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tseemann/01.configure

Created June 13, 2015 08:58
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01.configure
2015-06-13 18:57:26 +1000
./configure
--disable-debug
--disable-dependency-tracking
--disable-silent-rules
--prefix=/bio/linuxbrew/Cellar/uproc/1.1.2
configure: WARNING: unrecognized options: --disable-debug
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for GNU make... make
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... /bio/linuxbrew/bin/gcc-5
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /bio/linuxbrew/bin/gcc-5 accepts -g... yes
checking for /bio/linuxbrew/bin/gcc-5 option to accept ISO C89... none needed
checking whether /bio/linuxbrew/bin/gcc-5 understands -c and -o together... yes
checking dependency style of /bio/linuxbrew/bin/gcc-5... none
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by /bio/linuxbrew/bin/gcc-5... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from /bio/linuxbrew/bin/gcc-5 object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... /bio/linuxbrew/bin/gcc-5 -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if /bio/linuxbrew/bin/gcc-5 supports -fno-rtti -fno-exceptions... yes
checking for /bio/linuxbrew/bin/gcc-5 option to produce PIC... -fPIC -DPIC
checking if /bio/linuxbrew/bin/gcc-5 PIC flag -fPIC -DPIC works... yes
checking if /bio/linuxbrew/bin/gcc-5 static flag -static works... no
checking if /bio/linuxbrew/bin/gcc-5 supports -c -o file.o... yes
checking if /bio/linuxbrew/bin/gcc-5 supports -c -o file.o... (cached) yes
checking whether the /bio/linuxbrew/bin/gcc-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for /bio/linuxbrew/bin/gcc-5 option to accept ISO C99... none needed
checking for __attribute__... yes
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for vprintf... yes
checking for _doprnt... no
checking for mkdir... yes
checking for _mkdir... no
checking whether mkdir takes one argument... no
checking for atexit... yes
checking for munmap... yes
checking for pow... no
checking for strchr... yes
checking for strerror... yes
checking for posix_madvise... yes
checking for getopt_long... yes
checking for library containing log2... -lm
checking for library containing gzopen... -lz
checking for library containing clock_gettime... none required
checking for clock_gettime... yes
checking for /bio/linuxbrew/bin/gcc-5 option to support OpenMP... -fopenmp
checking for pkg-config... /bio/linuxbrew/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for CHECK... no
checking for doxygen... doxygen
checking for git... git
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating libuproc/Makefile
config.status: creating libuproc/include/Makefile
config.status: creating libuproc/tests/Makefile
config.status: creating libuproc/tests/data/Makefile
config.status: creating libuproc/docs/doxyfile
config.status: creating libuproc/docs/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-debug
Raw
02.make
2015-06-13 18:57:32 +1000
make
install
Making install in libuproc
make[1]: Entering directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc'
make install-recursive
make[2]: Entering directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc'
Making install in tests
make[3]: Entering directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/tests'
make[4]: Entering directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/tests'
make[5]: Entering directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/tests'
make[5]: Nothing to be done for `install-exec-am'.
make[5]: Nothing to be done for `install-data-am'.
make[5]: Leaving directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/tests'
make[4]: Leaving directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/tests'
make[3]: Leaving directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/tests'
Making install in include
make[3]: Entering directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/include'
make[4]: Entering directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/include'
make[4]: Nothing to be done for `install-exec-am'.
/usr/bin/mkdir -p '/bio/linuxbrew/Cellar/uproc/1.1.2/include'
/usr/bin/install -c -m 644 uproc.h '/bio/linuxbrew/Cellar/uproc/1.1.2/include/.'
/usr/bin/mkdir -p '/bio/linuxbrew/Cellar/uproc/1.1.2/include/uproc'
/usr/bin/install -c -m 644 uproc/alphabet.h uproc/bst.h uproc/codon.h uproc/common.h uproc/dnaclass.h uproc/ecurve.h uproc/error.h uproc/features.h uproc/idmap.h uproc/io.h uproc/list.h uproc/matrix.h uproc/orf.h uproc/protclass.h uproc/seqio.h uproc/substmat.h uproc/word.h '/bio/linuxbrew/Cellar/uproc/1.1.2/include/uproc'
make[4]: Leaving directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/include'
make[3]: Leaving directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/include'
Making install in docs
make[3]: Entering directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/docs'
doxygen doxyfile
echo Timestamp > doxygen.stamp
tar chozf libuproc.tar.gz libuproc
tar: value 1424802263 out of uid_t range 0..2097151
tar: Exiting with failure status due to previous errors
make[3]: *** [libuproc.tar.gz] Error 2
make[3]: Leaving directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc/docs'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/libuproc'
