* CPV: sci-biology/vaal-1.6 * REPO: gentoo * USE: elibc_glibc kernel_linux userland_GNU x86 >>> 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 ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805' ... * Running aclocal -I m4 ...  [ ok ] * Running libtoolize --copy --force --install --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-2.2.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 ... * econf: updating vaal-33805/config.guess with /usr/share/gnuconfig/config.guess * econf: updating vaal-33805/config.sub with /usr/share/gnuconfig/config.sub ./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 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... gcc3 checking for a sed that does not truncate output... /usr/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 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-ar... i686-pc-linux-gnu-ar 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 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++... gcc3 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_42 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 checking validity of OpenMP configuation.... 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 ... make -j4 Making all in src make[1]: Entering directory `/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/sh /var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/missing --run autoheader) rm -f stamp-h1 touch 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-33805/src' i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=2.6.31.14 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805 -fopenmp -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -MT Crash.o -MD -MP -MF .deps/Crash.Tpo -c -o Crash.o `test -f 'system/Crash.cc' || echo './'`system/Crash.cc i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=2.6.31.14 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805 -fopenmp -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -MT Mutmer.o -MD -MP -MF .deps/Mutmer.Tpo -c -o Mutmer.o `test -f 'pairwise_aligners/Mutmer.cc' || echo './'`pairwise_aligners/Mutmer.cc i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=2.6.31.14 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805 -fopenmp -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -MT Generic.o -MD -MP -MF .deps/Generic.Tpo -c -o Generic.o `test -f 'feudal/Generic.cc' || echo './'`feudal/Generic.cc i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=2.6.31.14 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805 -fopenmp -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -MT ReadPairing.o -MD -MP -MF .deps/ReadPairing.Tpo -c -o ReadPairing.o ReadPairing.cc distcc[9434] ERROR: nonblocking connect to 127.0.0.1:3632 failed: Connection refused distcc[9434] Warning: failed to distribute pairwise_aligners/Mutmer.cc to 127.0.0.1, running locally instead mv -f .deps/Crash.Tpo .deps/Crash.Po i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=2.6.31.14 -DMAKE_RELEASE=3.0 -DSVN_VERSION=33805 -fopenmp -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote . -MT FetchReadsAmb.o -MD -MP -MF .deps/FetchReadsAmb.Tpo -c -o FetchReadsAmb.o FetchReadsAmb.cc In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from ./system/System.h:16, from ./CoreTools.h:17, from ./feudal/FieldVec.h:20, from ./feudal/BaseVec.h:13, from ./Basevector.h:12, from ./pairwise_aligners/Mutmer.h:33, from pairwise_aligners/Mutmer.cc:9: ./feudal/SmallVec.h:443: warning: integer constant is too large for ‘long’ type In file included from ./feudal/BaseVec.h:13, from ./Basevector.h:12, from ./pairwise_aligners/Mutmer.h:33, from pairwise_aligners/Mutmer.cc:9: ./feudal/FieldVec.h:752: warning: integer constant is too large for ‘long’ type In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from ./system/System.h:16, from ./CoreTools.h:17, from ./feudal/FieldVec.h:20, from ./feudal/BaseVec.h:13, from ./Basevector.h:12, from ./pairwise_aligners/Mutmer.h:33, from pairwise_aligners/Mutmer.cc:9: ./feudal/SmallVec.h:443: warning: large integer implicitly truncated to unsigned type In file included from ./feudal/MasterVec.h:24, from ./VecString.h:14, from ./CoreTools.h:22, from ./feudal/FieldVec.h:20, from ./feudal/BaseVec.h:13, from ./Basevector.h:12, from ./pairwise_aligners/Mutmer.h:33, from