Bug#1058474: marked as pending in gubbins
Control: tag -1 pending Hello, Bug #1058474 in gubbins reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/gubbins/-/commit/bdb552a94232f55cca6da60196b62a2fe4d439a2 d/t/control: autopkgtests do not depend on python3-numba anymore. Closes: #1058474 (this message was generated automatically) -- Greetings https://bugs.debian.org/1058474
Bug#1071339: marked as pending in qrisk2
Control: tag -1 pending Hello, Bug #1071339 in qrisk2 reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/qrisk2/-/commit/2738a7d26d1280f7de5bc96f8c44922d1e52fc0c glibc-2.38.patch: new: fix ftbfs with glibc 2.38. Closes: #1071339 (this message was generated automatically) -- Greetings https://bugs.debian.org/1071339
Bug#1051534: marked as pending in analizo
Control: tag -1 pending Hello, Bug #1051534 in analizo reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/perl-team/modules/packages/analizo/-/commit/35bf8045a4f5bd366a25d63cd1539f9edacb3cdf doxygen-1.9.8.patch: new: update test item. A discrepancy tolerated in initial test results went resolved in recent doxygen versions, so this patch updates the new expected test result. Closes: #1051534 (this message was generated automatically) -- Greetings https://bugs.debian.org/1051534
Bug#1051534: analizo: Test failure in t/features.t during build and autopkgtests
Control: tags -1 + confirmed patch pending upstream
Hi,
gregor herrmann, on 2023-09-09:
> # Failed test 'Then analizo must report that the project has
> total_abstract_classes = 1'
> # at t/features/metrics/abstract_classes.feature line 19.
> # in step at t/features/metrics/abstract_classes.feature line 19.
> # not ok
> # # Failed test at
> /build/analizo-1.25.4/t/features/step_definitions/analizo_steps.pl line 143.
> # # got: 2
> # # expected: 1
Looking at t/features/metrics/abstract_classes.feature, ther is
a curious discrepancy between the csharp and the other
languages in terms of expected number of abstract classes:
Scenario: "Animals" project
Given I am in t/samples/animals/
When I run "analizo metrics ."
Then analizo must report that the project has total_abstract_classes =
Examples:
| language | total_abstract_classes |
| cpp | 2 |
| java | 2 |
| csharp | 1 |
Looking at the sample code which is under test, there does seem
to be two abstract classes for csharp samples:
$ grep 'abstract class' t/samples/animals/csharp/*
t/samples/animals/csharp/Animal.cs:public abstract class Animal {
t/samples/animals/csharp/Mammal.cs:public abstract class Mammal :
Animal {
Looking upstream, I ran into the commit introducing the csharp
support[1], which suggest there was something off at the time of
the introduction of the test with Doxygen:
>> doxyparse doesn't identify all abstract C# classes, the Mammal abstract
>> class defined in animals sample (below) wasn't identified:
>>
>> // Mammal.cs:
>> public abstract class Mammal : Animal {
>> public virtual void close() {}
>> }
This suggests the issue has been resolved with the recent upload
of doxygen that is currently staging in unstable. Therefore, I
believe it should be safe to update the test item so analizo is
expected to capture 2 abstract classes in csharp as well as the
other languages. I am preparing an upload to resolve that.
