Attachment 339506 Details for Bug 458488 – vaal-1.6:20130220-160841.log

vaal-1.6:20130220-160841.log

vaal-1.6:20130220-160841.log (text/plain), 33.36 KB, created by Agostino Sarubbo on 2013-02-20 16:13:15 UTC

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Creator: Agostino Sarubbo

Created: 2013-02-20 16:13:15 UTC

Size: 33.36 KB

patch

obsolete

> * Package:    sci-biology/vaal-1.6
> * Repository: gentoo
> * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
> * USE:        elibc_glibc kernel_linux openmp userland_GNU x86
> * FEATURES:   sandbox userpriv usersandbox
>>>> Unpacking source...
>>>> Unpacking VAAL.1.6.tgz to /var/tmp/portage/sci-biology/vaal-1.6/work
>>>> Unpacking VAAL_manual.doc to /var/tmp/portage/sci-biology/vaal-1.6/work
>unpack VAAL_manual.doc: file format not recognized. Ignoring.
>>>> Source unpacked in /var/tmp/portage/sci-biology/vaal-1.6/work
>>>> Preparing source in /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805 ...
> * Applying vaal-1.6-respect-flags.patch ...
> [ ok ]
> * Applying vaal-1.6-gcc47.patch ...
> [ ok ]
> * Running eautoreconf in '/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805' ...
> * Running libtoolize --install --copy --force --automake ...
> [ ok ]
> * Running aclocal -I m4 ...
> [ ok ]
> * Running autoconf ...
> [ ok ]
> * Running autoheader ...
> [ ok ]
> * Running automake --add-missing --copy --foreign ...
> [ ok ]
> * Running elibtoolize in: vaal-33805/
> *   Applying portage/1.2.0 patch ...
> *   Applying sed/1.5.6 patch ...
> *   Applying as-needed/2.2.6 patch ...
>>>> Source prepared.
>>>> Configuring source in /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805 ...
>>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-1.6_build"
> * econf: updating vaal-33805/config.sub with /usr/share/gnuconfig/config.sub
> * econf: updating vaal-33805/config.guess with /usr/share/gnuconfig/config.guess
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --docdir=/usr/share/doc/vaal-1.6 --enable-openmp
>checking for a BSD-compatible install... /usr/bin/install -c
>checking whether build environment is sane... yes
>checking for a thread-safe mkdir -p... /bin/mkdir -p
>checking for gawk... gawk
>checking whether make sets $(MAKE)... yes
>checking build system type... i686-pc-linux-gnu
>checking host system type... i686-pc-linux-gnu
>checking how to print strings... printf
>checking for style of include used by make... GNU
>checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc
>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 i686-pc-linux-gnu-gcc accepts -g... yes
>checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed
>checking dependency style of i686-pc-linux-gnu-gcc... none
>checking for a sed that does not truncate output... /bin/sed
>checking for grep that handles long lines and -e... /bin/grep
>checking for egrep... /bin/grep -E
>checking for fgrep... /bin/grep -F
>checking for ld used by i686-pc-linux-gnu-gcc... /usr/i686-pc-linux-gnu/bin/ld
>checking if the linker (/usr/i686-pc-linux-gnu/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 i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop
>checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop
>checking for /usr/i686-pc-linux-gnu/bin/ld option to reload object files... -r
>checking for i686-pc-linux-gnu-objdump... i686-pc-linux-gnu-objdump
>checking how to recognize dependent libraries... pass_all
>checking for i686-pc-linux-gnu-dlltool... no
>checking for dlltool... no
>checking how to associate runtime and link libraries... printf %s\n
>checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar
>checking for archiver @FILE support... @
>checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-strip
>checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib
>checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok
>checking for sysroot... no
>checking for i686-pc-linux-gnu-mt... no
>checking for mt... no
>checking if : is a manifest tool... no
>checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -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 i686-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
>checking for i686-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
>checking if i686-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
>checking if i686-pc-linux-gnu-gcc static flag -static works... yes
>checking if i686-pc-linux-gnu-gcc supports -c -o file.o... yes
>checking if i686-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
>checking whether the i686-pc-linux-gnu-gcc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
>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... no
>checking whether to build static libraries... yes
>checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++
>checking whether we are using the GNU C++ compiler... yes
>checking whether i686-pc-linux-gnu-g++ accepts -g... yes
>checking dependency style of i686-pc-linux-gnu-g++... none
>checking how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E
>checking for ld used by i686-pc-linux-gnu-g++... /usr/i686-pc-linux-gnu/bin/ld
>checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes
>checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
>checking for i686-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
>checking if i686-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
>checking if i686-pc-linux-gnu-g++ static flag -static works... yes
>checking if i686-pc-linux-gnu-g++ supports -c -o file.o... yes
>checking if i686-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
>checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
>checking dynamic linker characteristics... (cached) GNU/Linux ld.so
>checking how to hardcode library paths into programs... immediate
>checking whether byte ordering is bigendian... no
>g++ version is >= 4.3.3... yes
>checking for Boost headers version >= 103800... yes
>checking for Boost's header version... 1_49
>checking for the pthreads library -lpthreads... no
>checking whether pthreads work without any flags... no
>checking whether pthreads work with -Kthread... no
>checking whether pthreads work with -kthread... no
>checking for the pthreads library -llthread... no
>checking whether pthreads work with -pthread... yes
>checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
>checking if more special flags are required for pthreads... no
>checking for i686-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
>configure: creating ./config.status
>config.status: creating Makefile
>config.status: creating src/Makefile
>config.status: creating src/config.h
>config.status: executing depfiles commands
>config.status: executing libtool commands
