sci-biology:uchime-4.2.40:20210428-064758.log

sci-biology:uchime-4.2.40:20210428-064758.log (text/plain), 17.96 KB, created by Toralf Förster on 2021-04-28 07:16:31 UTC

 * Package:    sci-biology/uchime-4.2.40
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox

>>> Unpacking source...
>>> Unpacking uchime4.2.40_src.tar.gz to /var/tmp/portage/sci-biology/uchime-4.2.40/work
>>> Source unpacked in /var/tmp/portage/sci-biology/uchime-4.2.40/work
>>> Preparing source in /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src ...
 * Working in BUILD_DIR: "/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime-4.2.40_build"
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src ...
 * Working in BUILD_DIR: "/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime-4.2.40_build"
cmake -C /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime-4.2.40_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime-4.2.40_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src
loading initial cache file /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime-4.2.40_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 11.1.0
-- The CXX compiler identification is GNU 11.1.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -pipe -march=native -fno-diagnostics-color  -O2
C++             -pipe -march=native -fno-diagnostics-color  -O2 -D_FILE_OFFSET_BITS=64 -DUCHIMES=1
Linker flags:
Executable      -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Module          -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Shared          -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime-4.2.40_build
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src ...
 * Working in BUILD_DIR: "/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime-4.2.40_build"
ninja -v -j1 -l0
[1/23] /usr/bin/x86_64-pc-linux-gnu-g++    -pipe -march=native -fno-diagnostics-color  -O2 -D_FILE_OFFSET_BITS=64 -DUCHIMES=1 -MD -MT CMakeFiles/uchime.dir/addtargets2.cpp.o -MF CMakeFiles/uchime.dir/addtargets2.cpp.o.d -o CMakeFiles/uchime.dir/addtargets2.cpp.o -c /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp
FAILED: CMakeFiles/uchime.dir/addtargets2.cpp.o 
/usr/bin/x86_64-pc-linux-gnu-g++    -pipe -march=native -fno-diagnostics-color  -O2 -D_FILE_OFFSET_BITS=64 -DUCHIMES=1 -MD -MT CMakeFiles/uchime.dir/addtargets2.cpp.o -MF CMakeFiles/uchime.dir/addtargets2.cpp.o.d -o CMakeFiles/uchime.dir/addtargets2.cpp.o -c /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:176:1: error: reference to ‘byte’ is ambiguous
  176 | byte *ReadAllStdioFile(FILE *f, off_t &FileSize);
      | ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:61,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/char_traits.h:39,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/string:40,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:8,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/cpp_type_traits.h:404:30: note: candidates are: ‘enum class std::byte’
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:42:23: note:                 ‘typedef unsigned char byte’
   42 | typedef unsigned char byte;
      |                       ^~~~
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:177:1: error: reference to ‘byte’ is ambiguous
  177 | byte *ReadAllStdioFile(const string &FileName, off_t &FileSize);
      | ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:61,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/char_traits.h:39,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/string:40,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:8,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/cpp_type_traits.h:404:30: note: candidates are: ‘enum class std::byte’
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:42:23: note:                 ‘typedef unsigned char byte’
   42 | typedef unsigned char byte;
      |                       ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/chime.h:4,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:4:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/seq.h:9:15: error: reference to ‘byte’ is ambiguous
    9 |         const byte *Seq;
      |               ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:61,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/char_traits.h:39,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/string:40,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:8,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/cpp_type_traits.h:404:30: note: candidates are: ‘enum class std::byte’
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:42:23: note:                 ‘typedef unsigned char byte’
   42 | typedef unsigned char byte;
      |                       ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/chime.h:4,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:4:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/seq.h: In member function ‘void SeqData::Clear()’:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/seq.h:29:17: error: ‘Seq’ was not declared in this scope; did you mean ‘feq’?
   29 |                 Seq = 0;
      |                 ^~~
      |                 feq
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/ultra.h:4,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:5:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/seqdb.h: At global scope:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/seqdb.h:20:9: error: reference to ‘byte’ is ambiguous
   20 |         byte **m_Seqs;
      |         ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:61,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/char_traits.h:39,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/string:40,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:8,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/cpp_type_traits.h:404:30: note: candidates are: ‘enum class std::byte’
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:42:23: note:                 ‘typedef unsigned char byte’