make: *** [install-recursive] Error 1
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew
HEAD: d0844607d93192f6012cf19676c157cbfc31954d
Last commit: 3 days ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
CPU: 72-core 64-bit 6
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: N/A
System Ruby: 2.2.2 => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Perl: /usr/bin/perl
Python: /bio/python/bin/python
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Java: 1.7.0_79
CC: /bio/linuxbrew/bin/gcc-5 => /bio/linuxbrew/Cellar/gcc/5.1.0/bin/gcc-5
CXX: /bio/linuxbrew/bin/g++-5 => /bio/linuxbrew/Cellar/gcc/5.1.0/bin/g++-5
OBJC: /bio/linuxbrew/bin/gcc-5
OBJCXX: /bio/linuxbrew/bin/g++-5
CFLAGS: -Os -w -pipe -march=core2
CXXFLAGS: -Os -w -pipe -march=core2
CPPFLAGS: -isystem/bio/linuxbrew/include
LDFLAGS: -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib
MAKEFLAGS: -j72
CMAKE_PREFIX_PATH: /bio/linuxbrew
PKG_CONFIG_LIBDIR: /bio/linuxbrew/lib/pkgconfig
PATH: /home/tseemann/perl5/bin:/bio/python/bin:/bio/perl5/bin:/bio/linuxbrew/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bio/sw/hierBAPS:/bio/sw/brat:/bio/sw/mauve:/bio/sw/splitstree4:/bio/sw/vbc/fqa-tools:/bio/sw/vbc/misc:/bio/sw/MUMmer:/bio/sw/tablet:/bio/sw/nesoni/bin:/home/tseemann/git/wombac/bin:/home/tseemann/git/snippy/bin:/home/tseemann/git/barrnap/bin:/home/tseemann/git/nullarbor/bin:/home/tseemann/git/prokka/bin:/home/tseemann/git/mlst/bin:/home/tseemann/git/abricate/bin:/home/tseemann/git/mdu-tools/bin:/usr/local/sbin:/usr/sbin:/home/tseemann/.local/bin:/home/tseemann/bin:/bio/linuxbrew/Library/ENV/scm
Raw
config.log
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by uproc configure 1.1.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/bio/linuxbrew/Cellar/uproc/1.1.2
## --------- ##
## Platform. ##
## --------- ##
hostname = 526080-s598783.unimelb.edu.au
uname -m = x86_64
uname -r = 3.10.0-229.4.2.el7.x86_64
uname -s = Linux
uname -v = #1 SMP Fri Apr 24 15:26:38 EDT 2015
/usr/bin/uname -p = x86_64
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /home/tseemann/perl5/bin
PATH: /bio/python/bin
PATH: /bio/perl5/bin
PATH: /bio/linuxbrew/bin
PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bio/sw/hierBAPS
PATH: /bio/sw/brat
PATH: /bio/sw/mauve
PATH: /bio/sw/splitstree4
PATH: /bio/sw/vbc/fqa-tools
PATH: /bio/sw/vbc/misc
PATH: /bio/sw/MUMmer
PATH: /bio/sw/tablet
PATH: /bio/sw/nesoni/bin
PATH: /home/tseemann/git/wombac/bin
PATH: /home/tseemann/git/snippy/bin
PATH: /home/tseemann/git/barrnap/bin
PATH: /home/tseemann/git/nullarbor/bin
PATH: /home/tseemann/git/prokka/bin
PATH: /home/tseemann/git/mlst/bin
PATH: /home/tseemann/git/abricate/bin
PATH: /home/tseemann/git/mdu-tools/bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /home/tseemann/.local/bin
PATH: /home/tseemann/bin
PATH: /bio/linuxbrew/Library/ENV/scm
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2345: checking for a BSD-compatible install
configure:2413: result: /usr/bin/install -c
configure:2424: checking whether build environment is sane
configure:2479: result: yes
configure:2630: checking for a thread-safe mkdir -p
configure:2669: result: /usr/bin/mkdir -p
configure:2676: checking for gawk
configure:2692: found /usr/bin/gawk
configure:2703: result: gawk
configure:2714: checking whether make sets $(MAKE)
configure:2736: result: yes
configure:2765: checking whether make supports nested variables
configure:2782: result: yes
configure:2908: checking for GNU make
configure:2923: result: make
configure:2965: checking build system type
configure:2979: result: x86_64-unknown-linux-gnu
configure:2999: checking host system type
configure:3012: result: x86_64-unknown-linux-gnu
configure:3053: checking how to print strings
configure:3080: result: printf
configure:3113: checking for style of include used by make
configure:3141: result: GNU
configure:3212: checking for gcc
configure:3239: result: /bio/linuxbrew/bin/gcc-5
configure:3468: checking for C compiler version
configure:3477: /bio/linuxbrew/bin/gcc-5 --version >&5
gcc-5 (Homebrew gcc 5.1.0) 5.1.0
Copyright (C) 2015 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:3488: $? = 0
configure:3477: /bio/linuxbrew/bin/gcc-5 -v >&5
Reading specs from /bio/linuxbrew/Cellar/gcc/5.1.0/lib/gcc/x86_64-unknown-linux-gnu/5.1.0/specs
COLLECT_GCC=/bio/linuxbrew/bin/gcc-5
COLLECT_LTO_WRAPPER=/bio/linuxbrew/Cellar/gcc/5.1.0/libexec/gcc/x86_64-unknown-linux-gnu/5.1.0/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../configure --prefix=/bio/linuxbrew/Cellar/gcc/5.1.0 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/bio/linuxbrew/opt/gmp --with-mpfr=/bio/linuxbrew/opt/mpfr --with-mpc=/bio/linuxbrew/opt/libmpc --with-isl=/bio/linuxbrew/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew gcc 5.1.0' --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --disable-multilib
Thread model: posix
gcc version 5.1.0 (Homebrew gcc 5.1.0)
configure:3488: $? = 0
configure:3477: /bio/linuxbrew/bin/gcc-5 -V >&5
gcc-5: error: unrecognized command line option '-V'
gcc-5: fatal error: no input files
compilation terminated.
configure:3488: $? = 1
configure:3477: /bio/linuxbrew/bin/gcc-5 -qversion >&5
gcc-5: error: unrecognized command line option '-qversion'
gcc-5: fatal error: no input files
compilation terminated.
