config.log

config.log (text/plain), 30.24 KB, created by Toralf Förster on 2016-09-22 17:03:30 UTC

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by tophat configure 2.1.1, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/tophat-2.1.1-r1 --htmldir=/usr/share/doc/tophat-2.1.1-r1/html --libdir=/usr/lib64 --disable-debug

## --------- ##
## Platform. ##
## --------- ##

hostname = mr-fox
uname -m = x86_64
uname -r = 4.7.4-hardened
uname -s = Linux
uname -v = #1 SMP Sat Sep 17 16:52:39 CEST 2016

/usr/bin/uname -p = Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /var/tmp/portage/sci-biology/tophat-2.1.1-r1/temp/python2.7/bin
PATH: /usr/lib/portage/python2.7/ebuild-helpers/xattr
PATH: /usr/lib/portage/python2.7/ebuild-helpers
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /opt/bin
PATH: /usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2348: checking for a BSD-compatible install
configure:2416: result: /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c
configure:2427: checking whether build environment is sane
configure:2482: result: yes
configure:2633: checking for a thread-safe mkdir -p
configure:2672: result: /bin/mkdir -p
configure:2679: checking for gawk
configure:2695: found /usr/bin/gawk
configure:2706: result: gawk
configure:2717: checking whether make sets $(MAKE)
configure:2739: result: yes
configure:2768: checking whether make supports nested variables
configure:2785: result: yes
configure:2931: checking for x86_64-pc-linux-gnu-g++
configure:2947: found /usr/bin/x86_64-pc-linux-gnu-g++
configure:2958: result: x86_64-pc-linux-gnu-g++
configure:3029: checking for C++ compiler version
configure:3038: x86_64-pc-linux-gnu-g++ --version >&5
x86_64-pc-linux-gnu-g++ (Gentoo 6.2.0-r1 p1.1) 6.2.0
Copyright (C) 2016 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:3049: $? = 0
configure:3038: x86_64-pc-linux-gnu-g++ -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0/x86_64-pc-linux-gnu-g++
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/6.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-6.2.0-r1/work/gcc-6.2.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 6.2.0-r1 p1.1' --disable-esp --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --disable-libmpx --enable-vtable-verify --enable-libvtv --enable-lto --without-isl --enable-libsanitizer --disable-default-pie --disable-default-ssp
Thread model: posix
gcc version 6.2.0 (Gentoo 6.2.0-r1 p1.1) 
configure:3049: $? = 0
configure:3038: x86_64-pc-linux-gnu-g++ -V >&5
x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-V'
x86_64-pc-linux-gnu-g++: fatal error: no input files
compilation terminated.
configure:3049: $? = 1
configure:3038: x86_64-pc-linux-gnu-g++ -qversion >&5
x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-qversion'; did you mean '--version'?
x86_64-pc-linux-gnu-g++: fatal error: no input files
compilation terminated.
configure:3049: $? = 1
configure:3069: checking whether the C++ compiler works
configure:3091: x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -Wl,-O1 -Wl,--as-needed conftest.cpp  >&5
configure:3095: $? = 0
configure:3143: result: yes
configure:3146: checking for C++ compiler default output file name
configure:3148: result: a.out
configure:3154: checking for suffix of executables
configure:3161: x86_64-pc-linux-gnu-g++ -o conftest -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -Wl,-O1 -Wl,--as-needed conftest.cpp  >&5
configure:3165: $? = 0
configure:3187: result: 
configure:3209: checking whether we are cross compiling
configure:3217: x86_64-pc-linux-gnu-g++ -o conftest -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -Wl,-O1 -Wl,--as-needed conftest.cpp  >&5
configure:3221: $? = 0
configure:3228: ./conftest
configure:3232: $? = 0
configure:3247: result: no
configure:3252: checking for suffix of object files
configure:3274: x86_64-pc-linux-gnu-g++ -c -march=native -O2 -pipe  -I/usr/include/seqan-1.4 conftest.cpp >&5
configure:3278: $? = 0
configure:3299: result: o
configure:3303: checking whether we are using the GNU C++ compiler
configure:3322: x86_64-pc-linux-gnu-g++ -c -march=native -O2 -pipe  -I/usr/include/seqan-1.4 conftest.cpp >&5
configure:3322: $? = 0
configure:3331: result: yes
configure:3340: checking whether x86_64-pc-linux-gnu-g++ accepts -g
configure:3360: x86_64-pc-linux-gnu-g++ -c -g  -I/usr/include/seqan-1.4 conftest.cpp >&5
configure:3360: $? = 0
