[Debian-med-packaging] Bug#984243: Help: mothur: ftbfs with GCC-11

[Andreas Tille]

Control: tags -1 help

Hi,

I've solved one gcc-11 issue that was mentioned in this bug report but
now there are other gcc-11 issues that go beyond my C++ knowledge:

...
g++ -g -O2 -ffile-prefix-map=/build/mothur-1.46.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/      21\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/          datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/svm/svm.o source/svm/svm.cpp
cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd ..
make[3]: Entering directory '/build/mothur-1.46.1/source/uchime_src'
make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
make[3]: Leaving directory '/build/mothur-1.46.1/source/uchime_src'
make[3]: Entering directory '/build/mothur-1.46.1/source/uchime_src'
make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o addtargets2.o addtargets2.cpp
In file included from addtargets2.cpp:3:
myutils.h:176:1: error: reference to 'byte' is ambiguous
  176 | byte *ReadAllStdioFile(FILE *f, off_t &FileSize);
      | ^~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:61,
                 from /usr/include/c++/11/bits/char_traits.h:39,
                 from /usr/include/c++/11/string:40,
                 from myutils.h:8,
                 from addtargets2.cpp:3:
/usr/include/c++/11/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from addtargets2.cpp:3:
myutils.h:42:23: note:                 'typedef unsigned char byte'
   42 | typedef unsigned char byte;
      |                       ^~~~
myutils.h:177:1: error: reference to 'byte' is ambiguous
  177 | byte *ReadAllStdioFile(const string &FileName, off_t &FileSize);
      | ^~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:61,
                 from /usr/include/c++/11/bits/char_traits.h:39,
                 from /usr/include/c++/11/string:40,
                 from myutils.h:8,
                 from addtargets2.cpp:3:
/usr/include/c++/11/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte'
  404 |   enum class byte : unsigned char;
      |                              ^~~~
In file included from addtargets2.cpp:3:
myutils.h:42:23: note:                 'typedef unsigned char byte'
   42 | typedef unsigned char byte;
      |                       ^~~~


Any help is welcome

       Andreas.


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