configure:3488: $? = 1
configure:3508: checking whether the C compiler works
configure:3530: /bio/linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:3534: $? = 0
configure:3582: result: yes
configure:3585: checking for C compiler default output file name
configure:3587: result: a.out
configure:3593: checking for suffix of executables
configure:3600: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:3604: $? = 0
configure:3626: result:
configure:3648: checking whether we are cross compiling
configure:3656: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:3660: $? = 0
configure:3667: ./conftest
configure:3671: $? = 0
configure:3686: result: no
configure:3691: checking for suffix of object files
configure:3713: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:3717: $? = 0
configure:3738: result: o
configure:3742: checking whether we are using the GNU C compiler
configure:3761: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:3761: $? = 0
configure:3770: result: yes
configure:3779: checking whether /bio/linuxbrew/bin/gcc-5 accepts -g
configure:3799: /bio/linuxbrew/bin/gcc-5 -c -g -isystem/bio/linuxbrew/include conftest.c >&5
configure:3799: $? = 0
configure:3840: result: yes
configure:3857: checking for /bio/linuxbrew/bin/gcc-5 option to accept ISO C89
configure:3920: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:3920: $? = 0
configure:3933: result: none needed
configure:3958: checking whether /bio/linuxbrew/bin/gcc-5 understands -c and -o together
configure:3980: /bio/linuxbrew/bin/gcc-5 -c conftest.c -o conftest2.o
configure:3983: $? = 0
configure:3980: /bio/linuxbrew/bin/gcc-5 -c conftest.c -o conftest2.o
configure:3983: $? = 0
configure:3995: result: yes
configure:4014: checking dependency style of /bio/linuxbrew/bin/gcc-5
configure:4125: result: none
configure:4140: checking for a sed that does not truncate output
configure:4204: result: /usr/bin/sed
configure:4222: checking for grep that handles long lines and -e
configure:4280: result: /usr/bin/grep
configure:4285: checking for egrep
configure:4347: result: /usr/bin/grep -E
configure:4352: checking for fgrep
configure:4414: result: /usr/bin/grep -F
configure:4449: checking for ld used by /bio/linuxbrew/bin/gcc-5
configure:4516: result: /usr/bin/ld
configure:4523: checking if the linker (/usr/bin/ld) is GNU ld
configure:4538: result: yes
configure:4550: checking for BSD- or MS-compatible name lister (nm)
configure:4599: result: /usr/bin/nm -B
configure:4729: checking the name lister (/usr/bin/nm -B) interface
configure:4736: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:4739: /usr/bin/nm -B "conftest.o"
configure:4742: output
0000000000000000 B some_variable
configure:4749: result: BSD nm
configure:4752: checking whether ln -s works
configure:4756: result: yes
configure:4764: checking the maximum length of command line arguments
configure:4894: result: 1572864
configure:4911: checking whether the shell understands some XSI constructs
configure:4921: result: yes
configure:4925: checking whether the shell understands "+="
configure:4931: result: yes
configure:4966: checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format
configure:5006: result: func_convert_file_noop
configure:5013: checking how to convert x86_64-unknown-linux-gnu file names to toolchain format
configure:5033: result: func_convert_file_noop
configure:5040: checking for /usr/bin/ld option to reload object files
configure:5047: result: -r
configure:5121: checking for objdump
configure:5137: found /usr/bin/objdump
configure:5148: result: objdump
configure:5180: checking how to recognize dependent libraries
configure:5382: result: pass_all
configure:5467: checking for dlltool
configure:5497: result: no
configure:5527: checking how to associate runtime and link libraries
configure:5554: result: printf %s\n
configure:5615: checking for ar
configure:5631: found /usr/bin/ar
configure:5642: result: ar
configure:5679: checking for archiver @FILE support
configure:5696: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:5696: $? = 0
configure:5699: ar cru libconftest.a @conftest.lst >&5
configure:5702: $? = 0
configure:5707: ar cru libconftest.a @conftest.lst >&5
ar: conftest.o: No such file or directory
configure:5710: $? = 1
configure:5722: result: @
configure:5780: checking for strip
configure:5796: found /usr/bin/strip
configure:5807: result: strip
configure:5879: checking for ranlib
configure:5895: found /usr/bin/ranlib
configure:5906: result: ranlib
configure:6008: checking command to parse /usr/bin/nm -B output from /bio/linuxbrew/bin/gcc-5 object
configure:6128: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:6131: $? = 0
configure:6135: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' | sed '/ __gnu_lto/d' \> conftest.nm
configure:6138: $? = 0
configure:6204: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c conftstm.o >&5
configure:6207: $? = 0
configure:6245: result: ok
configure:6282: checking for sysroot
configure:6312: result: no
configure:6389: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:6392: $? = 0
configure:6568: checking for mt
configure:6598: result: no
configure:6618: checking if : is a manifest tool
configure:6624: : '-?'