>>>> Source configured.
>>>> Compiling source in /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805 ...
>>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-1.6_build"
>make -j4 
>Making all in src
>make[1]: Entering directory `/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-1.6_build/src'
>(CDPATH="${ZSH_VERSION+.}:" && cd /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805 && /bin/sh /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/missing --run autoheader)
>rm -f stamp-h1
>touch /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/config.h.in
>cd .. && /bin/sh ./config.status src/config.h
>config.status: creating src/config.h
>config.status: src/config.h is unchanged
>make  all-am
>make[2]: Entering directory `/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-1.6_build/src'
>i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src  -DRELEASE=3.0 -DMAKE_OS_RELEASE=3.4.6-hardened-r1-osl-guest-x86_64-1 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805  -fopenmp -O2 -pipe -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels  -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -c -o Crash.o `test -f 'system/Crash.cc' || echo '/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/'`system/Crash.cc
>i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src  -DRELEASE=3.0 -DMAKE_OS_RELEASE=3.4.6-hardened-r1-osl-guest-x86_64-1 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805  -fopenmp -O2 -pipe -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels  -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -c -o Mutmer.o `test -f 'pairwise_aligners/Mutmer.cc' || echo '/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/'`pairwise_aligners/Mutmer.cc
>i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src  -DRELEASE=3.0 -DMAKE_OS_RELEASE=3.4.6-hardened-r1-osl-guest-x86_64-1 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805  -fopenmp -O2 -pipe -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels  -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -c -o Generic.o `test -f 'feudal/Generic.cc' || echo '/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/'`feudal/Generic.cc
>i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src  -DRELEASE=3.0 -DMAKE_OS_RELEASE=3.4.6-hardened-r1-osl-guest-x86_64-1 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805  -fopenmp -O2 -pipe -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels  -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -c -o ReadPairing.o /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/ReadPairing.cc
>i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src  -DRELEASE=3.0 -DMAKE_OS_RELEASE=3.4.6-hardened-r1-osl-guest-x86_64-1 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805  -fopenmp -O2 -pipe -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels  -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -c -o FetchReadsAmb.o /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/FetchReadsAmb.cc
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:29:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:19,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/String.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/Generic.cc:20:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:443:39: warning: large integer implicitly truncated to unsigned type [-Woverflow]
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h: In member function âSmallVec<T, A>& SmallVec<T, A>::push_back(const T&, float, SmallVec<T, A>::size_type) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >, SmallVec<T, A>::size_type = unsigned int]â:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:215:36:   instantiated from âSmallVec<T, A>& SmallVec<T, A>::push_back(const T&) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >]â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:183:7:   instantiated from âFeudalString<charT, Traits>& FeudalString<charT, Traits>::push_back(FeudalString<charT, Traits>::value_type) [with charT = char, Traits = std::char_traits<char>, FeudalString<charT, Traits> = FeudalString<char, std::char_traits<char> >, FeudalString<charT, Traits>::value_type = char]â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:148:20:   instantiated from here
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:226:9: error: no matching function for call to âmax(long unsigned int, const unsigned int&)â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:226:9: note: candidates are:
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:210:5: note: template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)
>make[2]: *** [Generic.o] Error 1
>make[2]: *** Waiting for unfinished jobs....
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:29:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:19,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/String.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/system/System.h:16,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:17,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/ReadPairing.cc:14:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:443:39: warning: large integer implicitly truncated to unsigned type [-Woverflow]
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:29:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:19,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/String.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/system/System.h:16,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:17,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:20,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BitVec.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Bitvector.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/FetchReadsAmb.cc:22:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:443:39: warning: large integer implicitly truncated to unsigned type [-Woverflow]
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:29:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:19,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/String.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/system/System.h:16,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:17,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:20,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BaseVec.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Basevector.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/pairwise_aligners/Mutmer.h:33,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/pairwise_aligners/Mutmer.cc:9:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:443:39: warning: large integer implicitly truncated to unsigned type [-Woverflow]