configure:3401: result: yes
configure:3435: checking for style of include used by make
configure:3463: result: GNU
configure:3489: checking dependency style of x86_64-pc-linux-gnu-g++
configure:3600: result: none
configure:3632: checking for x86_64-pc-linux-gnu-gcc
configure:3648: found /usr/bin/x86_64-pc-linux-gnu-gcc
configure:3659: result: x86_64-pc-linux-gnu-gcc
configure:3928: checking for C compiler version
configure:3937: x86_64-pc-linux-gnu-gcc --version >&5
x86_64-pc-linux-gnu-gcc (Gentoo 6.2.0-r1 p1.1) 6.2.0
Copyright (C) 2016 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:3948: $? = 0
configure:3937: x86_64-pc-linux-gnu-gcc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0/x86_64-pc-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/6.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-6.2.0-r1/work/gcc-6.2.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 6.2.0-r1 p1.1' --disable-esp --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --disable-libmpx --enable-vtable-verify --enable-libvtv --enable-lto --without-isl --enable-libsanitizer --disable-default-pie --disable-default-ssp
Thread model: posix
gcc version 6.2.0 (Gentoo 6.2.0-r1 p1.1) 
configure:3948: $? = 0
configure:3937: x86_64-pc-linux-gnu-gcc -V >&5
x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-V'
x86_64-pc-linux-gnu-gcc: fatal error: no input files
compilation terminated.
configure:3948: $? = 1
configure:3937: x86_64-pc-linux-gnu-gcc -qversion >&5
x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-qversion'; did you mean '--version'?
x86_64-pc-linux-gnu-gcc: fatal error: no input files
compilation terminated.
configure:3948: $? = 1
configure:3952: checking whether we are using the GNU C compiler
configure:3971: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable  -I/usr/include/seqan-1.4 conftest.c >&5
configure:3971: $? = 0
configure:3980: result: yes
configure:3989: checking whether x86_64-pc-linux-gnu-gcc accepts -g
configure:4009: x86_64-pc-linux-gnu-gcc -c -g  -I/usr/include/seqan-1.4 conftest.c >&5
configure:4009: $? = 0
configure:4050: result: yes
configure:4067: checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89
configure:4130: x86_64-pc-linux-gnu-gcc  -c -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable  -I/usr/include/seqan-1.4 conftest.c >&5
configure:4130: $? = 0
configure:4143: result: none needed
configure:4168: checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together
configure:4190: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o
configure:4193: $? = 0
configure:4190: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o
configure:4193: $? = 0
configure:4205: result: yes
configure:4224: checking dependency style of x86_64-pc-linux-gnu-gcc
configure:4335: result: none
configure:4356: checking for x86_64-pc-linux-gnu-ar
configure:4372: found /usr/bin/x86_64-pc-linux-gnu-ar
configure:4383: result: x86_64-pc-linux-gnu-ar
configure:4453: checking the archiver (x86_64-pc-linux-gnu-ar) interface
configure:4469: x86_64-pc-linux-gnu-gcc -c -march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable  -I/usr/include/seqan-1.4 conftest.c >&5
configure:4469: $? = 0
configure:4471: x86_64-pc-linux-gnu-ar cru libconftest.a conftest.o >&5
configure:4474: $? = 0
configure:4502: result: ar
configure:4528: checking for gawk
configure:4555: result: gawk
configure:4678: checking for C++ compiler version
configure:4687: x86_64-pc-linux-gnu-g++ --version >&5
x86_64-pc-linux-gnu-g++ (Gentoo 6.2.0-r1 p1.1) 6.2.0
Copyright (C) 2016 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:4698: $? = 0
configure:4687: x86_64-pc-linux-gnu-g++ -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0/x86_64-pc-linux-gnu-g++
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/6.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-6.2.0-r1/work/gcc-6.2.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 6.2.0-r1 p1.1' --disable-esp --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --disable-libmpx --enable-vtable-verify --enable-libvtv --enable-lto --without-isl --enable-libsanitizer --disable-default-pie --disable-default-ssp
Thread model: posix
gcc version 6.2.0 (Gentoo 6.2.0-r1 p1.1) 
configure:4698: $? = 0
configure:4687: x86_64-pc-linux-gnu-g++ -V >&5
x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-V'
x86_64-pc-linux-gnu-g++: fatal error: no input files
compilation terminated.
