cv_header_string_h=yes | |
| ac_cv_header_strings_h=yes | |
| ac_cv_header_sys_select_h=yes | |
| ac_cv_header_sys_socket_h=yes | |
| ac_cv_header_sys_stat_h=yes | |
| ac_cv_header_sys_time_h=yes | |
| ac_cv_header_sys_types_h=yes | |
| ac_cv_header_time=yes | |
| ac_cv_header_unistd_h=yes | |
| ac_cv_header_wchar_h=yes | |
| ac_cv_header_xcurses_h=no | |
| ac_cv_header_zlib_h=yes | |
| ac_cv_lib_bz2_BZ2_bzRead=yes | |
| ac_cv_lib_error_at_line=no | |
| ac_cv_lib_m_pow=yes | |
| ac_cv_lib_pthread_pthread_create=yes | |
| ac_cv_lib_tcmalloc_malloc=yes | |
| ac_cv_lib_z_gzread=yes | |
| ac_cv_objext=o | |
| ac_cv_path_EGREP='/usr/bin/grep -E' | |
| ac_cv_path_GREP=/usr/bin/grep | |
| ac_cv_path_install='/usr/bin/install -c' | |
| ac_cv_prog_AWK=awk | |
| ac_cv_prog_CPP='/usr/bin/llvm-gcc -E' | |
| ac_cv_prog_ac_ct_CC=/usr/bin/llvm-gcc | |
| ac_cv_prog_cc__usr_bin_llvm_gcc_c_o=yes | |
| ac_cv_prog_cc_c89= | |
| ac_cv_prog_cc_g=yes | |
| ac_cv_prog_cxx_c_o=yes | |
| ac_cv_prog_cxx_g=yes | |
| ac_cv_prog_make_make_set=yes | |
| ac_cv_safe_to_define___extensions__=yes | |
| ac_cv_sizeof_int=0 | |
| ac_cv_sizeof_long_int=0 | |
| ac_cv_sizeof_short_int=0 | |
| ac_cv_sys_largefile_source=no | |
| ac_cv_type__Bool=yes | |
| ac_cv_type_off_t=yes | |
| ac_cv_type_signal=void | |
| ac_cv_type_size_t=yes | |
| ac_cv_type_ssize_t=yes | |
| ac_cv_working_alloca_h=yes | |
| am_cv_CC_dependencies_compiler_type=none | |
| am_cv_CXX_dependencies_compiler_type=none | |
| ## ----------------- ## | |
| ## Output variables. ## | |
| ## ----------------- ## | |
| ACLOCAL='${SHELL} /private/tmp/tmap-rhOV/config/missing --run aclocal-1.12' | |
| ALLOCA='' | |
| AMDEPBACKSLASH='' | |
| AMDEP_FALSE='' | |
| AMDEP_TRUE='#' | |
| AMTAR='$${TAR-tar}' | |
| AUTOCONF='${SHELL} /private/tmp/tmap-rhOV/config/missing --run autoconf' | |
| AUTOHEADER='${SHELL} /private/tmp/tmap-rhOV/config/missing --run autoheader' | |
| AUTOMAKE='${SHELL} /private/tmp/tmap-rhOV/config/missing --run automake-1.12' | |
| AWK='awk' | |
| CC='/usr/bin/llvm-gcc' | |
| CCDEPMODE='depmode=none' | |
| CFLAGS='-Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN' | |
| CPP='/usr/bin/llvm-gcc -E' | |
| CPPFLAGS='' | |
| CXX='/usr/bin/llvm-g++' | |
| CXXDEPMODE='depmode=none' | |
| CXXFLAGS='-Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS' | |
| CYGPATH_W='echo' | |
| DEFS='-DHAVE_CONFIG_H' | |
| DEPDIR='.deps' | |
| ECHO_C='\c' | |
| ECHO_N='' | |
| ECHO_T='' | |
| EGREP='/usr/bin/grep -E' | |
| EXEEXT='' | |
| GREP='/usr/bin/grep' | |
| INSTALL_DATA='${INSTALL} -m 644' | |
| INSTALL_PROGRAM='${INSTALL}' | |
| INSTALL_SCRIPT='${INSTALL}' | |
| INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' | |
| LDFLAGS='-L/usr/local/lib' | |
| LIBOBJS=' ${LIBOBJDIR}malloc$U.o ${LIBOBJDIR}realloc$U.o ${LIBOBJDIR}error$U.o ${LIBOBJDIR}memcmp$U.o ${LIBOBJDIR}lstat$U.o ${LIBOBJDIR}stat$U.o ${LIBOBJDIR}strtod$U.o' | |
| LIBS='-lpthread -lm -lz -ltcmalloc -lbz2 -lprofiler' | |
| LTLIBOBJS=' ${LIBOBJDIR}malloc$U.lo ${LIBOBJDIR}realloc$U.lo ${LIBOBJDIR}error$U.lo ${LIBOBJDIR}memcmp$U.lo ${LIBOBJDIR}lstat$U.lo ${LIBOBJDIR}stat$U.lo ${LIBOBJDIR}strtod$U.lo' | |
| MAKEINFO='${SHELL} /private/tmp/tmap-rhOV/config/missing --run makeinfo' | |
| MKDIR_P='config/install-sh -c -d' | |
| OBJEXT='o' | |
| PACKAGE='tmap' | |
| PACKAGE_BUGREPORT='nils.homer@lifetech.com' | |
| PACKAGE_NAME='tmap' | |
| PACKAGE_STRING='tmap 3.2.0' | |
| PACKAGE_TARNAME='tmap' | |
| PACKAGE_URL='' | |
| PACKAGE_VERSION='3.2.0' | |
| PATH_SEPARATOR=':' | |
| POW_LIB='' | |
| SET_MAKE='' | |
