[Debian-med-packaging] Bug#1053411: sra-sdk: FTBFS with re2 >= 20230601 (which requires abseil)

[Stefano Rivera]

Source: sra-sdk
Version: 3.0.3+dfsg-6
Severity: normal
Tags: upstream
Control: affects -1 + src:re2

The next RE2 transition is waiting for sra-sdk to support libre2-11
(re2 >= 20230601), available in experimental.

Upstream, RE2 added a dependency on Abseil, changing its API a little.

It looks like only sharq in sra-tools requires re2, and it currently
expects 2021-09-01:
https://github.com/ncbi/sra-tools/blob/6d1e74850ad399f671da13e8aee39bcef926e551/tools/loaders/sharq/CMakeLists.txt#L89

[ 78%] Linking CXX static library ../../../lib/libncbi-ngs-c++.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -P CMakeFiles/ncbi
-ngs-c++.dir/cmake_clean_target.cmake
In file included from /<<PKGBUILDDIR>>/test/loaders/sharq/test-regexpr.cpp:30:
/<<PKGBUILDDIR>>/test/loaders/sharq/../../../tools/loaders/sharq/regexpr.hpp: In member functi
on ‘bool CRegExprMatcher::Matches(const std::string_view&)’:
/<<PKGBUILDDIR>>/test/loaders/sharq/../../../tools/loaders/sharq/regexpr.hpp:56:40: error: cannot convert ‘const std::string_view’ {aka ‘const std::basic_string_view<char>’} to ‘absl::debian3::string_view’
   56 |         return re2::RE2::PartialMatchN(input, *re, args.empty() ? nullptr : &args[0], (int)args.size());
      |                                        ^~~~~
      |                                        |
      |                                        const std::string_view {aka const std::basic_string_view<char>}
In file included from /<<PKGBUILDDIR>>/test/loaders/sharq/../../../tools/loaders/sharq/regexpr.hpp:13:
/usr/include/re2/re2.h:343:47: note:   initializing argument 1 of ‘static bool re2::RE2::PartialMatchN(absl::debian3::string_view, const re2::RE2&, const Arg* const*, int)’
  343 |   static bool PartialMatchN(absl::string_view text, const RE2& re,
      |                             ~~~~~~~~~~~~~~~~~~^~~~

Stefano
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