configure:6632: result: no
configure:7274: checking how to run the C preprocessor
configure:7305: /bio/linuxbrew/bin/gcc-5 -E -isystem/bio/linuxbrew/include conftest.c
configure:7305: $? = 0
configure:7319: /bio/linuxbrew/bin/gcc-5 -E -isystem/bio/linuxbrew/include conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:7319: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:7344: result: /bio/linuxbrew/bin/gcc-5 -E
configure:7364: /bio/linuxbrew/bin/gcc-5 -E -isystem/bio/linuxbrew/include conftest.c
configure:7364: $? = 0
configure:7378: /bio/linuxbrew/bin/gcc-5 -E -isystem/bio/linuxbrew/include conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:7378: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:7407: checking for ANSI C header files
configure:7427: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7427: $? = 0
configure:7500: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:7500: $? = 0
configure:7500: ./conftest
configure:7500: $? = 0
configure:7511: result: yes
configure:7524: checking for sys/types.h
configure:7524: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7524: $? = 0
configure:7524: result: yes
configure:7524: checking for sys/stat.h
configure:7524: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7524: $? = 0
configure:7524: result: yes
configure:7524: checking for stdlib.h
configure:7524: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7524: $? = 0
configure:7524: result: yes
configure:7524: checking for string.h
configure:7524: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7524: $? = 0
configure:7524: result: yes
configure:7524: checking for memory.h
configure:7524: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7524: $? = 0
configure:7524: result: yes
configure:7524: checking for strings.h
configure:7524: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7524: $? = 0
configure:7524: result: yes
configure:7524: checking for inttypes.h
configure:7524: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7524: $? = 0
configure:7524: result: yes
configure:7524: checking for stdint.h
configure:7524: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7524: $? = 0
configure:7524: result: yes
configure:7524: checking for unistd.h
configure:7524: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7524: $? = 0
configure:7524: result: yes
configure:7538: checking for dlfcn.h
configure:7538: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:7538: $? = 0
configure:7538: result: yes
configure:7744: checking for objdir
configure:7759: result: .libs
configure:8030: checking if /bio/linuxbrew/bin/gcc-5 supports -fno-rtti -fno-exceptions
configure:8048: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -fno-rtti -fno-exceptions conftest.c >&5
configure:8052: $? = 0
configure:8065: result: yes
configure:8392: checking for /bio/linuxbrew/bin/gcc-5 option to produce PIC
configure:8399: result: -fPIC -DPIC
configure:8407: checking if /bio/linuxbrew/bin/gcc-5 PIC flag -fPIC -DPIC works
configure:8425: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -fPIC -DPIC -DPIC conftest.c >&5
configure:8429: $? = 0
configure:8442: result: yes
configure:8471: checking if /bio/linuxbrew/bin/gcc-5 static flag -static works
configure:8499: result: no
configure:8514: checking if /bio/linuxbrew/bin/gcc-5 supports -c -o file.o
configure:8535: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -o out/conftest2.o conftest.c >&5
configure:8539: $? = 0
configure:8561: result: yes
configure:8569: checking if /bio/linuxbrew/bin/gcc-5 supports -c -o file.o
configure:8616: result: yes
configure:8649: checking whether the /bio/linuxbrew/bin/gcc-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:9802: result: yes
configure:9839: checking whether -lc should be explicitly linked in
configure:9847: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:9850: $? = 0
configure:9865: /bio/linuxbrew/bin/gcc-5 -shared -fPIC -DPIC conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /usr/bin/grep -lc \>/dev/null 2\>\&1
configure:9868: $? = 0
configure:9882: result: no
configure:10042: checking dynamic linker characteristics
configure:10553: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib -Wl,-rpath -Wl,/foo conftest.c >&5
configure:10553: $? = 0
configure:10775: result: GNU/Linux ld.so
configure:10882: checking how to hardcode library paths into programs
configure:10907: result: immediate
configure:11447: checking whether stripping libraries is possible
configure:11452: result: yes
configure:11487: checking if libtool supports shared libraries
configure:11489: result: yes
configure:11492: checking whether to build shared libraries
configure:11513: result: yes
configure:11516: checking whether to build static libraries
configure:11520: result: yes
configure:11564: checking for /bio/linuxbrew/bin/gcc-5 option to accept ISO C99
configure:11713: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:11713: $? = 0
configure:11726: result: none needed
configure:11744: checking for __attribute__
configure:11769: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:11769: $? = 0
configure:11780: result: yes
configure:12091: checking for ANSI C header files
configure:12195: result: yes
configure:12206: checking fcntl.h usability
configure:12206: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12206: $? = 0
configure:12206: result: yes
configure:12206: checking fcntl.h presence
configure:12206: /bio/linuxbrew/bin/gcc-5 -E -isystem/bio/linuxbrew/include conftest.c
configure:12206: $? = 0
configure:12206: result: yes
configure:12206: checking for fcntl.h
configure:12206: result: yes
configure:12206: checking for inttypes.h
configure:12206: result: yes
configure:12206: checking limits.h usability
configure:12206: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12206: $? = 0
configure:12206: result: yes
configure:12206: checking limits.h presence
configure:12206: /bio/linuxbrew/bin/gcc-5 -E -isystem/bio/linuxbrew/include conftest.c
configure:12206: $? = 0
configure:12206: result: yes
configure:12206: checking for limits.h
configure:12206: result: yes
configure:12206: checking for stdint.h
configure:12206: result: yes
configure:12206: checking for stdlib.h
configure:12206: result: yes
configure:12206: checking for string.h
configure:12206: result: yes
configure:12219: checking for unistd.h
configure:12219: result: yes
configure:12219: checking zlib.h usability
configure:12219: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12219: $? = 0
configure:12219: result: yes
configure:12219: checking zlib.h presence
configure:12219: /bio/linuxbrew/bin/gcc-5 -E -isystem/bio/linuxbrew/include conftest.c
configure:12219: $? = 0
configure:12219: result: yes
configure:12219: checking for zlib.h
configure:12219: result: yes
configure:12219: checking getopt.h usability
configure:12219: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12219: $? = 0