pairwise_aligners/Mutmer.cc:9: ./feudal/OuterVec.h: In member function ‘size_t OuterVec::max_size() const’: ./feudal/OuterVec.h:196: warning: left shift count >= width of type In file included from ./feudal/BaseVec.h:13, from ./Basevector.h:12, from ./pairwise_aligners/Mutmer.h:33, from pairwise_aligners/Mutmer.cc:9: ./feudal/FieldVec.h: At global scope: ./feudal/FieldVec.h:752: warning: large integer implicitly truncated to unsigned type ./feudal/FieldVec.h: In member function ‘FieldVec& FieldVec::push_back(unsigned char, float, unsigned int) [with int N = 2, A = MempoolAllocator]’: ./feudal/FieldVec.h:494: instantiated from ‘FieldVec& FieldVec::push_back(unsigned char) [with int N = 2, A = MempoolAllocator]’ ./feudal/BaseVec.h:184: instantiated from here ./feudal/FieldVec.h:506: error: no matching function for call to ‘max(long unsigned int, const unsigned int&)’ In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from ./system/System.h:16, from ./CoreTools.h:17, from ./feudal/FieldVec.h:20, from ./feudal/BaseVec.h:13, from ./Basevector.h:12, from ./pairwise_aligners/Mutmer.h:33, from pairwise_aligners/Mutmer.cc:9: ./feudal/SmallVec.h: In member function ‘SmallVec& SmallVec::push_back(const T&, float, unsigned int) [with T = char, A = MempoolAllocator]’: ./feudal/SmallVec.h:215: instantiated from ‘SmallVec& SmallVec::push_back(const T&) [with T = char, A = MempoolAllocator]’ ./Fastavector.h:59: instantiated from here ./feudal/SmallVec.h:226: error: no matching function for call to ‘max(long unsigned int, const unsigned int&)’ distcc[9434] ERROR: compile pairwise_aligners/Mutmer.cc on localhost failed make[2]: *** [Mutmer.o] Error 1 make[2]: *** Waiting for unfinished jobs.... distcc[9435] ERROR: compile feudal/Generic.cc on 195.113.57.236 failed distcc[9435] (dcc_build_somewhere) Warning: remote compilation of 'feudal/Generic.cc' failed, retrying locally distcc[9435] Warning: failed to distribute feudal/Generic.cc to 195.113.57.236, running locally instead In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from feudal/Generic.cc:20: ./feudal/SmallVec.h:443: warning: integer constant is too large for ‘long’ type ./feudal/SmallVec.h:443: warning: large integer implicitly truncated to unsigned type ./feudal/SmallVec.h: In member function ‘SmallVec& SmallVec::push_back(const T&, float, unsigned int) [with T = char, A = MempoolAllocator]’: ./feudal/SmallVec.h:215: instantiated from ‘SmallVec& SmallVec::push_back(const T&) [with T = char, A = MempoolAllocator]’ ./feudal/FeudalString.h:183: instantiated from ‘FeudalString& FeudalString::push_back(charT) [with charT = char, Traits = std::char_traits]’ ./feudal/CharString.h:148: instantiated from here ./feudal/SmallVec.h:226: error: no matching function for call to ‘max(long unsigned int, const unsigned int&)’ distcc[9435] ERROR: compile feudal/Generic.cc on localhost failed make[2]: *** [Generic.o] Error 1 distcc[9436] ERROR: compile ReadPairing.cc on 192.168.251.1,lzo failed distcc[9436] (dcc_build_somewhere) Warning: remote compilation of 'ReadPairing.cc' failed, retrying locally distcc[9436] Warning: failed to distribute ReadPairing.cc to 192.168.251.1,lzo, running locally instead In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from system/System.h:16, from CoreTools.h:17, from ReadPairing.cc:14: ./feudal/SmallVec.h:443: warning: integer constant is too large for ‘long’ type In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from system/System.h:16, from CoreTools.h:17, from ReadPairing.cc:14: ./feudal/SmallVec.h:443: warning: large integer implicitly truncated to unsigned type In file included from feudal/MasterVec.h:24, from VecString.h:14, from CoreTools.h:22, from ReadPairing.cc:14: ./feudal/OuterVec.h: In member function ‘size_t OuterVec::max_size() const’: ./feudal/OuterVec.h:196: warning: left shift count >= width of type ReadPairing.cc: In function ‘void ReadsToPairs(const String&, const vec&, vec&, const String&)’: ReadPairing.cc:115: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result In file included from CoreTools.h:20, from ReadPairing.cc:14: Vec.h: In function ‘void BinaryReadSubset(const String&, const vec&, vec&) [with T = int]’: ReadPairing.cc:105: instantiated from here Vec.h:872: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from