* Package: sci-biology/uchime-4.2.40 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * 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'