configure:12219: result: yes
configure:12219: checking getopt.h presence
configure:12219: /bio/linuxbrew/bin/gcc-5 -E -isystem/bio/linuxbrew/include conftest.c
configure:12219: $? = 0
configure:12219: result: yes
configure:12219: checking for getopt.h
configure:12219: result: yes
configure:12219: checking time.h usability
configure:12219: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12219: $? = 0
configure:12219: result: yes
configure:12219: checking time.h presence
configure:12219: /bio/linuxbrew/bin/gcc-5 -E -isystem/bio/linuxbrew/include conftest.c
configure:12219: $? = 0
configure:12219: result: yes
configure:12219: checking for time.h
configure:12219: result: yes
configure:12230: checking for stdbool.h that conforms to C99
configure:12297: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12297: $? = 0
configure:12304: result: yes
configure:12306: checking for _Bool
configure:12306: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12306: $? = 0
configure:12306: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:71:20: error: expected expression before ')' token
if (sizeof ((_Bool)))
^
configure:12306: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE___ATTRIBUTE__ 1
| #define STDC_HEADERS 1
| #define HAVE_FCNTL_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_GETOPT_H 1
| #define HAVE_TIME_H 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((_Bool)))
| return 0;
| ;
| return 0;
| }
configure:12306: result: yes
configure:12323: checking for an ANSI C-conforming const
configure:12389: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12389: $? = 0
configure:12396: result: yes
configure:12404: checking for size_t
configure:12404: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12404: $? = 0
configure:12404: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:73:21: error: expected expression before ')' token
if (sizeof ((size_t)))
^
configure:12404: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE___ATTRIBUTE__ 1
| #define STDC_HEADERS 1
| #define HAVE_FCNTL_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_GETOPT_H 1
| #define HAVE_TIME_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((size_t)))
| return 0;
| ;
| return 0;
| }
configure:12404: result: yes
configure:12423: checking for stdlib.h
configure:12423: result: yes
configure:12423: checking for unistd.h
configure:12423: result: yes
configure:12423: checking for sys/param.h
configure:12423: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
configure:12423: $? = 0
configure:12423: result: yes
configure:12443: checking for getpagesize
configure:12443: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12443: $? = 0
configure:12443: result: yes
configure:12452: checking for working mmap
configure:12599: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12599: $? = 0
configure:12599: ./conftest
configure:12599: $? = 0
configure:12609: result: yes
configure:12620: checking for vprintf
configure:12620: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12620: $? = 0
configure:12620: result: yes
configure:12626: checking for _doprnt
configure:12626: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
/tmp/cckWBwra.o: In function `main':
conftest.c:(.text.startup+0x4): undefined reference to `_doprnt'
collect2: error: ld returned 1 exit status
configure:12626: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE___ATTRIBUTE__ 1
| #define STDC_HEADERS 1
| #define HAVE_FCNTL_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_GETOPT_H 1
| #define HAVE_TIME_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MMAP 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:12626: result: no
configure:12640: checking for mkdir
configure:12640: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12640: $? = 0
configure:12640: result: yes
configure:12640: checking for _mkdir
configure:12640: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
/tmp/ccui3yf6.o: In function `main':
conftest.c:(.text.startup+0x4): undefined reference to `_mkdir'
collect2: error: ld returned 1 exit status
configure:12640: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE___ATTRIBUTE__ 1
| #define STDC_HEADERS 1
| #define HAVE_FCNTL_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_GETOPT_H 1
| #define HAVE_TIME_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MMAP 1
| #define HAVE_VPRINTF 1
| #define HAVE_MKDIR 1
| /* end confdefs.h. */
| /* Define _mkdir to an innocuous variant, in case <limits.h> declares _mkdir.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define _mkdir innocuous__mkdir
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char _mkdir (); 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 _mkdir
|
| /* 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 _mkdir ();
| /* 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__mkdir || defined __stub____mkdir
| choke me
| #endif
|
| int
| main ()
| {
| return _mkdir ();
| ;
| return 0;
| }
configure:12640: result: no
configure:12649: checking whether mkdir takes one argument
configure:12670: /bio/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:53:1: error: too few arguments to function 'mkdir'
mkdir (".");
^
In file included from conftest.c:45:0:
/usr/include/sys/stat.h:322:12: note: declared here
extern int mkdir (const char *__path, __mode_t __mode)
^
configure:12670: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE___ATTRIBUTE__ 1
| #define STDC_HEADERS 1
| #define HAVE_FCNTL_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_GETOPT_H 1
| #define HAVE_TIME_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MMAP 1
| #define HAVE_VPRINTF 1
| #define HAVE_MKDIR 1
| /* end confdefs.h. */
|
| #include <sys/stat.h>
| #if HAVE_UNISTD_H
| # include <unistd.h>
| #endif
|
| int
| main ()
| {
| mkdir (".");
| ;
| return 0;
| }
configure:12677: result: no
configure:12689: checking for atexit
configure:12689: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12689: $? = 0
configure:12689: result: yes
configure:12689: checking for munmap
configure:12689: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12689: $? = 0
configure:12689: result: yes
configure:12689: checking for pow
configure:12689: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
/tmp/ccH8Epxg.o: In function `main':
conftest.c:(.text.startup+0x4): undefined reference to `pow'
collect2: error: ld returned 1 exit status
configure:12689: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE___ATTRIBUTE__ 1
| #define STDC_HEADERS 1
| #define HAVE_FCNTL_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_GETOPT_H 1
| #define HAVE_TIME_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MMAP 1
| #define HAVE_VPRINTF 1
| #define HAVE_MKDIR 1
| #define HAVE_ATEXIT 1
| #define HAVE_MUNMAP 1
| /* end confdefs.h. */
| /* Define pow to an innocuous variant, in case <limits.h> declares pow.