system/System.h:16, from CoreTools.h:17, from ReadPairing.cc:14: ./feudal/SmallVec.h: In member function ‘SmallVec& SmallVec::push_back(const T&, float, unsigned int) [with T = char, A = MempoolAllocator]’: ./feudal/SmallVec.h:215: instantiated from ‘SmallVec& SmallVec::push_back(const T&) [with T = char, A = MempoolAllocator]’ ./feudal/FeudalString.h:183: instantiated from ‘FeudalString& FeudalString::push_back(charT) [with charT = char, Traits = std::char_traits]’ ./feudal/CharString.h:148: instantiated from here ./feudal/SmallVec.h:226: error: no matching function for call to ‘max(long unsigned int, const unsigned int&)’ distcc[9436] ERROR: compile ReadPairing.cc on localhost failed make[2]: *** [ReadPairing.o] Error 1 distcc[9451] ERROR: compile FetchReadsAmb.cc on 195.113.57.236 failed distcc[9451] (dcc_build_somewhere) Warning: remote compilation of 'FetchReadsAmb.cc' failed, retrying locally distcc[9451] Warning: failed to distribute FetchReadsAmb.cc to 195.113.57.236, running locally instead In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from ./system/System.h:16, from ./CoreTools.h:17, from ./feudal/FieldVec.h:20, from feudal/BitVec.h:12, from Bitvector.h:12, from FetchReadsAmb.cc:22: ./feudal/SmallVec.h:443: warning: integer constant is too large for ‘long’ type In file included from feudal/BitVec.h:12, from Bitvector.h:12, from FetchReadsAmb.cc:22: ./feudal/FieldVec.h:752: warning: integer constant is too large for ‘long’ type In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from ./system/System.h:16, from ./CoreTools.h:17, from ./feudal/FieldVec.h:20, from feudal/BitVec.h:12, from Bitvector.h:12, from FetchReadsAmb.cc:22: ./feudal/SmallVec.h:443: warning: large integer implicitly truncated to unsigned type In file included from ./feudal/MasterVec.h:24, from ./VecString.h:14, from ./CoreTools.h:22, from ./feudal/FieldVec.h:20, from feudal/BitVec.h:12, from Bitvector.h:12, from FetchReadsAmb.cc:22: ./feudal/OuterVec.h: In member function ‘size_t OuterVec::max_size() const’: ./feudal/OuterVec.h:196: warning: left shift count >= width of type In file included from feudal/BitVec.h:12, from Bitvector.h:12, from FetchReadsAmb.cc:22: ./feudal/FieldVec.h: At global scope: ./feudal/FieldVec.h:752: warning: large integer implicitly truncated to unsigned type ./feudal/FieldVec.h: In member function ‘FieldVec& FieldVec::push_back(unsigned char, float, unsigned int) [with int N = 2, A = MempoolAllocator]’: ./feudal/FieldVec.h:494: instantiated from ‘FieldVec& FieldVec::push_back(unsigned char) [with int N = 2, A = MempoolAllocator]’ feudal/BaseVec.h:184: instantiated from here ./feudal/FieldVec.h:506: error: no matching function for call to ‘max(long unsigned int, const unsigned int&)’ In file included from ./feudal/FeudalString.h:29, from ./feudal/CharString.h:19, from ./String.h:13, from ./system/System.h:16, from ./CoreTools.h:17, from ./feudal/FieldVec.h:20, from feudal/BitVec.h:12, from Bitvector.h:12, from FetchReadsAmb.cc:22: ./feudal/SmallVec.h: In member function ‘SmallVec& SmallVec::push_back(const T&, float, unsigned int) [with T = char, A = MempoolAllocator]’: ./feudal/SmallVec.h:215: instantiated from ‘SmallVec& SmallVec::push_back(const T&) [with T = char, A = MempoolAllocator]’ ./feudal/FeudalString.h:183: instantiated from ‘FeudalString& FeudalString::push_back(charT) [with charT = char, Traits = std::char_traits]’ ./feudal/CharString.h:148: instantiated from here ./feudal/SmallVec.h:226: error: no matching function for call to ‘max(long unsigned int, const unsigned int&)’ distcc[9451] ERROR: compile FetchReadsAmb.cc on localhost failed make[2]: *** [FetchReadsAmb.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805/src' make: *** [all-recursive] Error 1 emake failed * ERROR: sci-biology/vaal-1.6 failed: * died running emake, base_src_make * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 2952: Called base_src_compile * environment, line 418: Called base_src_make * environment, line 456: Called die * The specific snippet of code: * emake "$@" || die "died running emake, $FUNCNAME"; * * 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/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'. * S: '/var/tmp/portage/sci-biology/vaal-1.6/work/vaal-33805'