Your message dated Mon, 06 May 2024 03:05:12 +0000
with message-id <[email protected]>
and subject line Bug#1053411: fixed in sra-sdk 3.0.9+dfsg-3
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
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: 3.0.9+dfsg-3
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 22:45:27 -0400
Source: sra-sdk
Architecture: source
Version: 3.0.9+dfsg-3
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Closes: 1053411
Changes:
sra-sdk (3.0.9+dfsg-3) experimental; 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.)
Checksums-Sha1:
def52049a16c20c6412cd27206138a04d2e239ec 3001 sra-sdk_3.0.9+dfsg-3.dsc
17ab684c176f54008d31904806d636324a8d19dc 3791512
sra-sdk_3.0.9+dfsg-3.debian.tar.xz
Checksums-Sha256:
af7a8a1daa38ee1b60086e112252654841d3674f9d0505caff4043551534500d 3001
sra-sdk_3.0.9+dfsg-3.dsc
f8e21a36ee630e7a16210509d8a7fd6b0da126a3a88ab8e19e9b8e3542380ae7 3791512
sra-sdk_3.0.9+dfsg-3.debian.tar.xz
Files:
d6469ab30dfe99b00f42c777940c3553 3001 science optional sra-sdk_3.0.9+dfsg-3.dsc
d088594605289fc209b445000a2ab324 3791512 science optional
sra-sdk_3.0.9+dfsg-3.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmY4RikACgkQHnCRsfFK
ZKICPQ//TsQBVaXDrrlEFzp3hupAxicmISXJFXgnpg3wWXxqblFByvrH08fMdZUV
hV4DQnXNKhgBjMWQFFu4EGgIxGg0dnaFeKU44nCrxj3CnUO8JfWnb/hpIxqwrS7e
C9fQkE0juilnQetO0I0sg2nhyuhowZmZAF34QW69Grbj3wf7mDax8rRXTIIVz4vq
JEmaZY6dCMu60ZQ+aZCbgq0ZxIg0OJJbDeEx4D7VKyw50LVO5l0XQCux+OHoR5fN
e+j/mvN1aBS0i1llbGko4vn7fnxGKfECJbUKPwOqt26bVEt+hlh1i50HGdgThd0O
VcvZCKt3K1e+xl1Rr5uJ7dLFAcFVBfhK7annct7PBfB1yskRfhBWnpcrhyoUMluQ
SV9nV6sAteUd+05ydi/X875z1vnYSGGcl4igBRmDXiK6UxxeHyUv0JWbvNrRe3BT
F1WjXrmgEq5TDC4vxoANv4v3bJnnAY53V1X3WggIOyELJ/HvB46JjGdfstdoLwa3
GWDRb/pBr8v5nocf8BHo7HAng/IBqvDNDFpMdpXR97krw/dgD6Ci7mlvBgO0NNn+
VWrtiRF16Li9fuurExh9qFazQwYLrfsfz48v8GEuMzq5bX42qZQom7MbNjUz1C8V
rXMiXSWOGBj92TxB6aU25Tqo74/Q+yFSL54kcXuZ3eMMo+Yr35Y=
=ysO1
-----END PGP SIGNATURE-----
pgpJCA1E1lrnP.pgp
Description: PGP signature
--- End Message ---