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/MasterVec.h:24:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/VecString.h:14,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:22,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/ReadPairing.cc:14:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/OuterVec.h: In member function âOuterVec<T, A>::size_type OuterVec<T, A>::max_size() constâ:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/OuterVec.h:196:21: warning: left shift count >= width of type [enabled by default]
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/MasterVec.h:24:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/VecString.h:14,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:22,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:20,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BitVec.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Bitvector.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/FetchReadsAmb.cc:22:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/OuterVec.h: In member function âOuterVec<T, A>::size_type OuterVec<T, A>::max_size() constâ:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/OuterVec.h:196:21: warning: left shift count >= width of type [enabled by default]
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/MasterVec.h:24:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/VecString.h:14,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:22,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:20,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BaseVec.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Basevector.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/pairwise_aligners/Mutmer.h:33,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/pairwise_aligners/Mutmer.cc:9:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/OuterVec.h: In member function âOuterVec<T, A>::size_type OuterVec<T, A>::max_size() constâ:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/OuterVec.h:196:21: warning: left shift count >= width of type [enabled by default]
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BitVec.h:12:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Bitvector.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/FetchReadsAmb.cc:22:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h: At global scope:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:752:39: warning: large integer implicitly truncated to unsigned type [-Woverflow]
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BaseVec.h:13:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Basevector.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/pairwise_aligners/Mutmer.h:33,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/pairwise_aligners/Mutmer.cc:9:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h: At global scope:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:752:39: warning: large integer implicitly truncated to unsigned type [-Woverflow]
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:29:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:19,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/String.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/system/System.h:16,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:17,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/ReadPairing.cc:14:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h: In member function âSmallVec<T, A>& SmallVec<T, A>::push_back(const T&, float, SmallVec<T, A>::size_type) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >, SmallVec<T, A>::size_type = unsigned int]â:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:215:36:   instantiated from âSmallVec<T, A>& SmallVec<T, A>::push_back(const T&) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >]â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:183:7:   instantiated from âFeudalString<charT, Traits>& FeudalString<charT, Traits>::push_back(FeudalString<charT, Traits>::value_type) [with charT = char, Traits = std::char_traits<char>, FeudalString<charT, Traits> = FeudalString<char, std::char_traits<char> >, FeudalString<charT, Traits>::value_type = char]â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:148:20:   instantiated from here
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:226:9: error: no matching function for call to âmax(long unsigned int, const unsigned int&)â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:226:9: note: candidates are:
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:210:5: note: template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h: In member function âFieldVec<N, A>& FieldVec<N, A>::push_back(FieldVec<N, A>::value_type, float, FieldVec<N, A>::size_type) [with int N = 2, A = MempoolAllocator<unsigned char>, FieldVec<N, A> = FieldVec<2, MempoolAllocator<unsigned char> >, FieldVec<N, A>::value_type = unsigned char, FieldVec<N, A>::size_type = unsigned int]â:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:494:40:   instantiated from âFieldVec<N, A>& FieldVec<N, A>::push_back(FieldVec<N, A>::value_type) [with int N = 2, A = MempoolAllocator<unsigned char>, FieldVec<N, A> = FieldVec<2, MempoolAllocator<unsigned char> >, FieldVec<N, A>::value_type = unsigned char]â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BaseVec.h:184:58:   instantiated from here
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:506:13: error: no matching function for call to âmax(long unsigned int, const unsigned int&)â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:506:13: note: candidates are:
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:210:5: note: template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:29:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:19,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/String.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/system/System.h:16,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:17,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:20,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BitVec.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Bitvector.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/FetchReadsAmb.cc:22:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h: In member function âSmallVec<T, A>& SmallVec<T, A>::push_back(const T&, float, SmallVec<T, A>::size_type) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >, SmallVec<T, A>::size_type = unsigned int]â:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:215:36:   instantiated from âSmallVec<T, A>& SmallVec<T, A>::push_back(const T&) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >]â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:183:7:   instantiated from âFeudalString<charT, Traits>& FeudalString<charT, Traits>::push_back(FeudalString<charT, Traits>::value_type) [with charT = char, Traits = std::char_traits<char>, FeudalString<charT, Traits> = FeudalString<char, std::char_traits<char> >, FeudalString<charT, Traits>::value_type = char]â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:148:20:   instantiated from here