| For example, HP-UX 11i <limits.h> declares gettimeofday. */
| #define pow innocuous_pow
|
| /* System header to define __stub macros and hopefully few prototypes,
| which can conflict with char pow (); below.
| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
| <limits.h> exists even on freestanding compilers. */
|
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|
| #undef pow
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char pow ();
| /* The GNU C library defines this for functions which it implements
| to always fail with ENOSYS. Some functions are actually named
| something starting with __ and the normal name is an alias. */
| #if defined __stub_pow || defined __stub___pow
| choke me
| #endif
|
| int
| main ()
| {
| return pow ();
| ;
| return 0;
| }
configure:12689: result: no
configure:12689: checking for strchr
configure:12689: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12689: $? = 0
configure:12689: result: yes
configure:12689: checking for strerror
configure:12689: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12689: $? = 0
configure:12689: result: yes
configure:12689: checking for posix_madvise
configure:12689: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12689: $? = 0
configure:12689: result: yes
configure:12689: checking for getopt_long
configure:12689: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
configure:12689: $? = 0
configure:12689: result: yes
configure:12700: checking for library containing log2
configure:12731: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c >&5
/tmp/cchKoycu.o: In function `main':
conftest.c:(.text.startup+0x4): undefined reference to `log2'
collect2: error: ld returned 1 exit status
configure:12731: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE___ATTRIBUTE__ 1
| #define STDC_HEADERS 1
| #define HAVE_FCNTL_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_GETOPT_H 1
| #define HAVE_TIME_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MMAP 1
| #define HAVE_VPRINTF 1
| #define HAVE_MKDIR 1
| #define HAVE_ATEXIT 1
| #define HAVE_MUNMAP 1
| #define HAVE_STRCHR 1
| #define HAVE_STRERROR 1
| #define HAVE_POSIX_MADVISE 1
| #define HAVE_GETOPT_LONG 1
| /* end confdefs.h. */
|
| /* 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 log2 ();
| int
| main ()
| {
| return log2 ();
| ;
| return 0;
| }
configure:12731: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c -lm >&5
configure:12731: $? = 0
configure:12748: result: -lm
configure:12756: checking for library containing gzopen
configure:12787: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c -lm >&5
/tmp/ccGmseMy.o: In function `main':
conftest.c:(.text.startup+0x4): undefined reference to `gzopen'
collect2: error: ld returned 1 exit status
configure:12787: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE___ATTRIBUTE__ 1
| #define STDC_HEADERS 1
| #define HAVE_FCNTL_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_GETOPT_H 1
| #define HAVE_TIME_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MMAP 1
| #define HAVE_VPRINTF 1
| #define HAVE_MKDIR 1
| #define HAVE_ATEXIT 1
| #define HAVE_MUNMAP 1
| #define HAVE_STRCHR 1
| #define HAVE_STRERROR 1
| #define HAVE_POSIX_MADVISE 1
| #define HAVE_GETOPT_LONG 1
| /* end confdefs.h. */
|
| /* 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 gzopen ();
| int
| main ()
| {
| return gzopen ();
| ;
| return 0;
| }
configure:12787: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c -lz -lm >&5
configure:12787: $? = 0
configure:12804: result: -lz
configure:12814: checking for library containing clock_gettime
configure:12845: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c -lz -lm >&5
configure:12845: $? = 0
configure:12862: result: none required
configure:12872: checking for clock_gettime
configure:12872: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c -lz -lm >&5
configure:12872: $? = 0
configure:12872: result: yes
configure:12890: checking for /bio/linuxbrew/bin/gcc-5 option to support OpenMP
configure:12905: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c -lz -lm >&5
conftest.c:53:2: error: unknown type name 'choke'
choke me
^
In file included from conftest.c:55:0:
/bio/linuxbrew/Cellar/gcc/5.1.0/lib/gcc/x86_64-unknown-linux-gnu/5.1.0/include/omp.h:35:1: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'typedef'
typedef struct
^
configure:12905: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "uproc"
| #define PACKAGE_TARNAME "uproc"
| #define PACKAGE_VERSION "1.1.2"
| #define PACKAGE_STRING "uproc 1.1.2"
| #define PACKAGE_BUGREPORT "uproc@gobics.de"
| #define PACKAGE_URL ""
| #define PACKAGE "uproc"
| #define VERSION "1.1.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE___ATTRIBUTE__ 1
| #define STDC_HEADERS 1
| #define HAVE_FCNTL_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ZLIB_H 1
| #define HAVE_GETOPT_H 1
| #define HAVE_TIME_H 1
| #define HAVE__BOOL 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_GETPAGESIZE 1
| #define HAVE_MMAP 1
| #define HAVE_VPRINTF 1
| #define HAVE_MKDIR 1
| #define HAVE_ATEXIT 1
| #define HAVE_MUNMAP 1
| #define HAVE_STRCHR 1
| #define HAVE_STRERROR 1
| #define HAVE_POSIX_MADVISE 1
| #define HAVE_GETOPT_LONG 1
| #define HAVE_CLOCK_GETTIME 1
| /* end confdefs.h. */
|
| #ifndef _OPENMP
| choke me
| #endif
| #include <omp.h>
| int main () { return omp_get_num_threads (); }
|
configure:12923: /bio/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=core2 -fopenmp -isystem/bio/linuxbrew/include -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.c -lz -lm >&5
configure:12923: $? = 0
configure:12937: result: -fopenmp
configure:13004: checking for pkg-config
configure:13022: found /bio/linuxbrew/bin/pkg-config
configure:13034: result: /bio/linuxbrew/bin/pkg-config
configure:13059: checking pkg-config is at least version 0.9.0
configure:13062: result: yes
configure:13072: checking for CHECK
configure:13079: $PKG_CONFIG --exists --print-errors "check >= 0.9.4"
Package check was not found in the pkg-config search path.
