Attachment 576690 Details for Bug 685980 – sci-biology:vaal-46233-r2:20190514-185706.log

sci-biology:vaal-46233-r2:20190514-185706.log

sci-biology:vaal-46233-r2:20190514-185706.log (text/plain), 26.10 KB, created by Toralf Förster on 2019-05-14 19:25:31 UTC

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Creator: Toralf Förster

Created: 2019-05-14 19:25:31 UTC

Size: 26.10 KB

patch

obsolete

> * Package:    sci-biology/vaal-46233-r2
> * Repository: gentoo
> * Maintainer: sci-biology@gentoo.org
> * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux openmp userland_GNU
> * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>>> Unpacking source...
>>>> Unpacking vaal-46233.tar.gz to /var/tmp/portage/sci-biology/vaal-46233-r2/work
>>>> Unpacking VAAL_manual.doc to /var/tmp/portage/sci-biology/vaal-46233-r2/work
>unpack VAAL_manual.doc: file format not recognized. Ignoring.
>>>> Unpacking vaal-46233_remove-namespace-std.patch.bz2 to /var/tmp/portage/sci-biology/vaal-46233-r2/work
>>>> Source unpacked in /var/tmp/portage/sci-biology/vaal-46233-r2/work
>>>> Preparing source in /var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233 ...
> * Applying vaal-46233-libieee.patch ...
> [ ok ]
> * Applying vaal-46233_remove-namespace-std.patch ...
> [ ok ]
> * Running eautoreconf in '/var/tmp/portage/sci-biology/vaal-46233-r2/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-r2/work/vaal-46233 ...
> * econf: updating vaal-46233/config.sub with /usr/share/gnuconfig/config.sub
> * econf: updating vaal-46233/config.guess with /usr/share/gnuconfig/config.guess
>./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/vaal-46233-r2 --htmldir=/usr/share/doc/vaal-46233-r2/html --libdir=/usr/lib64 --enable-openmp
>checking for a BSD-compatible install... /usr/lib/portage/python3.6/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 whether make supports the include directive... yes (GNU style)
>checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
>checking whether the C compiler works... yes
>checking for C compiler default output file name... a.out
>checking for suffix of executables... 
>checking whether we are cross compiling... no
>checking for suffix of object files... o
>checking whether we are using the GNU C compiler... yes
>checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
>checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
>checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
>checking dependency style of x86_64-pc-linux-gnu-gcc... none
>checking for a sed that does not truncate output... /bin/sed
>checking for grep that handles long lines and -e... /bin/grep
>checking for egrep... /bin/grep -E
>checking for fgrep... /bin/grep -F
>checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
>checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
>checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B
>checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm
>checking whether ln -s works... yes
>checking the maximum length of command line arguments... 1572864
>checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
>checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
>checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
>checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
>checking how to recognize dependent libraries... pass_all
>checking for x86_64-pc-linux-gnu-dlltool... no
>checking for dlltool... no
>checking how to associate runtime and link libraries... printf %s\n
>checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
>checking for archiver @FILE support... @
>checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
>checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
>checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok
>checking for sysroot... no
>checking for a working dd... /bin/dd
>checking how to truncate binary pipes... /bin/dd bs=4096 count=1
>checking for x86_64-pc-linux-gnu-mt... no
>checking for mt... 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-r2/work/vaal-46233 ...
>make -j1 
>Making all in src
>make[1]: Entering directory '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233/src'
>make  all-am
>make[2]: Entering directory '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233/src'
>x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -DRELEASE=3.0 -DMAKE_OS_RELEASE=5.1.2 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233  -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -fno-strict-aliasing -iquote .  -DNDEBUG -c -o VAAL0_5.o `test -f 'polymorphism/VAAL0_5.cc' || echo './'`polymorphism/VAAL0_5.cc
>In file included from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/BaseVec.h: In member function âBaseVec& BaseVec::Reverse(const BaseVec&)â:
>./feudal/BaseVec.h:202:15: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  202 |     { *this = b; return Reverse(); }
>      |               ^
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>./feudal/BaseVec.h: In member function âBaseVec& BaseVec::ReverseComplement(const BaseVec&)â:
>./feudal/BaseVec.h:284:23: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  284 |     { return (*this = bv).ReverseComplement(); }
>      |                       ^~
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>./feudal/BaseVec.h: In function âBaseVec Cat(const BaseVec&, const BaseVec&)â:
>./feudal/BaseVec.h:483:12: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  483 |     join = left;
>      |            ^~~~
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>./feudal/BaseVec.h: In function âBaseVec Cat(const BaseVec&, const BaseVec&, const BaseVec&)â:
>./feudal/BaseVec.h:493:12: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  493 |     join = b1;
>      |            ^~