configure:4698: $? = 1
configure:4687: x86_64-pc-linux-gnu-g++ -qversion >&5
x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-qversion'; did you mean '--version'?
x86_64-pc-linux-gnu-g++: fatal error: no input files
compilation terminated.
configure:4698: $? = 1
configure:4702: checking whether we are using the GNU C++ compiler
configure:4730: result: yes
configure:4739: checking whether x86_64-pc-linux-gnu-g++ accepts -g
configure:4800: result: yes
configure:4825: checking dependency style of x86_64-pc-linux-gnu-g++
configure:4936: result: none
configure:4959: checking for x86_64-pc-linux-gnu-gcc
configure:4986: result: x86_64-pc-linux-gnu-gcc
configure:5255: checking for C compiler version
configure:5264: x86_64-pc-linux-gnu-gcc --version >&5
x86_64-pc-linux-gnu-gcc (Gentoo 6.2.0-r1 p1.1) 6.2.0
Copyright (C) 2016 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:5275: $? = 0
configure:5264: x86_64-pc-linux-gnu-gcc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0/x86_64-pc-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/6.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-6.2.0-r1/work/gcc-6.2.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/6.2.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 6.2.0-r1 p1.1' --disable-esp --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --disable-libmpx --enable-vtable-verify --enable-libvtv --enable-lto --without-isl --enable-libsanitizer --disable-default-pie --disable-default-ssp
Thread model: posix
gcc version 6.2.0 (Gentoo 6.2.0-r1 p1.1) 
configure:5275: $? = 0
configure:5264: x86_64-pc-linux-gnu-gcc -V >&5
x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-V'
x86_64-pc-linux-gnu-gcc: fatal error: no input files
compilation terminated.
configure:5275: $? = 1
configure:5264: x86_64-pc-linux-gnu-gcc -qversion >&5
x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-qversion'; did you mean '--version'?
x86_64-pc-linux-gnu-gcc: fatal error: no input files
compilation terminated.
configure:5275: $? = 1
configure:5279: checking whether we are using the GNU C compiler
configure:5307: result: yes
configure:5316: checking whether x86_64-pc-linux-gnu-gcc accepts -g
configure:5377: result: yes
configure:5394: checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89
configure:5470: result: none needed
configure:5495: checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together
configure:5532: result: yes
configure:5551: checking dependency style of x86_64-pc-linux-gnu-gcc
configure:5662: result: none
configure:5677: checking whether make sets $(MAKE)
configure:5699: result: yes
configure:5711: checking for x86_64-pc-linux-gnu-ranlib
configure:5727: found /usr/bin/x86_64-pc-linux-gnu-ranlib
configure:5738: result: x86_64-pc-linux-gnu-ranlib
configure:5809: checking whether /usr/bin/python2.7 version is >= 2.4
configure:5820: /usr/bin/python2.7 -c import sys # split strings by '.' and convert to numeric. Append some zeros # because we need at least 4 digits for the hex conversion. # map returns an iterator in Python 3.0 and a list in 2.x minver = list(map(int, '2.4'.split('.'))) + [0, 0, 0] minverhex = 0 # xrange is not present in Python 3.0 and range returns an iterator for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[i] sys.exit(sys.hexversion < minverhex)
configure:5823: $? = 0
configure:5825: result: yes
configure:5918: checking for /usr/bin/python2.7 version
configure:5925: result: 2.7
configure:5937: checking for /usr/bin/python2.7 platform
configure:5944: result: linux2
configure:5970: checking for /usr/bin/python2.7 script directory
configure:6005: result: ${prefix}/lib64/python2.7/site-packages
configure:6014: checking for /usr/bin/python2.7 extension module directory
configure:6049: result: ${exec_prefix}/lib64/python2.7/site-packages