Perhaps you should add the directory containing `check.pc'
to the PKG_CONFIG_PATH environment variable
No package 'check' found
configure:13082: $? = 1
configure:13096: $PKG_CONFIG --exists --print-errors "check >= 0.9.4"
Package check was not found in the pkg-config search path.
Perhaps you should add the directory containing `check.pc'
to the PKG_CONFIG_PATH environment variable
No package 'check' found
configure:13099: $? = 1
configure:13113: result: no
No package 'check' found
configure:13201: checking for doxygen
configure:13217: found /usr/bin/doxygen
configure:13228: result: doxygen
configure:13255: checking for git
configure:13271: found /usr/bin/git
configure:13282: result: git
configure:13419: checking that generated files are newer than configure
configure:13425: result: done
configure:13460: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by uproc config.status 1.1.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on 526080-s598783.unimelb.edu.au
config.status:1133: creating Makefile
config.status:1133: creating libuproc/Makefile
config.status:1133: creating libuproc/include/Makefile
config.status:1133: creating libuproc/tests/Makefile
config.status:1133: creating libuproc/tests/data/Makefile
config.status:1133: creating libuproc/docs/doxyfile
config.status:1133: creating libuproc/docs/Makefile
config.status:1133: creating config.h
config.status:1362: executing depfiles commands
config.status:1362: executing libtool commands
configure:15691: WARNING: unrecognized options: --disable-debug
## ---------------- ##
## Cache variables. ##
## ---------------- ##
_cv_gnu_make_command=make
ac_cv___attribute__=yes
ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_env_CC_set=set
ac_cv_env_CC_value=/bio/linuxbrew/bin/gcc-5
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-Os -w -pipe -march=core2'
ac_cv_env_CHECK_CFLAGS_set=
ac_cv_env_CHECK_CFLAGS_value=
ac_cv_env_CHECK_LIBS_set=
ac_cv_env_CHECK_LIBS_value=
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=-isystem/bio/linuxbrew/include
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib'
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_PKG_CONFIG_LIBDIR_set=set
ac_cv_env_PKG_CONFIG_LIBDIR_value=/bio/linuxbrew/lib/pkgconfig
ac_cv_env_PKG_CONFIG_PATH_set=
ac_cv_env_PKG_CONFIG_PATH_value=
ac_cv_env_PKG_CONFIG_set=
ac_cv_env_PKG_CONFIG_value=
ac_cv_env_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__mkdir=no
ac_cv_func_atexit=yes
ac_cv_func_clock_gettime=yes
ac_cv_func_getopt_long=yes
ac_cv_func_getpagesize=yes
ac_cv_func_mkdir=yes
ac_cv_func_mmap_fixed_mapped=yes
ac_cv_func_munmap=yes
ac_cv_func_posix_madvise=yes
ac_cv_func_pow=no
ac_cv_func_strchr=yes
ac_cv_func_strerror=yes
ac_cv_func_vprintf=yes
ac_cv_header_dlfcn_h=yes
ac_cv_header_fcntl_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_stdbool_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_param_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_time_h=yes
ac_cv_header_unistd_h=yes
ac_cv_header_zlib_h=yes
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_mkdir_takes_one_arg=no
ac_cv_objext=o
ac_cv_path_EGREP='/usr/bin/grep -E'
ac_cv_path_FGREP='/usr/bin/grep -F'
ac_cv_path_GREP=/usr/bin/grep
ac_cv_path_SED=/usr/bin/sed
ac_cv_path_ac_pt_PKG_CONFIG=/bio/linuxbrew/bin/pkg-config
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/usr/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='/bio/linuxbrew/bin/gcc-5 -E'
ac_cv_prog_DOXYGEN=doxygen
ac_cv_prog_GIT=git
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_CC=/bio/linuxbrew/bin/gcc-5
ac_cv_prog_ac_ct_OBJDUMP=objdump
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_c_openmp=-fopenmp
ac_cv_prog_cc_c89=
ac_cv_prog_cc_c99=
ac_cv_prog_cc_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_search_clock_gettime='none required'
ac_cv_search_gzopen=-lz
ac_cv_search_log2=-lm
ac_cv_type__Bool=yes
ac_cv_type_size_t=yes
am_cv_CC_dependencies_compiler_type=none
am_cv_make_support_nested_variables=yes
am_cv_prog_cc_c_o=yes
lt_cv_ar_at_file=@
lt_cv_archive_cmds_need_lc=no
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_nm_interface='BSD nm'
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/bin/ld
lt_cv_path_NM='/usr/bin/nm -B'
lt_cv_path_mainfest_tool=no
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_pic='-fPIC -DPIC'
lt_cv_prog_compiler_pic_works=yes
lt_cv_prog_compiler_rtti_exceptions=yes
lt_cv_prog_compiler_static_works=no
lt_cv_prog_gnu_ld=yes
lt_cv_sharedlib_from_linklib_cmd='printf %s\n'
lt_cv_shlibpath_overrides_runpath=no
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'' | sed '\''/ __gnu_lto/d'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_max_cmd_len=1572864