   42 | typedef unsigned char byte;
      |                       ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/ultra.h:4,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:5:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/seqdb.h:35:50: error: reference to ‘byte’ is ambiguous
   35 |         unsigned AddSeq(const char *Label, const byte *Seq, unsigned L);
      |                                                  ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:61,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/char_traits.h:39,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/string:40,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:8,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/cpp_type_traits.h:404:30: note: candidates are: ‘enum class std::byte’
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:42:23: note:                 ‘typedef unsigned char byte’
   42 | typedef unsigned char byte;
      |                       ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/ultra.h:4,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:5:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/seqdb.h:37:9: error: reference to ‘byte’ is ambiguous
   37 |         byte *GetSeq(unsigned SeqIndex) const
      |         ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:61,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/char_traits.h:39,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/string:40,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:8,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/cpp_type_traits.h:404:30: note: candidates are: ‘enum class std::byte’
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:42:23: note:                 ‘typedef unsigned char byte’
   42 | typedef unsigned char byte;
      |                       ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/ultra.h:4,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:5:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/seqdb.h:106:12: error: ‘bool isgap’ redeclared as different kind of entity
  106 | bool isgap(byte c);
      |            ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:4:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/chime.h:93:20: note: previous declaration ‘bool isgap(char)’
   93 | static bool inline isgap(char c)
      |                    ^~~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/ultra.h:4,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:5:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/seqdb.h:106:12: error: reference to ‘byte’ is ambiguous
  106 | bool isgap(byte c);
      |            ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:61,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/char_traits.h:39,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/string:40,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:8,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/cpp_type_traits.h:404:30: note: candidates are: ‘enum class std::byte’
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:42:23: note:                 ‘typedef unsigned char byte’
   42 | typedef unsigned char byte;
      |                       ^~~~
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:12:34: error: reference to ‘byte’ is ambiguous
   12 | double GetFractIdGivenPath(const byte *A, const byte *B, const char *Path);
      |                                  ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:61,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/char_traits.h:39,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/string:40,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:8,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/cpp_type_traits.h:404:30: note: candidates are: ‘enum class std::byte’
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:42:23: note:                 ‘typedef unsigned char byte’
   42 | typedef unsigned char byte;
      |                       ^~~~
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:12:49: error: reference to ‘byte’ is ambiguous
   12 | double GetFractIdGivenPath(const byte *A, const byte *B, const char *Path);
      |                                                 ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:61,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/char_traits.h:39,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/string:40,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:8,
                 from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/cpp_type_traits.h:404:30: note: candidates are: ‘enum class std::byte’
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from /var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/addtargets2.cpp:3:
/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src/myutils.h:42:23: note:                 ‘typedef unsigned char byte’
   42 | typedef unsigned char byte;
      |                       ^~~~
ninja: build stopped: subcommand failed.
 * ERROR: sci-biology/uchime-4.2.40::gentoo failed (compile phase):
 *   ninja -v -j1 -l0 failed
 * 
 * Call stack:
 *     ebuild.sh, line  125:  Called src_compile
 *   environment, line 2104:  Called cmake_src_compile
 *   environment, line  800:  Called cmake_build
 *   environment, line  769:  Called eninja
 *   environment, line 1221:  Called die
 * The specific snippet of code:
 *       "$@" || die "${nonfatal_args[@]}" "${*} failed"
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/uchime-4.2.40::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/uchime-4.2.40::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:uchime-4.2.40:20210428-064758.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/uchime-4.2.40/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/uchime-4.2.40/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime-4.2.40_build'
 * S: '/var/tmp/portage/sci-biology/uchime-4.2.40/work/uchime4.2.40_src'