configure:6150: checking for boostlib >= 1.38.0
configure:6204: x86_64-pc-linux-gnu-g++ -c -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -I/usr/include conftest.cpp >&5
configure:6204: $? = 0
configure:6206: result: yes
configure:6341: checking whether the compiler implements namespaces
configure:6364: x86_64-pc-linux-gnu-g++ -c -march=native -O2 -pipe  -I/usr/include/seqan-1.4 conftest.cpp >&5
configure:6364: $? = 0
configure:6378: result: yes
configure:6405: checking whether the Boost::Thread library is available
configure:6421: x86_64-pc-linux-gnu-g++ -c -pthread -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -I/usr/include conftest.cpp >&5
configure:6421: $? = 0
configure:6429: result: yes
configure:6450: checking for main in -lboost_thread
configure:6469: x86_64-pc-linux-gnu-g++ -o conftest -pthread -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.cpp -lboost_thread   >&5
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_thread
collect2: error: ld returned 1 exit status
configure:6469: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "tophat"
| #define PACKAGE_TARNAME "tophat"
| #define PACKAGE_VERSION "2.1.1"
| #define PACKAGE_STRING "tophat 2.1.1"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL ""
| #define SVN_REVISION ""
| #define PACKAGE "tophat"
| #define VERSION "2.1.1"
| #define HAVE_BOOST /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_BOOST_THREAD /**/
| /* end confdefs.h.  */
| 
| 
| int
| main ()
| {
| return main ();
|   ;
|   return 0;
| }
configure:6479: result: no
configure:6450: checking for main in -lboost_thread-mt
configure:6469: x86_64-pc-linux-gnu-g++ -o conftest -pthread -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.cpp -lboost_thread-mt   >&5
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_thread-mt
collect2: error: ld returned 1 exit status
configure:6469: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "tophat"
| #define PACKAGE_TARNAME "tophat"
| #define PACKAGE_VERSION "2.1.1"
| #define PACKAGE_STRING "tophat 2.1.1"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL ""
| #define SVN_REVISION ""
| #define PACKAGE "tophat"
| #define VERSION "2.1.1"
| #define HAVE_BOOST /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_BOOST_THREAD /**/
| /* end confdefs.h.  */
| 
| 
| int
| main ()
| {
| return main ();
|   ;
|   return 0;
| }
configure:6479: result: no
configure:6488: checking whether Boost::Thread needs Boost::System library
configure:6505: x86_64-pc-linux-gnu-g++ -o conftest -pthread -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.cpp   >&5
/var/tmp/portage/sci-biology/tophat-2.1.1-r1/temp/ccssN2IP.o: In function `boost::thread_group::~thread_group()':
conftest.cpp:(.text._ZN5boost12thread_groupD2Ev[_ZN5boost12thread_groupD5Ev]+0x46): undefined reference to `boost::thread::detach()'
/var/tmp/portage/sci-biology/tophat-2.1.1-r1/temp/ccssN2IP.o: In function `main':
conftest.cpp:(.text.startup+0x11d): undefined reference to `boost::system::system_category()'
conftest.cpp:(.text.startup+0x1a9): undefined reference to `boost::system::system_category()'
conftest.cpp:(.text.startup+0x201): undefined reference to `boost::system::system_category()'
conftest.cpp:(.text.startup+0x30a): undefined reference to `boost::system::system_category()'
conftest.cpp:(.text.startup+0x397): undefined reference to `boost::system::system_category()'
/var/tmp/portage/sci-biology/tophat-2.1.1-r1/temp/ccssN2IP.o:conftest.cpp:(.text.startup+0x411): more undefined references to `boost::system::system_category()' follow
/var/tmp/portage/sci-biology/tophat-2.1.1-r1/temp/ccssN2IP.o: In function `_GLOBAL__sub_I_main':
conftest.cpp:(.text.startup+0x565): undefined reference to `boost::system::generic_category()'
conftest.cpp:(.text.startup+0x56a): undefined reference to `boost::system::generic_category()'
