* Package: sci-biology/vaal-46233 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux openmp userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking vaal-46233.tar.gz to /var/tmp/portage/sci-biology/vaal-46233/work >>> Unpacking VAAL_manual.doc to /var/tmp/portage/sci-biology/vaal-46233/work unpack VAAL_manual.doc: file format not recognized. Ignoring. >>> Source unpacked in /var/tmp/portage/sci-biology/vaal-46233/work >>> Preparing source in /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233 ... * Running eautoreconf in '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233' ... * Running libtoolize --install --copy --force --automake ... [ ok ] * Running aclocal -I m4 ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --foreign --force-missing ... [ ok ] * Running elibtoolize in: vaal-46233/ * Applying portage/1.2.0 patch ... * Applying sed/1.5.6 patch ... * Applying as-needed/2.4.3 patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233_build" * econf: updating vaal-46233/config.sub with /usr/share/gnuconfig/config.sub * econf: updating vaal-46233/config.guess with /usr/share/gnuconfig/config.guess /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/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 --libdir=/usr/lib64 --docdir=/usr/share/doc/vaal-46233 --enable-openmp checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/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 whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for style of include used by make... GNU checking for x86_64-pc-linux-gnu-gcc... x86_64-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 x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-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 x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-pc-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... x86_64-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 x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) 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 x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking dependency style of x86_64-pc-linux-gnu-g++... none checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) 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 >= 4.7... yes 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 x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp checking that generated files are newer than configure... done 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-46233/work/vaal-46233 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233_build" make -j1 Making all in src make[1]: Entering directory '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233_build/src' make all-am make[2]: Entering directory '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233_build/src' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.8.17-hardened-r2 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ErrNo.o `test -f 'system/ErrNo.cc' || echo '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/'`system/ErrNo.cc x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.8.17-hardened-r2 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Mutmer.o `test -f 'pairwise_aligners/Mutmer.cc' || echo '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/'`pairwise_aligners/Mutmer.cc In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:170:20: error: reference to ‘align’ is ambiguous packalign( const align& a ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:155:7: note: candidates are: class align class align; ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:221:21: error: reference to ‘align’ is ambiguous void SetToFlipOf( align a ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:155:7: note: candidates are: class align class align; ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:221:21: error: ‘align’ has not been declared void SetToFlipOf( align a ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:223:28: error: reference to ‘align’ is ambiguous void SetToReverseFlipOf( align a, int b1_len, int b2_len ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:155:7: note: candidates are: class align class align; ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:223:28: error: ‘align’ has not been declared void SetToReverseFlipOf( align a, int b1_len, int b2_len ); ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:12:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BinaryStreamTraits.h:77:37: error: template argument 1 is invalid template <> struct Serializability \ ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:595:1: note: in expansion of macro ‘SELF_SERIALIZABLE’ SELF_SERIALIZABLE(align); ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:597:42: error: reference to ‘align’ is ambiguous ostream & operator<<(ostream & os, const align & a); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:599:20: error: reference to ‘align’ is ambiguous Bool Proper( const align& a, int len1, int len2 ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:601:27: error: reference to ‘align’ is ambiguous void RequireProper( const align& a, int id1, int id2, Bool rc2, ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:604:27: error: reference to ‘align’ is ambiguous void RequireProper( const align& a, int id1, int id2, Bool rc2, ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:611:25: error: reference to ‘align’ is ambiguous const align& a, int mismatch_penalty = 1, int gap_penalty = 2 ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:615:25: error: reference to ‘align’ is ambiguous const align& a, int mismatch_penalty = 1, int gap_penalty = 2 ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:618:25: error: reference to ‘align’ is ambiguous const align& a, int mismatch_penalty = 1, int gap_penalty = 2 ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:620:25: error: reference to ‘align’ is ambiguous const align& a, int mismatch_penalty = 1, int gap_penalty = 2 ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:622:25: error: reference to ‘align’ is ambiguous const align& a, int mismatch_penalty = 1, int gap_penalty = 2 ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:624:25: error: reference to ‘align’ is ambiguous const align& a, int mismatch_penalty = 1, int gap_penalty = 2 ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:626:16: error: reference to ‘align’ is ambiguous int Bandwidth( align& a ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:626:23: error: ‘a’ was not declared in this scope int Bandwidth( align& a ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:628:31: error: reference to ‘align’ is ambiguous int CorrelatePositions( const align& a, int x1 ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:633:12: error: reference to ‘align’ is ambiguous const align & a, int startOn1, int len, ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:634:30: error: reference to ‘align’ is ambiguous basevector & trimmedb1, align & trimmeda); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:634:30: error: ‘align’ has not been declared basevector & trimmedb1, align & trimmeda); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h: In function ‘std::ostream& operator<<(std::ostream&, const placement_mark&)’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:716:22: error: ambiguous overload for ‘operator<<’ (operand types are ‘std::ostream {aka std::basic_ostream}’ and ‘int’) { return out << m.Tig( ) << " " << m.Pos( ) << " " ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:166:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:170:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:174:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(bool __n) ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:638:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/ostream.tcc:91:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char; _Traits = std::char_traits] basic_ostream<_CharT, _Traits>:: ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:181:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned short __n) ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:638:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/ostream.tcc:105:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char; _Traits = std::char_traits] basic_ostream<_CharT, _Traits>:: ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:192:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned int __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:201:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:205:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned long long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:220:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(double __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:224:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(float __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:232:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long double __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:502:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, char) [with _CharT = char; _Traits = std::char_traits] operator<<(basic_ostream<_CharT, _Traits>& __out, char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:508:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:514:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, signed char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, signed char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:519:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, unsigned char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, unsigned char __c) ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:597:11: note: candidate: std::ostream& operator<<(std::ostream&, const int&) ostream & operator<<(ostream & os, const align & a); ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:132:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/HoInterval.h:319:11: note: candidate: std::ostream& operator<<(std::ostream&, const HoIntervalWithId&) ostream & operator<< (ostream & os, const HoIntervalWithId & i) { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/MasterVec.h:28:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/VecString.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:22, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Functions.h:406:18: note: candidate: std::ostream& operator<<(std::ostream&, const NormalDistribution&) inline ostream & operator<<(ostream & os, const ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Functions.h:13:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/MasterVec.h:28, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/VecString.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:22, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Arith.h:138:10: note: candidate: std::ostream& operator<<(std::ostream&, const Float&) ostream& operator<< ( ostream& out, const Float& aFloat ) { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h: At global scope: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:82:22: error: reference to ‘align’ is ambiguous void Set( const align& al ) ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:86:22: error: reference to ‘align’ is ambiguous void Set( const align& al, int errors ) ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h: In member function ‘void alignment::Set(const int&)’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:83:30: error: request for member ‘pos1’ in ‘al’, which is of non-class type ‘const int’ { packalign::Set( al.pos1( ), al.pos2( ), al.Gaps( ), al.Lengths( ), ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:83:42: error: request for member ‘pos2’ in ‘al’, which is of non-class type ‘const int’ { packalign::Set( al.pos1( ), al.pos2( ), al.Gaps( ), al.Lengths( ), ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:83:54: error: request for member ‘Gaps’ in ‘al’, which is of non-class type ‘const int’ { packalign::Set( al.pos1( ), al.pos2( ), al.Gaps( ), al.Lengths( ), ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:83:66: error: request for member ‘Lengths’ in ‘al’, which is of non-class type ‘const int’ { packalign::Set( al.pos1( ), al.pos2( ), al.Gaps( ), al.Lengths( ), ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:84:19: error: request for member ‘Nblocks’ in ‘al’, which is of non-class type ‘const int’ al.Nblocks( ) ); } ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h: In member function ‘void alignment::Set(const int&, int)’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:87:30: error: request for member ‘pos1’ in ‘al’, which is of non-class type ‘const int’ { packalign::Set( al.pos1( ), al.pos2( ), al.Gaps( ), al.Lengths( ), ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:87:42: error: request for member ‘pos2’ in ‘al’, which is of non-class type ‘const int’ { packalign::Set( al.pos1( ), al.pos2( ), al.Gaps( ), al.Lengths( ), ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:87:54: error: request for member ‘Gaps’ in ‘al’, which is of non-class type ‘const int’ { packalign::Set( al.pos1( ), al.pos2( ), al.Gaps( ), al.Lengths( ), ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:87:66: error: request for member ‘Lengths’ in ‘al’, which is of non-class type ‘const int’ { packalign::Set( al.pos1( ), al.pos2( ), al.Gaps( ), al.Lengths( ), ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:88:19: error: request for member ‘Nblocks’ in ‘al’, which is of non-class type ‘const int’ al.Nblocks( ) ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h: In function ‘int ActualErrors(const BASEVEC&, const BASEVEC&, const alignment&, int, int)’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:137:37: error: reference to ‘align’ is ambiguous { return ActualErrors( rd1, rd2, align(packalign(a)), mismatch_penalty, ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h: At global scope: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:209:30: error: reference to ‘align’ is ambiguous void SetToSwapOf( const align& x, int id1, int id2, Bool rc2, ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:326:29: error: ‘int Bandwidth(alignment&)’ redeclared as different kind of symbol int Bandwidth( alignment& a ); ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:626:5: note: previous declaration ‘int Bandwidth’ int Bandwidth( align& a ); ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:333:26: error: variable or field ‘TrimAlignmentFront’ declared void void TrimAlignmentFront( align& a, int n ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:333:26: error: reference to ‘align’ is ambiguous In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:333:33: error: ‘a’ was not declared in this scope void TrimAlignmentFront( align& a, int n ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:333:36: error: expected primary-expression before ‘int’ void TrimAlignmentFront( align& a, int n ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:338:25: error: variable or field ‘TrimAlignmentBack’ declared void void TrimAlignmentBack( align& a, int n ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:338:25: error: reference to ‘align’ is ambiguous In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:338:32: error: ‘a’ was not declared in this scope void TrimAlignmentBack( align& a, int n ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:338:35: error: expected primary-expression before ‘int’ void TrimAlignmentBack( align& a, int n ); ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:340:44: error: reference to ‘align’ is ambiguous int MaxPerfectMatch( Bool rd1_is_rc, const align& a, const basevector& rd1, ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10:0: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:24:33: error: reference to ‘align’ is ambiguous const BASEVEC2& rd2, const align& a, ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10:0: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:36:33: error: reference to ‘align’ is ambiguous const BASEVEC2& rd2, const align& a, ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10:0: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:66:47: error: reference to ‘align’ is ambiguous const BASEVEC1& rd1, BASEVEC2 rd2, const align& a, ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10:0: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h: In function ‘void PrintVisualAlignment(Bool, std::ostream&, const BASEVEC1&, const BASEVEC2&, const alignment&, const qualvector&, const qualvector&, int, Bool, int, Bool, float)’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:79:55: error: reference to ‘align’ is ambiguous { PrintVisualAlignment( abbreviate, out, rd1, rd2, align(packalign(a)), ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10:0: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h: In function ‘void PrintVisualAlignment(Bool, Bool, std::ostream&, const BASEVEC1&, BASEVEC2, const alignment&, const qualvector&, qualvector, int, Bool, int, Bool, float)’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:91:11: error: reference to ‘align’ is ambiguous align(packalign(a)), scores1, scores2, begin, one_frame, ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc: In member function ‘void mutmer::Print(std::ostream&, const basevector&, const basevector&)’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:14:3: error: reference to ‘align’ is ambiguous align a; ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:298:7: note: candidates are: class align class align { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:34:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:20, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/memory:115:1: note: void* std::align(std::size_t, std::size_t, void*&, std::size_t&) align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept ^ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:15:3: error: ‘a’ was not declared in this scope a.Setpos1( pos1_ ); ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BinaryStream.h:22:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FeudalString.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/CharString.h:19, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/String.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h: In instantiation of ‘void Assert::reportAndDie(const T&, const U&, const char*, const char*) [with T = int; U = int]’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h:41:32: required from ‘void Assert::ge(const T&, const U&, const char*, const char*) [with T = int; U = int]’ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:896:11: required from here /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h:24:44: error: ambiguous overload for ‘operator<<’ (operand types are ‘std::basic_ostream’ and ‘const int’) { std::ostringstream oss; oss << "arg1 = " << t << " and arg2 = " << u; ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:166:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:170:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:174:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(bool __n) ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:638:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/ostream.tcc:91:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char; _Traits = std::char_traits] basic_ostream<_CharT, _Traits>:: ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:181:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned short __n) ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:638:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/ostream.tcc:105:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char; _Traits = std::char_traits] basic_ostream<_CharT, _Traits>:: ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:192:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned int __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:201:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:205:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned long long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:220:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(double __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:224:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(float __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:232:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long double __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:502:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, char) [with _CharT = char; _Traits = std::char_traits] operator<<(basic_ostream<_CharT, _Traits>& __out, char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:508:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:514:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, signed char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, signed char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:519:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, unsigned char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, unsigned char __c) ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:597:11: note: candidate: std::ostream& operator<<(std::ostream&, const int&) ostream & operator<<(ostream & os, const align & a); ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:132:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/HoInterval.h:319:11: note: candidate: std::ostream& operator<<(std::ostream&, const HoIntervalWithId&) ostream & operator<< (ostream & os, const HoIntervalWithId & i) { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/MasterVec.h:28:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/VecString.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:22, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Functions.h:406:18: note: candidate: std::ostream& operator<<(std::ostream&, const NormalDistribution&) inline ostream & operator<<(ostream & os, const ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Functions.h:13:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/MasterVec.h:28, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/VecString.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:22, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Arith.h:138:10: note: candidate: std::ostream& operator<<(std::ostream&, const Float&) ostream& operator<< ( ostream& out, const Float& aFloat ) { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BinaryStream.h:22:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FeudalString.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/CharString.h:19, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/String.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h: In instantiation of ‘void Assert::reportAndDie(const T&, const U&, const char*, const char*) [with T = int; U = long int]’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h:45:31: required from ‘void Assert::lt(const T&, const U&, const char*, const char*) [with T = int; U = long int]’ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Vec.h:897:11: required from here /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h:24:44: error: ambiguous overload for ‘operator<<’ (operand types are ‘std::basic_ostream’ and ‘const int’) { std::ostringstream oss; oss << "arg1 = " << t << " and arg2 = " << u; ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:166:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:170:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:174:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(bool __n) ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:638:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/ostream.tcc:91:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char; _Traits = std::char_traits] basic_ostream<_CharT, _Traits>:: ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:181:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned short __n) ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:638:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/ostream.tcc:105:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char; _Traits = std::char_traits] basic_ostream<_CharT, _Traits>:: ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:192:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned int __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:201:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:205:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned long long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:220:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(double __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:224:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(float __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:232:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long double __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:502:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, char) [with _CharT = char; _Traits = std::char_traits] operator<<(basic_ostream<_CharT, _Traits>& __out, char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:508:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:514:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, signed char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, signed char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:519:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, unsigned char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, unsigned char __c) ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:597:11: note: candidate: std::ostream& operator<<(std::ostream&, const int&) ostream & operator<<(ostream & os, const align & a); ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:132:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/HoInterval.h:319:11: note: candidate: std::ostream& operator<<(std::ostream&, const HoIntervalWithId&) ostream & operator<< (ostream & os, const HoIntervalWithId & i) { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/MasterVec.h:28:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/VecString.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:22, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Functions.h:406:18: note: candidate: std::ostream& operator<<(std::ostream&, const NormalDistribution&) inline ostream & operator<<(ostream & os, const ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Functions.h:13:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/MasterVec.h:28, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/VecString.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:22, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Arith.h:138:10: note: candidate: std::ostream& operator<<(std::ostream&, const Float&) ostream& operator<< ( ostream& out, const Float& aFloat ) { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BinaryStream.h:22:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FeudalString.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/CharString.h:19, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/String.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h: In instantiation of ‘void Assert::reportAndDie(const T&, const U&, const char*, const char*) [with T = long int; U = int]’: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h:41:32: required from ‘void Assert::ge(const T&, const U&, const char*, const char*) [with T = long int; U = int]’ /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/HoInterval.h:25:11: required from here /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h:24:67: error: ambiguous overload for ‘operator<<’ (operand types are ‘std::basic_ostream’ and ‘const int’) { std::ostringstream oss; oss << "arg1 = " << t << " and arg2 = " << u; ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:166:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:170:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:174:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(bool __n) ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:638:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/ostream.tcc:91:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char; _Traits = std::char_traits] basic_ostream<_CharT, _Traits>:: ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:181:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned short __n) ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:638:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/bits/ostream.tcc:105:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char; _Traits = std::char_traits] basic_ostream<_CharT, _Traits>:: ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/istream:39:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/fstream:38, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/System.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:17, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:192:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned int __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:201:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:205:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(unsigned long long __n) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:220:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(double __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:224:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(float __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:232:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] operator<<(long double __f) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:502:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, char) [with _CharT = char; _Traits = std::char_traits] operator<<(basic_ostream<_CharT, _Traits>& __out, char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:508:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:514:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, signed char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, signed char __c) ^ /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5/ostream:519:5: note: candidate: std::basic_ostream& std::operator<<(std::basic_ostream&, unsigned char) [with _Traits = std::char_traits] operator<<(basic_ostream& __out, unsigned char __c) ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:597:11: note: candidate: std::ostream& operator<<(std::ostream&, const int&) ostream & operator<<(ostream & os, const align & a); ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:132:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:10: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/HoInterval.h:319:11: note: candidate: std::ostream& operator<<(std::ostream&, const HoIntervalWithId&) ostream & operator<< (ostream & os, const HoIntervalWithId & i) { ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/MasterVec.h:28:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/VecString.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:22, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Functions.h:406:18: note: candidate: std::ostream& operator<<(std::ostream&, const NormalDistribution&) inline ostream & operator<<(ostream & os, const ^ In file included from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Functions.h:13:0, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/MasterVec.h:28, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/VecString.h:14, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/CoreTools.h:22, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/FieldVec.h:21, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/feudal/BaseVec.h:13, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Basevector.h:12, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.h:33, from /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:9: /var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/math/Arith.h:138:10: note: candidate: std::ostream& operator<<(std::ostream&, const Float&) ostream& operator<< ( ostream& out, const Float& aFloat ) { ^ make[2]: *** [Makefile:1136: Mutmer.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233_build/src' make[1]: *** [Makefile:739: all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233_build/src' make: *** [Makefile:389: all-recursive] Error 1 * ERROR: sci-biology/vaal-46233::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/vaal-46233::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/vaal-46233::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:vaal-46233:20170123-190519.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/vaal-46233/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/vaal-46233/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233_build' * S: '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233'