[1]:
https://github.com/analizo/analizo/commit/6cdd646d723106bddc4f9f01cbbbf9370e347925
Have a nice day, :)
--
.''`. Étienne Mollier
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Bug#1069691: [Debian-med-packaging] Bug#1069691: libmaus2: FTBFS on arm64: what(): AutoArray failed to allocate 1398102 elements (11184816 bytes)
Control: tags -1 + confirmed upstream Control: forwarded -1 https://gitlab.com/german.tischler/libmaus2/-/issues/40 In the end, I could reproduce the test failures affecting libmaus2 on amdahl and informed upstream. We'll see how things go. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/3, please excuse my verbosity `-on air: Silent Memorial - Retrospective signature.asc Description: PGP signature
Bug#1069370: shasta: FTBFS: dpkg-shlibdeps: error: cannot continue due to the error above
Hi, With the error rewrapped to facilitate readability: > dpkg-shlibdeps: error: > cannot find library shasta.cpython-311-aarch64-linux-gnu.so > needed by debian/shasta/usr/bin/shasta > (ELF format: 'elf64-littleaarch64' > abi: 'ELF:64:l:arm64:0'; > RPATH: '/usr/lib/python3/dist-packages') The problem seems to stem from the shasta binary having its DT_RUNPATH set to /usr/lib/python3/dist-packages. This is prompting dpkg-shlibdeps to scan the cython shared object to derive from which package obtaining the library, and fail. Now to mitigate properly, it might be helpful to see whether other options than setting the RPATH are acceptable. Otherwise dpkg-shlibdeps may have to be instructed to ignore shasta, which in turn will lead to manual maintenance of library dependencies in the package. I see if I can get somewhere… In hope this helps, -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/3, please excuse my verbosity `-on air: Saga - Framed signature.asc Description: PGP signature
Bug#1070387: [Debian-med-packaging] Bug#1070387: gdcm: CVE-2024-25569 CVE-2024-22373 CVE-2024-22391
Control: found -1 3.0.21-1 Control: found -1 3.0.8-2 Control: fixed -1 3.0.24-1 Hi Moritz, Thanks for the tracking and the triaging of these issues! Moritz Mühlenhoff, on 2024-05-04: > Please adjust the affected versions in the BTS as needed. Done with the present email; an upload of 3.0.24-1 is on the way in unstable. I'm afraid I'm not sure how to test those vulnerabilities, but mitigations brought by Mathieu apply with no fuzz, or just a little, to gdcm in stable and oldstable (and possibly oldoldstable), so I'm inclined to assume they are affected. Hi Mathieu, don't hesitate to chime in if you have some insights on applying the mitigations on older versions. I'm still running extensive tests at the moment against (build) reverse dependencies, but there were no issues directly induced by the newer gdcm version so far. I'm considering liaising with Stable Release Managers to get gdcm fixed there too in upcoming point releases, if that helps. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: Alta Forma - Apocalyptus signature.asc Description: PGP signature
Bug#1070334: marked as pending in libnet-frame-device-perl
Control: tag -1 pending Hello, Bug #1070334 in libnet-frame-device-perl reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/perl-team/modules/packages/libnet-frame-device-perl/-/commit/b13569b50af94c9f812be0ba383eeb950557d914 loopback-test.patch: new: fix test failures. The test suite relies on the existence of network interfaces leading to Internet. However this may not be the case in Debian build environment. This changes slightly alter the test suite to allow running against loopback interfaces, which are expected to be always available. Closes: #1070334 (this message was generated automatically) -- Greetings https://bugs.debian.org/1070334
Bug#1070334: libnet-frame-device-perl needs network access during build
Control: tags -1 + patch
Étienne Mollier, on 2024-05-03:
> Has someone an idea of better approach?
Answering to myself, the test suite does not actually attempt to
access the Internet, but it does attempt to access the device on
the build machine that can route by default to 1.1.1.1. This is
not because it is a Cloudflare DNS, but merely because it is the
first usable ipv4 available at hand. Especially in chroot-mode
unshare, there are no device leading to Internet exposed, thus
no device able to route to 1.1.1.1 with the default object
instanciation routine.
It turns out that the class can be told to construct objects
that refer to the loopback interface by asking for routes to the
loopback network (127/8 in ipv4, ::1/64 in ipv6). I prepared a
patch in this direction and consider uploading soon.
Have a nice day, :)
--
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`-on air: Allman Brothers Band - Statesboro Blues
Description: fix build failure when no network interfaces are available.
On buildd systems using sbuild chroot mode unshare, the network interface
leading to Internet is not exposed. However the default construction method
for instanciating Net::Frame::Devices relies on the existence of a network
interface able to route to 1.1.1.1. This change adjusts the test suite items
failing when not such interfaces are available, by trying to refer to loopback
interfaces instead. Note this slightly changes the meaning of the
t/04-new-default.t, as it does not test the default behavior anymore, but it
tests the behavior with ipv6 targets instead.
.
This addresses a Debian infrastructure specific behavior, probably not much
worth forwarding upstream.
