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Gentoo's Bugzilla – Attachment 419362 Details for
Bug 568438
sci-biology/vaal-46233: gcc-5 issue
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emerge log
x.log (text/plain), 129.33 KB, created by
Toralf Förster
on 2015-12-16 15:19:59 UTC
(
hide
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Description:
emerge log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2015-12-16 15:19:59 UTC
Size:
129.33 KB
patch
obsolete
> > * Package: sci-biology/vaal-46233 > * Repository: gentoo > * Maintainer: sci-biology > * 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... x86_64-pc-linux-gnu-dlltool >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... mt >checking if mt 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=4.2.7-hardened -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -march=native -O2 -pipe -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=4.2.7-hardened -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -march=native -O2 -pipe -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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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: âalignâ 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 âalignâ 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/5.3.0/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: âalignâ 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<T> \ > ^ >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:595:1: note: in expansion of macro âSELF_SERIALIZABLEâ > 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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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: âaâ 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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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: âalignâ has not been declared > basevector & trimmedb1, align & trimmeda); > ^ >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h: In function âstd::ostream& operator<<(std::ostream&, const placement_mark&)â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PackAlign.h:716:22: error: ambiguous overload for âoperator<<â (operand types are âstd::ostream {aka std::basic_ostream<char>}â and âintâ) > { return out << m.Tig( ) << " " << m.Pos( ) << " " > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(bool __n) > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>] > basic_ostream<_CharT, _Traits>:: > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned short __n) > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>] > basic_ostream<_CharT, _Traits>:: > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned int __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(double __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(float __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long double __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>] > operator<<(basic_ostream<_CharT, _Traits>& __out, char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:508:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __out, char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:514:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, signed char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __out, signed char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:519:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, unsigned char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âvoid alignment::Set(const int&)â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:83:30: error: request for member âpos1â in âalâ, which is of non-class type âconst intâ > { 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 âpos2â in âalâ, which is of non-class type âconst intâ > { 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 âGapsâ in âalâ, which is of non-class type âconst intâ > { 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 âLengthsâ in âalâ, which is of non-class type âconst intâ > { 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 âNblocksâ in âalâ, which is of non-class type âconst intâ > al.Nblocks( ) ); } > ^ >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h: In member function âvoid alignment::Set(const int&, int)â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:87:30: error: request for member âpos1â in âalâ, which is of non-class type âconst intâ > { 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 âpos2â in âalâ, which is of non-class type âconst intâ > { 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 âGapsâ in âalâ, which is of non-class type âconst intâ > { 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 âLengthsâ in âalâ, which is of non-class type âconst intâ > { 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 âNblocksâ in âalâ, which is of non-class type âconst intâ > al.Nblocks( ) ); > ^ >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h: In function âint ActualErrors(const BASEVEC&, const BASEVEC&, const alignment&, int, int)â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:137:37: error: reference to âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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: âint Bandwidth(alignment&)â 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 âint Bandwidthâ > 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 âTrimAlignmentFrontâ 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 âalignâ 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/5.3.0/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: âaâ 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 âintâ > 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 âTrimAlignmentBackâ 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 âalignâ 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/5.3.0/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: âaâ 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 âintâ > void TrimAlignmentBack( align& a, int n ); > ^ >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/Alignment.h:340:44: error: reference to âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âalignâ 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/5.3.0/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 âvoid PrintVisualAlignment(Bool, std::ostream&, const BASEVEC1&, const BASEVEC2&, const alignment&, const qualvector&, const qualvector&, int, Bool, int, Bool, float)â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:79:55: error: reference to âalignâ 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/5.3.0/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 âvoid PrintVisualAlignment(Bool, Bool, std::ostream&, const BASEVEC1&, BASEVEC2, const alignment&, const qualvector&, qualvector, int, Bool, int, Bool, float)â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/PrintAlignment.h:91:11: error: reference to âalignâ 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/5.3.0/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 