| SHELL='/bin/sh' | |
| STRIP='' | |
| VERSION='3.2.0' | |
| ac_ct_CC='/usr/bin/llvm-gcc' | |
| ac_ct_CXX='' | |
| 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='' | |
| am__quote='' | |
| am__tar='$${TAR-tar} chof - "$$tardir"' | |
| am__untar='$${TAR-tar} xf -' | |
| bindir='${exec_prefix}/bin' | |
| build='x86_64-apple-darwin12.2.0' | |
| build_alias='' | |
| build_cpu='x86_64' | |
| build_os='darwin12.2.0' | |
| build_vendor='apple' | |
| datadir='${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='${SHELL} /private/tmp/tmap-rhOV/config/install-sh' | |
| libdir='${exec_prefix}/lib' | |
| libexecdir='${exec_prefix}/libexec' | |
| localedir='${datarootdir}/locale' | |
| localstatedir='${prefix}/var' | |
| mandir='${datarootdir}/man' | |
| mkdir_p='$(MKDIR_P)' | |
| oldincludedir='/usr/include' | |
| pdfdir='${docdir}' | |
| prefix='/usr/local/Cellar/tmap/3.2.0' | |
| 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 "tmap" | |
| #define PACKAGE_TARNAME "tmap" | |
| #define PACKAGE_VERSION "3.2.0" | |
| #define PACKAGE_STRING "tmap 3.2.0" | |
| #define PACKAGE_BUGREPORT "nils.homer@lifetech.com" | |
| #define PACKAGE_URL "" | |
| #define PACKAGE "tmap" | |
| #define VERSION "3.2.0" | |
| #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 __EXTENSIONS__ 1 | |
| #define _ALL_SOURCE 1 | |
| #define _GNU_SOURCE 1 | |
| #define _POSIX_PTHREAD_SEMANTICS 1 | |
| #define _TANDEM_SOURCE 1 | |
| #define HAVE_LIBBZ2 1 | |
| #define HAVE_LIBTCMALLOC 1 | |
| #define HAVE_STDLIB_H 1 | |
| #define HAVE_MALLOC 0 | |
| #define malloc rpl_malloc | |
| #define HAVE_STDLIB_H 1 | |
| #define HAVE_REALLOC 0 | |
| #define realloc rpl_realloc | |
| #define HAVE_ALLOCA_H 1 | |
| #define HAVE_ALLOCA 1 | |
| #define HAVE_FSEEKO 1 | |
| #define HAVE_SYS_SELECT_H 1 | |
| #define HAVE_SYS_SOCKET_H 1 | |
| #define SELECT_TYPE_ARG1 int | |
| #define SELECT_TYPE_ARG234 (fd_set *) | |
| #define SELECT_TYPE_ARG5 (struct timeval *) | |
| #define HAVE_STAT_EMPTY_STRING_BUG 1 | |
| #define HAVE_VPRINTF 1 | |
| #define HAVE_LIBZ 1 | |
| #define HAVE_LIBM 1 | |
| #define HAVE_LIBPTHREAD 1 | |
| #define HAVE_POW 1 | |
| #define HAVE_STRDUP 1 | |
| #define HAVE_MEMSET 1 | |
| #define HAVE_STRCHR 1 | |
| #define HAVE_STRDUP 1 | |
| #define HAVE_STRSTR 1 | |
| #define HAVE_MEMMOVE 1 | |
| #define HAVE_GETOPT_LONG 1 | |
| #define HAVE_GETTIMEOFDAY 1 | |
| #define HAVE_GETHOSTBYADDR 1 | |
| #define HAVE_GETHOSTBYNAME 1 | |
| #define HAVE_MEMCHR 1 | |
| #define HAVE_SELECT 1 | |
| #define HAVE_SOCKET 1 | |
| #define HAVE_SQRT 1 | |
| #define HAVE_STRERROR 1 | |
| #define HAVE_STRTOL 1 | |
| #define RETSIGTYPE void | |
| #define SIZEOF_SHORT_INT 0 | |
| #define SIZEOF_INT 0 | |
| #define SIZEOF_LONG_INT 0 | |
| #define STDC_HEADERS 1 | |
| #define HAVE__BOOL 1 | |
| #define HAVE_STDBOOL_H 1 | |
| #define TIME_WITH_SYS_TIME 1 | |
| #define HAVE_STDLIB_H 1 | |
| #define HAVE_STDIO_H 1 | |
| #define HAVE_STDINT_H 1 | |
| #define HAVE_STRING_H 1 | |
| #define HAVE_SYS_TIME_H 1 | |
| #define HAVE_UNISTD_H 1 | |
| #define HAVE_FLOAT_H 1 | |
| #define HAVE_ZLIB_H 1 | |
| #define HAVE_BZLIB_H 1 | |
| #define HAVE_PTHREAD_H 1 | |
| #define HAVE_LIMITS_H 1 | |
| #define HAVE_NETINET_IN_H 1 | |
| #define HAVE_EMMINTRIN_H 1 | |
| #define HAVE_GETOPT_H 1 | |
| #define HAVE_ARPA_INET_H 1 | |
| #define HAVE_FCNTL_H 1 | |
| #define HAVE_NETDB_H 1 | |
| #define HAVE_STDDEF_H 1 | |
| #define HAVE_SYS_SOCKET_H 1 | |
| #define HAVE_WCHAR_H 1 | |
| #define HAVE_CURSES_H 1 | |
| configure: exit 0 |
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