Author: Étienne Mollier
Bug-Debian: https://bugs.debian.org/1070334
Forwarded: not-needed
Last-Update: 2024-05-04
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- libnet-frame-device-perl.orig/t/05-new-target.t
+++ libnet-frame-device-perl/t/05-new-target.t
@@ -2,7 +2,7 @@
BEGIN { plan(tests => 1) }
use Net::Frame::Device;
-my $d = Net::Frame::Device->new(target => '2.2.2.2') or die("Device::new");
+my $d = Net::Frame::Device->new(target => '127.1.1.1') or die("Device::new");
print $d->cgDumper if $d->can('cgDumper');
ok(1);
--- libnet-frame-device-perl.orig/t/04-new-default.t
+++ libnet-frame-device-perl/t/04-new-default.t
@@ -2,7 +2,7 @@
BEGIN { plan(tests => 1) }
use Net::Frame::Device;
-my $d = Net::Frame::Device->new or die("Device::new");
+my $d = Net::Frame::Device->new(target6 => '::1') or die("Device::new");
print $d->cgDumper if $d->can('cgDumper');
ok(1);
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Bug#1070334: libnet-frame-device-perl needs network access during build
Control: tags -1 + confirmed
Jochen Sprickerhof, on 2024-05-03:
> libnet-frame-device-perl fails to build with no network connection:
>
> 1..1
> # Running under perl version 5.038002 for linux
> # Current time local: Sat Apr 27 12:53:04 2024
> # Current time GMT: Sat Apr 27 12:53:04 2024
> # Using Test.pm version 1.31
> ok 1 # skip Test::Pod 1.00 required for testing
> ok
> Net::Frame::Device: updateFromDefault: unable to get dnet
>
> This can be tested with the sbuild unshare backend.
Interesting, the test suite looks to expect to find non loopback
interfaces being configured, at least one I assume. If I run
the build in chroot-mode schroot, it captures details of the
network configuration of the interface:
$VAR1 = {
'subnet6' => 'fe80::/64',
'gatewayMac6' => undef,
'target6' => undef,
'gatewayIp6' => 'fe80::1234:56ff:fe78:9abc',
'ip6' => 'fe80::cba9:87ff:fe65:4321',
'mac' => 'cb:a9:87:65:43:21',
'gatewayMac' => '12:34:56:67:9a:bc',
'target' => undef,
'dev' => 'enp1s0',
'subnet' => '192.168.1.0/24',
'_dnet' => undef,
'gatewayIp' => '192.168.1.254',
'ip' => '192.168.1.1'
};
instead of the error below, which I also witnessed on my end in
chroot-mode unshare:
Net::Frame::Device: updateFromDefault: unable to get dnet
I don't really have any good suggestion apart from not running
the affected tests at build time:
t/04-new-default.t (Wstat: 25856 (exited 101) Tests: 0 Failed: 0)
Non-zero exit status: 101
Parse errors: Bad plan. You planned 1 tests but ran 0.
t/05-new-target.t (Wstat: 25856 (exited 101) Tests: 0 Failed: 0)
Non-zero exit status: 101
Parse errors: Bad plan. You planned 1 tests but ran 0.
Has someone an idea of better approach?