lt_cv_to_host_file_cmd=func_convert_file_noop
lt_cv_to_tool_file_cmd=func_convert_file_noop
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/missing aclocal-1.14'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE='#'
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AR='ar'
AS='as'
AUTOCONF='${SHELL} /tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/missing autoconf'
AUTOHEADER='${SHELL} /tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/missing autoheader'
AUTOMAKE='${SHELL} /tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/missing automake-1.14'
AWK='gawk'
CC='/bio/linuxbrew/bin/gcc-5'
CCDEPMODE='depmode=none'
CFLAGS='-Os -w -pipe -march=core2'
CHECK_CFLAGS=''
CHECK_LIBS=''
CPP='/bio/linuxbrew/bin/gcc-5 -E'
CPPFLAGS='-isystem/bio/linuxbrew/include'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
DLLTOOL='false'
DOXYGEN='doxygen'
DSYMUTIL=''
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/usr/bin/grep -E'
EXEEXT=''
FGREP='/usr/bin/grep -F'
GIT='git'
GREP='/usr/bin/grep'
HAVE_CHECK_FALSE=''
HAVE_CHECK_TRUE='#'
HAVE_DOXYGEN_FALSE='#'
HAVE_DOXYGEN_TRUE=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LD='/usr/bin/ld -m elf_x86_64'
LDFLAGS='-L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib'
LIBOBJS=''
LIBS='-lz -lm '
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LIPO=''
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/missing makeinfo'
MANIFEST_TOOL=':'
MKDIR_P='/usr/bin/mkdir -p'
NM='/usr/bin/nm -B'
NMEDIT=''
OBJDUMP='objdump'
OBJEXT='o'
OPENMP_CFLAGS='-fopenmp'
OTOOL64=''
OTOOL=''
PACKAGE='uproc'
PACKAGE_BUGREPORT='uproc@gobics.de'
PACKAGE_NAME='uproc'
PACKAGE_STRING='uproc 1.1.2'
PACKAGE_TARNAME='uproc'
PACKAGE_URL=''
PACKAGE_VERSION='1.1.2'
PATH_SEPARATOR=':'
PKG_CONFIG='/bio/linuxbrew/bin/pkg-config'
PKG_CONFIG_LIBDIR='/bio/linuxbrew/lib/pkgconfig'
PKG_CONFIG_PATH=''
RANLIB='ranlib'
SED='/usr/bin/sed'
SET_MAKE=''
SHARED_LIBUPROC_FALSE='#'
SHARED_LIBUPROC_TRUE=''
SHELL='/bin/sh'
STRIP='strip'
VERSION='1.1.2'
ac_ct_AR='ar'
ac_ct_CC='/bio/linuxbrew/bin/gcc-5'
ac_ct_DUMPBIN=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE=''
am__fastdepCC_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='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
htmldir='${docdir}'
ifGNUmake=''
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /tmp/uproc20150613-140460-q9lvqg/uproc-1.1.2/install-sh'
libdir='${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='/bio/linuxbrew/Cellar/uproc/1.1.2'
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 "uproc"
#define PACKAGE_TARNAME "uproc"
#define PACKAGE_VERSION "1.1.2"
#define PACKAGE_STRING "uproc 1.1.2"
#define PACKAGE_BUGREPORT "uproc@gobics.de"
#define PACKAGE_URL ""
#define PACKAGE "uproc"
#define VERSION "1.1.2"
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_DLFCN_H 1
#define LT_OBJDIR ".libs/"
#define HAVE___ATTRIBUTE__ 1
#define STDC_HEADERS 1
#define HAVE_FCNTL_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_LIMITS_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_UNISTD_H 1
#define HAVE_ZLIB_H 1
#define HAVE_GETOPT_H 1
#define HAVE_TIME_H 1
#define HAVE__BOOL 1
#define HAVE_STDBOOL_H 1
#define HAVE_STDLIB_H 1
#define HAVE_UNISTD_H 1
#define HAVE_SYS_PARAM_H 1
#define HAVE_GETPAGESIZE 1
#define HAVE_MMAP 1
#define HAVE_VPRINTF 1
#define HAVE_MKDIR 1
#define HAVE_ATEXIT 1
#define HAVE_MUNMAP 1
#define HAVE_STRCHR 1
#define HAVE_STRERROR 1
#define HAVE_POSIX_MADVISE 1
#define HAVE_GETOPT_LONG 1
#define HAVE_CLOCK_GETTIME 1
#define USE_MMAP 1
#define UPROC_VERSION "1.1.2"
configure: exit 0
Raw
config.out
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew
HEAD: d0844607d93192f6012cf19676c157cbfc31954d
Last commit: 3 days ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
CPU: 72-core 64-bit 6
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: N/A
System Ruby: 2.2.2 => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Perl: /usr/bin/perl
Python: /bio/python/bin/python
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Java: 1.7.0_79
Raw
doctor.out
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
/bio/python/bin/python-config
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
python
python3
asciidoc
Warning: Homebrew's sbin was not found in your PATH but you have installed
formulae that put executables in /bio/linuxbrew/sbin.
Consider setting the PATH for example like so
echo 'export PATH="/bio/linuxbrew/sbin:$PATH"' >> ~/.bash_profile
Raw
tap.out
Formula: uproc
Tap: homebrew/homebrew-science
Path: /bio/linuxbrew/Library/Taps/homebrew/homebrew-science/uproc.rb
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