conftest.cpp:(.text.startup+0x56f): undefined reference to `boost::system::system_category()'
collect2: error: ld returned 1 exit status
configure:6505: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "tophat"
| #define PACKAGE_TARNAME "tophat"
| #define PACKAGE_VERSION "2.1.1"
| #define PACKAGE_STRING "tophat 2.1.1"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL ""
| #define SVN_REVISION ""
| #define PACKAGE "tophat"
| #define VERSION "2.1.1"
| #define HAVE_BOOST /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_BOOST_THREAD /**/
| /* end confdefs.h.  */
| #include <boost/thread/thread.hpp>
| int
| main ()
| {
| boost::thread_group thrds; return 0;
|   ;
|   return 0;
| }
configure:6522: x86_64-pc-linux-gnu-g++ -o conftest -pthread -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.cpp    -lboost_system >&5
/var/tmp/portage/sci-biology/tophat-2.1.1-r1/temp/ccwcKElD.o: In function `boost::thread_group::~thread_group()':
conftest.cpp:(.text._ZN5boost12thread_groupD2Ev[_ZN5boost12thread_groupD5Ev]+0x46): undefined reference to `boost::thread::detach()'
collect2: error: ld returned 1 exit status
configure:6522: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "tophat"
| #define PACKAGE_TARNAME "tophat"
| #define PACKAGE_VERSION "2.1.1"
| #define PACKAGE_STRING "tophat 2.1.1"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL ""
| #define SVN_REVISION ""
| #define PACKAGE "tophat"
| #define VERSION "2.1.1"
| #define HAVE_BOOST /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_BOOST_THREAD /**/
| /* end confdefs.h.  */
| 
|                     #include <boost/thread/thread.hpp>
| int
| main ()
| {
| boost::thread_group thrds; return 0;
|   ;
|   return 0;
| }
| 
configure:6540: x86_64-pc-linux-gnu-g++ -o conftest -pthread -march=native -O2 -pipe  -I/usr/include/seqan-1.4 -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.cpp    -lboost_system  -lboost_system -lrt >&5
/var/tmp/portage/sci-biology/tophat-2.1.1-r1/temp/ccSdZupl.o: In function `boost::thread_group::~thread_group()':
conftest.cpp:(.text._ZN5boost12thread_groupD2Ev[_ZN5boost12thread_groupD5Ev]+0x46): undefined reference to `boost::thread::detach()'
collect2: error: ld returned 1 exit status
configure:6540: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "tophat"
| #define PACKAGE_TARNAME "tophat"
| #define PACKAGE_VERSION "2.1.1"
| #define PACKAGE_STRING "tophat 2.1.1"
| #define PACKAGE_BUGREPORT "[e-mail]"
| #define PACKAGE_URL ""
| #define SVN_REVISION ""
| #define PACKAGE "tophat"
| #define VERSION "2.1.1"
| #define HAVE_BOOST /**/
| #define HAVE_NAMESPACES /**/
| #define HAVE_BOOST_THREAD /**/
| /* end confdefs.h.  */
| 
| 		                    #include <boost/thread/thread.hpp>
| int
| main ()
| {
| boost::thread_group thrds; return 0;
|   ;
|   return 0;
| }
| 
configure:6544: error: Cannot use Boost::Thread

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_cxx_namespaces=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable'
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=' -I/usr/include/seqan-1.4'
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=set
ac_cv_env_CXXFLAGS_value='-march=native -O2 -pipe'
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-Wl,-O1 -Wl,--as-needed'
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_PYTHON_set=set
ac_cv_env_PYTHON_value=/usr/bin/python2.7
ac_cv_env_build_alias_set=set
ac_cv_env_build_alias_value=x86_64-pc-linux-gnu
ac_cv_env_host_alias_set=set
ac_cv_env_host_alias_value=x86_64-pc-linux-gnu
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_lib_boost_thread___main=no
ac_cv_lib_boost_thread_mt___main=no
ac_cv_objext=o
ac_cv_path_install='/usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AR=x86_64-pc-linux-gnu-ar
ac_cv_prog_AWK=gawk