âvoid mutmer::Print(std::ostream&, const basevector&, const basevector&)â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/pairwise_aligners/Mutmer.cc:14:3: error: reference to âalignâ 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/5.3.0/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: âaâ 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 âvoid Assert::reportAndDie(const T&, const U&, const char*, const char*) [with T = int; U = int]â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h:41:32: required from âvoid Assert::ge(const T&, const U&, const char*, const char*) [with T = int; U = int]â >/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 âoperator<<â (operand types are âstd::basic_ostream<char>â and âconst intâ) > { std::ostringstream oss; oss << "arg1 = " << t << " and arg2 = " << u; > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(bool __n) > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>] > basic_ostream<_CharT, _Traits>:: > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned short __n) > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>] > basic_ostream<_CharT, _Traits>:: > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned int __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(double __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(float __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long double __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>] > operator<<(basic_ostream<_CharT, _Traits>& __out, char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:508:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __out, char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:514:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, signed char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __out, signed char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:519:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, unsigned char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __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 âvoid Assert::reportAndDie(const T&, const U&, const char*, const char*) [with T = int; U = long int]â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h:45:31: required from âvoid Assert::lt(const T&, const U&, const char*, const char*) [with T = int; U = long int]â >/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 âoperator<<â (operand types are âstd::basic_ostream<char>â and âconst intâ) > { std::ostringstream oss; oss << "arg1 = " << t << " and arg2 = " << u; > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(bool __n) > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>] > basic_ostream<_CharT, _Traits>:: > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned short __n) > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>] > basic_ostream<_CharT, _Traits>:: > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned int __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(double __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(float __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long double __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>] > operator<<(basic_ostream<_CharT, _Traits>& __out, char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:508:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __out, char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:514:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, signed char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __out, signed char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:519:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, unsigned char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __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 âvoid Assert::reportAndDie(const T&, const U&, const char*, const char*) [with T = long int; U = int]â: >/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233/src/system/Assert.h:41:32: required from âvoid Assert::ge(const T&, const U&, const char*, const char*) [with T = long int; U = int]â >/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 âoperator<<â (operand types are âstd::basic_ostream<char>â and âconst intâ) > { std::ostringstream oss; oss << "arg1 = " << t << " and arg2 = " << u; > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(bool __n) > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>] > basic_ostream<_CharT, _Traits>:: > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned short __n) > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>] > basic_ostream<_CharT, _Traits>:: > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned int __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long long __n) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(double __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(float __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long double __f) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/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<char>] > operator<<(basic_ostream<_CharT, _Traits>& __out, char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:508:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __out, char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:514:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, signed char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __out, signed char __c) > ^ >/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/ostream:519:5: note: candidate: std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, unsigned char) [with _Traits = std::char_traits<char>] > operator<<(basic_ostream<char, _Traits>& __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 ) { > ^ >Makefile:1136: recipe for target 'Mutmer.o' failed >make[2]: *** [Mutmer.o] Error 1 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233_build/src' >Makefile:739: recipe for target 'all' failed >make[1]: *** [all] Error 2 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/vaal-46233/work/vaal-46233_build/src' >Makefile:389: recipe for target 'all-recursive' failed >make: *** [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-46233:20151216-151036.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' > > * Regenerating GNU info directory index... > * Processed 341 info files. > * > * revdep-rebuild failed to emerge all packages. > * you have the following choices: > * - If emerge failed during the build, fix the problems and re-run revdep-rebuild. > * - Use /etc/portage/package.keywords to unmask a newer version of the package. > * (and remove 5_order.rr to be evaluated again) > * - Modify the above emerge command and run it manually. > * - Compile or unmerge unsatisfied packages manually, > * remove temporary files, and try again. > * (you can edit package/ebuild list first) > * > * To remove temporary files, please run: > * rm /var/cache/revdep-rebuild/*.rr
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bug 568438
: 419362