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:226:9: error: no matching function for call to âmax(long unsigned int, const unsigned int&)â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:226:9: note: candidates are:
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:210:5: note: template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/system/System.h:13:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:17,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/ReadPairing.cc:14:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/ReadPairing.cc: In function âvoid ReadsToPairs(const String&, const vec<int>&, vec<read_pairing>&, const String&)â:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/ReadPairing.cc:115:59: warning: ignoring return value of âssize_t read(int, void*, size_t)â, declared with attribute warn_unused_result [-Wunused-result]
>In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/i686-pc-linux-gnu/bits/c++allocator.h:34:0,
>                 from /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/allocator.h:48,
>                 from /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/string:43,
>                 from /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/locale_classes.h:42,
>                 from /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/ios_base.h:43,
>                 from /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/iomanip:42,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/system/System.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:17,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/ReadPairing.cc:14:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Vec.h: In function âvoid BinaryReadSubset(const String&, const vec<int>&, vec<T>&) [with T = int, String = FeudalString<char, std::char_traits<char> >]â:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Vec.h:872:11: warning: ignoring return value of âssize_t read(int, void*, size_t)â, declared with attribute warn_unused_result [-Wunused-result]
>make[2]: *** [ReadPairing.o] Error 1
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h: In member function âFieldVec<N, A>& FieldVec<N, A>::push_back(FieldVec<N, A>::value_type, float, FieldVec<N, A>::size_type) [with int N = 2, A = MempoolAllocator<unsigned char>, FieldVec<N, A> = FieldVec<2, MempoolAllocator<unsigned char> >, FieldVec<N, A>::value_type = unsigned char, FieldVec<N, A>::size_type = unsigned int]â:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:494:40:   instantiated from âFieldVec<N, A>& FieldVec<N, A>::push_back(FieldVec<N, A>::value_type) [with int N = 2, A = MempoolAllocator<unsigned char>, FieldVec<N, A> = FieldVec<2, MempoolAllocator<unsigned char> >, FieldVec<N, A>::value_type = unsigned char]â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BaseVec.h:184:58:   instantiated from here
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:506:13: error: no matching function for call to âmax(long unsigned int, const unsigned int&)â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:506:13: note: candidates are:
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:210:5: note: template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)
>make[2]: *** [FetchReadsAmb.o] Error 1
>In file included from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FeudalString.h:29:0,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/CharString.h:19,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/String.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/system/System.h:16,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/CoreTools.h:17,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/FieldVec.h:20,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/BaseVec.h:13,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Basevector.h:12,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/pairwise_aligners/Mutmer.h:33,
>                 from /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/pairwise_aligners/Mutmer.cc:9:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h: In member function âSmallVec<T, A>& SmallVec<T, A>::push_back(const T&, float, SmallVec<T, A>::size_type) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >, SmallVec<T, A>::size_type = unsigned int]â:
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:215:36:   instantiated from âSmallVec<T, A>& SmallVec<T, A>::push_back(const T&) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >]â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/Fastavector.h:59:38:   instantiated from here
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:226:9: error: no matching function for call to âmax(long unsigned int, const unsigned int&)â
>/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src/feudal/SmallVec.h:226:9: note: candidates are:
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:210:5: note: template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)
>/usr/lib/gcc/i686-pc-linux-gnu/4.6.3/include/g++-v4/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)
>make[2]: *** [Mutmer.o] Error 1
>make[2]: Leaving directory `/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-1.6_build/src'
>make[1]: *** [all] Error 2
>make[1]: Leaving directory `/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-1.6_build/src'
>make: *** [all-recursive] Error 1
> * ERROR: sci-biology/vaal-1.6 failed (compile phase):
> *   emake failed
> * 
> * If you need support, post the output of `emerge --info '=sci-biology/vaal-1.6'`,
> * the complete build log and the output of `emerge -pqv '=sci-biology/vaal-1.6'`.
> * The complete build log is located at '/var/log/log/build/sci-biology/vaal-1.6:20130220-160841.log'.
> * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/vaal-1.6/temp/build.log'.
> * The ebuild environment file is located at '/var/tmp/portage/sci-biology/vaal-1.6/temp/environment'.
> * Working directory: '/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-1.6_build'
> * S: '/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805'

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Attachments on bug 458488: 339506