ac_cv_prog_CC=x86_64-pc-linux-gnu-gcc
ac_cv_prog_CXX=x86_64-pc-linux-gnu-g++
ac_cv_prog_RANLIB=x86_64-pc-linux-gnu-ranlib
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
am_cv_CC_dependencies_compiler_type=none
am_cv_CXX_dependencies_compiler_type=none
am_cv_ar_interface=ar
am_cv_make_support_nested_variables=yes
am_cv_prog_cc_c_o=yes
am_cv_python_platform=linux2
am_cv_python_pyexecdir='${exec_prefix}/lib64/python2.7/site-packages'
am_cv_python_pythondir='${prefix}/lib64/python2.7/site-packages'
am_cv_python_version=2.7
ax_cv_boost_thread=yes

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1/missing aclocal-1.15'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE='#'
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AR='x86_64-pc-linux-gnu-ar'
AUTOCONF='${SHELL} /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1/missing autoconf'
AUTOHEADER='${SHELL} /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1/missing autoheader'
AUTOMAKE='${SHELL} /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1/missing automake-1.15'
AWK='gawk'
BOOST_CPPFLAGS='-pthread -I/usr/include'
BOOST_LDFLAGS='-L/usr/lib'
BOOST_THREAD_LIBS=''
CC='x86_64-pc-linux-gnu-gcc'
CCDEPMODE='depmode=none'
CFLAGS='-march=native -O2 -pipe -Wno-unused-but-set-variable -Wno-unused-variable'
CPPFLAGS=' -I/usr/include/seqan-1.4 -I/usr/include'
CXX='x86_64-pc-linux-gnu-g++'
CXXCPP=''
CXXDEPMODE='depmode=none'
CXXFLAGS='-pthread -march=native -O2 -pipe'
CYGPATH_W='echo'
DEFS=''
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
EXEEXT=''
GREP=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS='-Wl,-O1 -Wl,--as-needed -L/usr/lib'
LIBOBJS=''
LIBS='   -lboost_system  -lboost_system -lrt'
LTLIBOBJS=''
MAKEINFO='${SHELL} /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1/missing makeinfo'
MKDIR_P='/bin/mkdir -p'
OBJEXT='o'
PACKAGE='tophat'
PACKAGE_BUGREPORT='[e-mail]'
PACKAGE_NAME='tophat'
PACKAGE_STRING='tophat 2.1.1'
PACKAGE_TARNAME='tophat'
PACKAGE_URL=''
PACKAGE_VERSION='2.1.1'
PATH_SEPARATOR=':'
PYTHON='/usr/bin/python2.7'
PYTHON_EXEC_PREFIX='${exec_prefix}'
PYTHON_PLATFORM='linux2'
PYTHON_PREFIX='${prefix}'
PYTHON_VERSION='2.7'
RANLIB='x86_64-pc-linux-gnu-ranlib'
SET_MAKE=''
SHELL='/bin/sh'
STRIP=''
VERSION='2.1.1'
ac_ct_AR=''
ac_ct_CC=''
ac_ct_CXX=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE='#'
am__fastdepCXX_FALSE=''
am__fastdepCXX_TRUE='#'
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep=''
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-pc-linux-gnu'
build_alias='x86_64-pc-linux-gnu'
build_cpu=''
build_os=''
build_vendor=''
datadir='/usr/share'
datarootdir='${prefix}/share'
docdir='/usr/share/doc/tophat-2.1.1-r1'
dvidir='${docdir}'
exec_prefix='NONE'
host='x86_64-pc-linux-gnu'
host_alias='x86_64-pc-linux-gnu'
host_cpu=''
host_os=''
host_vendor=''
htmldir='/usr/share/doc/tophat-2.1.1-r1/html'
includedir='${prefix}/include'
infodir='/usr/share/info'
install_sh='${SHELL} /var/tmp/portage/sci-biology/tophat-2.1.1-r1/work/tophat-2.1.1/install-sh'
libdir='/usr/lib64'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='/var/lib'
mandir='/usr/share/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
pkgpyexecdir='${pyexecdir}/tophat'
pkgpythondir='${pythondir}/tophat'
prefix='/usr'
program_transform_name='s,x,x,'
psdir='${docdir}'
pyexecdir='${exec_prefix}/lib64/python2.7/site-packages'
pythondir='${prefix}/lib64/python2.7/site-packages'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "tophat"
#define PACKAGE_TARNAME "tophat"
#define PACKAGE_VERSION "2.1.1"
#define PACKAGE_STRING "tophat 2.1.1"
#define PACKAGE_BUGREPORT "[e-mail]"
#define PACKAGE_URL ""
#define SVN_REVISION ""
#define PACKAGE "tophat"
#define VERSION "2.1.1"
#define HAVE_BOOST /**/
#define HAVE_NAMESPACES /**/
#define HAVE_BOOST_THREAD /**/

configure: exit 1