Your message dated Mon, 06 May 2024 03:04:39 +0000
with message-id <[email protected]>
and subject line Bug#1053411: fixed in sra-sdk 3.0.3+dfsg-7
has caused the Debian Bug report #1053411,
regarding sra-sdk: FTBFS with re2 >= 20230601 (which requires abseil)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1053411: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1053411
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
sra-sdk_3.0.3+dfsg-6_amd64.build.xz
Description: application/xz
--- End Message ---
--- Begin Message ---
Source: sra-sdk
Source-Version: 3.0.3+dfsg-7
Done: Aaron M. Ucko <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sra-sdk, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <[email protected]> (supplier of updated sra-sdk package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 05 May 2024 22:15:17 -0400
Source: sra-sdk
Architecture: source
Version: 3.0.3+dfsg-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Closes: 1053411
Changes:
sra-sdk (3.0.3+dfsg-7) unstable; urgency=medium
.
* debian/control: Build depend on libabsl-dev so binaries using libre2
(sharq and relevant tests) can unconditionally link against
-labsl_string_view for simplicitly.
* debian/patches/support_libre2-11.patch (new): Prepare for (but don't
require!) newer libre2 versions where re2::StringPiece has changed
from a custom class to a typedef for absl::string_view, whose API is
somewhat different. (Closes: #1053411.)
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Files:
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