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>./feudal/BaseVec.h: In function âBaseVec Cat(const BaseVec&, const BaseVec&, const BaseVec&, const BaseVec&)â:
>./feudal/BaseVec.h:505:12: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  505 |     join = b1;
>      |            ^~
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>./feudal/BaseVec.h: In function âBaseVec TrimCat(int, const BaseVec&, const BaseVec&)â:
>./feudal/BaseVec.h:520:12: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  520 |     join = b1;
>      |            ^~
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>./feudal/BaseVec.h: In function âBaseVec TrimCat(int, const BaseVec&, const BaseVec&, const BaseVec&)â:
>./feudal/BaseVec.h:531:12: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  531 |     join = b1;
>      |            ^~
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>./feudal/BaseVec.h: In function âBaseVec TrimCat(int, const BaseVec&, const BaseVec&, const BaseVec&, const BaseVec&)â:
>./feudal/BaseVec.h:544:12: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  544 |     join = b1;
>      |            ^~
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>./feudal/BaseVec.h: In function âBaseVec TrimCat(int, const BaseVec&, const BaseVec&, const BaseVec&, const BaseVec&, const BaseVec&)â:
>./feudal/BaseVec.h:560:12: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  560 |     join = b1;
>      |            ^~
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>In file included from ./Fastavector.h:18,
>                 from ./Alignment.h:32,
>                 from polymorphism/VAAL0_5.cc:26:
>./Superb.h: At global scope:
>./Superb.h:240:18: error: friend declaration of âvoid WriteSuperbsAndSummary(const String&, const vec<superb>&, Bool, const String&)â specifies default arguments and isnât a definition [-fpermissive]
>  240 |      friend void WriteSuperbsAndSummary( const String & dir,
>      |                  ^~~~~~~~~~~~~~~~~~~~~~
>./Superb.h:245:18: error: friend declaration of âvoid WriteSummary(const String&, const vec<superb>&, const vecBoolvector&)â specifies default arguments and isnât a definition [-fpermissive]
>  245 |      friend void WriteSummary( const String & fn, const vec<superb> & s,
>      |                  ^~~~~~~~~~~~
>./Superb.h:252:18: error: friend declaration of âvoid WriteSupercontigFiles(const String&, const vec<superb>&, Bool)â specifies default arguments and isnât a definition [-fpermissive]
>  252 |      friend void WriteSupercontigFiles( const String& dir,
>      |                  ^~~~~~~~~~~~~~~~~~~~~
>In file included from ./Alignment.h:32,
>                 from polymorphism/VAAL0_5.cc:26:
>./Fastavector.h:302:18: error: friend declaration of âvoid LoadRegionsFromIndexedFastaFile(const String&, const String&, const vec<std::tuple<FeudalString<char, std::char_traits<char> >, int, int> >&, vec<fastavector>&, int, vec<std::pair<int, int> >*)â specifies default arguments and isnât a definition [-fpermissive]
>  302 |      friend void LoadRegionsFromIndexedFastaFile( const String& fasta, const String& index,
>      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>./Fastavector.h:323:18: error: friend declaration of âvoid WriteScaffoldedFasta(const String&, const vec<fastavector>&, const vec<superb>&, const vec<unsigned char>&, int, char, Bool)â specifies default arguments and isnât a definition [-fpermissive]
>  323 |      friend void WriteScaffoldedFasta( const String &out_file,
>      |                  ^~~~~~~~~~~~~~~~~~~~
>In file included from ./paths/KmerPath.h:20,
>                 from ./paths/KmerBaseBroker.h:16,
>                 from ./paths/HyperKmerPath.h:17,
>                 from ./polymorphism/VAALTools.h:17,
>                 from polymorphism/VAAL0_5.cc:34:
>./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â:
>./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=]
>  359 |      {    data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback;    }
>      |                                        ~~~~~~~~~~^~~~~
>polymorphism/VAAL0_5.cc: In constructor âpoly_event::poly_event(int, int, basevector, poly_event::ConstructorBehavior)â:
>polymorphism/VAAL0_5.cc:67:20: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>   67 |           bases_ = insertion;    }
>      |                    ^~~~~~~~~
>In file included from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>polymorphism/VAAL0_5.cc: In function âint main(int, char**)â:
>polymorphism/VAAL0_5.cc:401:30: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  401 |                ref_edit[z] = ref_orig;
>      |                              ^~~~~~~~
>In file included from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>polymorphism/VAAL0_5.cc:414:52: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  414 |                          ref_edit[z] = Cat( b1, b2 );
>      |                                                    ^
>In file included from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>polymorphism/VAAL0_5.cc:421:68: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  421 |                          ref_edit[z] = Cat( b1, p.Insertion( ), b2 );
>      |                                                                    ^
>In file included from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>polymorphism/VAAL0_5.cc:442:48: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  442 |           ref2[tig] = Cat( r1, ref_edit[z], r2 );
>      |                                                ^
>In file included from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>In file included from ./feudal/MasterVec.h:24,
>                 from ./VecString.h:14,
>                 from ./CoreTools.h:22,
>                 from ./feudal/FieldVec.h:21,
>                 from ./feudal/BaseVec.h:13,
