Your message dated Tue, 12 Dec 2023 19:00:13 +0000
with message-id <[email protected]>
and subject line Bug#1010358: fixed in ugene 49.1+dfsg-1
has caused the Debian Bug report #1010358,
regarding ugene: Fix for non-constant SIGSTKSZ
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
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--
1010358: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1010358
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: ugene
Severity: normal
Tags: patch
User: [email protected]
Usertags: origin-ubuntu kinetic ubuntu-patch
Dear Maintainer,
ugene 40.1+dfsg-1 fails to build on Ubuntu.
* Fix for non-constant SIGSTKSZ (LP: #1970417)
* Build on amd64 only.
Thanks for considering the patch.
-- System Information:
Debian Release: bookworm/sid
APT prefers jammy-updates
APT policy: (500, 'jammy-updates'), (500, 'jammy-security'), (500, 'jammy')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.15.0-27-generic (SMP w/32 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
diff -Nru ugene-40.1+dfsg/debian/control ugene-40.1+dfsg/debian/control
--- ugene-40.1+dfsg/debian/control 2021-10-19 12:55:46.000000000 +0200
+++ ugene-40.1+dfsg/debian/control 2022-04-26 14:25:30.000000000 +0200
@@ -1,9 +1,9 @@
Source: ugene
-Maintainer: Debian Med Packaging Team
<[email protected]>
+Maintainer: Maintainer: Debian Med Packaging Team
<[email protected]>
Uploaders: Steffen Moeller <[email protected]>,
Andreas Tille <[email protected]>,
Olivier Sallou <[email protected]>
-Section: non-free/science
+Section: multiverse/science
XS-Autobuild: yes
Priority: optional
Build-Depends: qtbase5-dev,
@@ -30,7 +30,7 @@
Rules-Requires-Root: no
Package: ugene
-Architecture: any
+Architecture: amd64
Depends: ${shlibs:Depends},
ugene-data,
${misc:Depends}
diff -Nru ugene-40.1+dfsg/debian/patches/Fix-for-non-constant-SIGSTKSZ.patch
ugene-40.1+dfsg/debian/patches/Fix-for-non-constant-SIGSTKSZ.patch
--- ugene-40.1+dfsg/debian/patches/Fix-for-non-constant-SIGSTKSZ.patch
1970-01-01 01:00:00.000000000 +0100
+++ ugene-40.1+dfsg/debian/patches/Fix-for-non-constant-SIGSTKSZ.patch
2022-04-26 14:24:36.000000000 +0200
@@ -0,0 +1,32 @@
+From: David Faure <[email protected]>
+Date: Wed, 15 Dec 2021 22:26:40 +0100
+Subject: [PATCH] Fix for non-constant SIGSTKSZ
+
+On glibc > 2.33, `SIGSTKSZ` might not be constant (in which case
+it expands to a call to `sysconf` which returns a `long int`); see
+https://sourceware.org/pipermail/libc-alpha/2020-October/118513.html
+
+Pass unsigned explicitly to std::max, to avoid relying on template
+argument deduction. This works both with the old-style constant
+`SIGSTKSZ` and the new configurable one.
+
+Initially based on https://chromium-review.googlesource.com/c/2776379
+
+Change-Id: I9fc95337f973e871b84735ce822b5e11ba73ea8c
+Reviewed-on:
https://chromium-review.googlesource.com/c/breakpad/breakpad/+/3340721
+Reviewed-by: Mark Mentovai <[email protected]>
+---
+ src/client/linux/handler/exception_handler.cc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+--- a/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc
++++ b/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc
+@@ -141,7 +141,7 @@
+ // SIGSTKSZ may be too small to prevent the signal handlers from overrunning
+ // the alternative stack. Ensure that the size of the alternative stack is
+ // large enough.
+- static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ);
++ const unsigned kSigStackSize = std::max<unsigned>(16384, SIGSTKSZ);
+
+ // Only set an alternative stack if there isn't already one, or if the
current
+ // one is too small.
diff -Nru ugene-40.1+dfsg/debian/patches/series
ugene-40.1+dfsg/debian/patches/series
--- ugene-40.1+dfsg/debian/patches/series 2021-10-19 12:55:46.000000000
+0200
+++ ugene-40.1+dfsg/debian/patches/series 2022-04-26 14:25:30.000000000
+0200
@@ -3,3 +3,4 @@
do_not_build_phylip.patch
# only partly addressed by upstream
use_debian_sqlite.patch
+Fix-for-non-constant-SIGSTKSZ.patch
--- End Message ---
--- Begin Message ---
Source: ugene
Source-Version: 49.1+dfsg-1
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ugene, 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.
Pierre Gruet <[email protected]> (supplier of updated ugene 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: Tue, 12 Dec 2023 14:49:53 +0100
Source: ugene
Binary: ugene ugene-data ugene-dbgsym
Architecture: source all amd64
Version: 49.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Description:
ugene - integrated bioinformatics toolkit
ugene-data - required data for UGENE - integrated bioinformatics toolkit
Closes: 1010358 1018252 1032688
Changes:
ugene (49.1+dfsg-1) unstable; urgency=medium
.
* Team upload
* New upstream version 49.1+dfsg
* Refreshing patches
* Shipping to main instead of non-free (Closes: #1018252):
- Excluding files with non-free license (*.so and psipred)
- Rewriting d/copyright
* Updating install paths
* Setting the runpaths so that private shared libraries can be found
* Fixing spelling mistakes
* Using python3 instead of python in shebangs
* Fixing Lintian override syntax
* Overriding Lintian warnings about spelling errors due to false positives
.
[ Andreas Tille ]
* Fix watch file
* Standards-Version: 4.6.2 (routine-update)
* Build-Depends: s/libprocps-dev/libproc2-dev/ (Closes: #1032688)
.
[ Michael R. Crusoe ]
* debian/patches/Fix-for-non-constant-SIGSTKSZ.patch: from Ubuntu,
Closes: #1010358
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