>                 from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/OuterVec.h: In instantiation of âT* OuterVec<T, S, A>::copy(Itr, const Itr&) [with Itr = const BaseVec*; T = BaseVec; S = MempoolOwner<unsigned char>; A = std::allocator<BaseVec>]â:
>./feudal/OuterVec.h:106:16:   required from âOuterVec<T, S, A>::OuterVec(const OuterVec<T, S, A>&) [with T = BaseVec; S = MempoolOwner<unsigned char>; A = std::allocator<BaseVec>]â
>./feudal/MasterVec.h:44:7:   required from here
>./feudal/OuterVec.h:418:42: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>  418 |       { *(new (dest++) T(mSubAllocator)) = *first;
>      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
>In file included from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>polymorphism/VAAL0_5.cc: In instantiation of âvoid std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<poly_event*, std::vector<poly_event, std::allocator<poly_event> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]â:
>/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/stl_algo.h:1874:25:   required from âvoid std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<poly_event*, std::vector<poly_event, std::allocator<poly_event> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]â
>/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/stl_algo.h:1960:31:   required from âvoid std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<poly_event*, std::vector<poly_event, std::allocator<poly_event> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]â
>/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/stl_algo.h:4818:18:   required from âvoid std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<poly_event*, std::vector<poly_event, std::allocator<poly_event> > >]â
>./Vec.h:746:24:   required from âvoid Sort(vec<U>&) [with T = poly_event]â
>polymorphism/VAAL0_5.cc:294:16:   required from here
>polymorphism/VAAL0_5.cc:37:7: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>   37 | class poly_event {
>      |       ^~~~~~~~~~
>In file included from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/algorithm:62,
>                 from ./Compare.h:18,
>                 from ./feudal/FieldVec.h:20,
>                 from ./feudal/BaseVec.h:13,
>                 from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/stl_algo.h:1841:17: note: synthesized method âpoly_event& poly_event::operator=(poly_event&&)â first required here
> 1841 |        *__first = _GLIBCXX_MOVE(__val);
>      |                 ^
>polymorphism/VAAL0_5.cc: In instantiation of âstatic _OI std::__copy_move<false, false, std::random_access_iterator_tag>::__copy_m(_II, _II, _OI) [with _II = const poly_event*; _OI = poly_event*]â:
>/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/stl_algobase.h:404:30:   required from â_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const poly_event*; _OI = poly_event*]â
>/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/stl_algobase.h:441:30:   required from â_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const poly_event*, std::vector<poly_event, std::allocator<poly_event> > >; _OI = __gnu_cxx::__normal_iterator<poly_event*, std::vector<poly_event, std::allocator<poly_event> > >]â
>/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/stl_algobase.h:474:7:   required from â_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const poly_event*, std::vector<poly_event, std::allocator<poly_event> > >; _OI = __gnu_cxx::__normal_iterator<poly_event*, std::vector<poly_event, std::allocator<poly_event> > >]â
>/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/vector.tcc:238:31:   required from âstd::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = poly_event; _Alloc = std::allocator<poly_event>]â
>./Vec.h:64:26:   required from here
>polymorphism/VAAL0_5.cc:37:7: warning: implicitly-declared âBaseVec& BaseVec::operator=(const BaseVec&)â is deprecated [-Wdeprecated-copy]
>   37 | class poly_event {
>      |       ^~~~~~~~~~
>In file included from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>./feudal/BaseVec.h:123:5: note: because âBaseVecâ has user-provided âBaseVec::BaseVec(const BaseVec&)â
>  123 |     BaseVec(BaseVec const& bv) :
>      |     ^~~~~~~
>In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/algorithm:61,
>                 from ./Compare.h:18,
>                 from ./feudal/FieldVec.h:20,
>                 from ./feudal/BaseVec.h:13,
>                 from ./Basevector.h:12,
>                 from ./Alignment.h:30,
>                 from polymorphism/VAAL0_5.cc:26:
>/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/stl_algobase.h:342:18: note: synthesized method âpoly_event& poly_event::operator=(const poly_event&)â first required here
>  342 |        *__result = *__first;
>      |        ~~~~~~~~~~^~~~~~~~~~
>make[2]: *** [Makefile:2927: VAAL0_5.o] Error 1
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233/src'
>make[1]: *** [Makefile:830: all] Error 2
>make[1]: Leaving directory '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233/src'
>make: *** [Makefile:389: all-recursive] Error 1
> * ERROR: sci-biology/vaal-46233-r2::gentoo failed (compile phase):
> *   emake failed
> * 
> * If you need support, post the output of `emerge --info '=sci-biology/vaal-46233-r2::gentoo'`,
> * the complete build log and the output of `emerge -pqv '=sci-biology/vaal-46233-r2::gentoo'`.
> * The complete build log is located at '/var/log/portage/sci-biology:vaal-46233-r2:20190514-185706.log'.
> * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/vaal-46233-r2/temp/build.log'.
> * The ebuild environment file is located at '/var/tmp/portage/sci-biology/vaal-46233-r2/temp/environment'.
> * Working directory: '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233'
> * S: '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233'

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