Have a nice day, :)
--
.''`. Étienne Mollier
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Bug#1069756: readability: build time test error: lxml.html.clean module is now a separate project lxml_html_clean
Hi Colin, Colin Watson, on 2024-04-26: > Based on https://github.com/buriy/python-readability/issues/179, it > looks as though upstream intends to switch to bleach; I think we can > just patch setup.py in Debian in the meantime though. I'll do that. Looks good to me, thanks for tackling this! Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/3, please excuse my verbosity `-on air: Saga - Give 'Em The Money signature.asc Description: PGP signature
Bug#1069691: [Debian-med-packaging] Bug#1069691: libmaus2: FTBFS on arm64: what(): AutoArray failed to allocate 1398102 elements (11184816 bytes)
Control: found -1 2.0.813+ds-3 Hmn, this is annoying. I do not manage to reproduce the error with qemu-user. The test error is reproducible on buildd's real hardware in the meantime[1], or at least on two of the Arm build machines hosted by Conova. There could be something hardware specific. I'd have to check how things go on porterbox next. [1]: https://buildd.debian.org/status/fetch.php?pkg=libmaus2=arm64=2.0.813%2Bds-3=1713977128=0 Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/0, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1069756: readability: build time test error: lxml.html.clean module is now a separate project lxml_html_clean
Source: readability Version: 0.8.1+dfsg1-3 Severity: serious Tags: ftbfs Justification: ftbfs Dear Maintainer, Attempt to run readability tests at build time results in the following error: == ERROR: readability (unittest.loader._FailedTest.readability) -- ImportError: Failed to import test module: readability Traceback (most recent call last): File "/usr/lib/python3.11/unittest/loader.py", line 452, in _find_test_path package = self._get_module_from_name(name) File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/<>/.pybuild/cpython3_3.11/build/readability/__init__.py", line 3, in from .readability import Document File "/<>/.pybuild/cpython3_3.11/build/readability/readability.py", line 11, in from .cleaners import clean_attributes File "/<>/.pybuild/cpython3_3.11/build/readability/cleaners.py", line 3, in from lxml.html.clean import Cleaner File "/usr/lib/python3/dist-packages/lxml/html/clean.py", line 18, in raise ImportError( ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. As far as I could witness, replacing the python3-lxml build dependency by python3-lxml-html-clean resolved the issue at least for the bulid time test. The package is subject to autodep8 python3 test, which raises that the binary package will also need it dependencies adjusted; this suggests the setup.py would probably need patching so this is addressed appropriately at a larger scale than Debian's. The missing dependency on python3-lxml-html-clean is also causing a regression in offpunk autopkgtest[1], although that could be easily worked around by pulling the missing dependency there. [1]: https://ci.debian.net/packages/o/offpunk/unstable/amd64/44684161/ Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/4, please excuse my verbosity `-on air: Mike Oldfield - Lion signature.asc Description: PGP signature
Bug#1066369: marked as pending in obitools
Control: tag -1 pending Hello, Bug #1066369 in obitools reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/obitools/-/commit/fb6053e4a8742128194a416438fa695959b2e0ff qsort.patch: new: replace heapsort by qsort. Closes: #1066369 (this message was generated automatically) -- Greetings https://bugs.debian.org/1066369
Bug#1066369: obitools: FTBFS: error: implicit declaration of function ‘heapsort’
Hi, Lucas Nussbaum, on 2024-03-13: > > build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:6320:3: > > error: implicit declaration of function ‘heapsort’ > > [-Werror=implicit-function-declaration] Interesting, if I trust the Debian online manual of heapsort[1], this is a Berkeley function optimized for "almost" sorted arrays. I see two options here: either try to implement the libbsd compatibility layer in cython context, or replace heapsort by qsort[2] (and remove the heapsort function declaration from the .pyx); the two functions look to have compatible argument passing. I would consider implementing the replacement by qsort: this may affect the memory consumption, and possibly performances of obitools; on the other hand I wonder how come the program managed to do the sorting without appropriate function available in the application binary interface in the first place. [1]: https://manpages.debian.org/bookworm/libbsd-dev/heapsort.3bsd.en.html [2]: https://manpages.debian.org/bookworm/manpages-fr-dev/qsort.3.fr.html Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `-on air: Genesis - Throwing it All Away signature.asc Description: PGP signature
Bug#1066377: argtable2: FTBFS: arg_int.c:60:12: error: implicit declaration of functions
Control: tag -1 + patch Hi Shachar, I wrapped up a patch to resolve #1066377, the recently caught build failure affecting argtable2. You will find the diff in attachment. Hope this helps, -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `- Description: fix multiple implicit function declarations. Author: Étienne Mollier Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066377 Forwarded: no Last-Update: 2024-03-25 --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ --- argtable2-13.orig/src/arg_int.c +++ argtable2-13/src/arg_int.c @@ -29,6 +29,7 @@ /* #endif */ #include "argtable2.h" +#include #include /* local error codes */ --- argtable2-13.orig/tests/fntests.c +++ argtable2-13/tests/fntests.c @@ -1,5 +1,6 @@ #include "../src/argtable2.h" #include +#include /* for memory leak debugging */ #ifdef DMALLOC --- argtable2-13.orig/tests/test_file.c +++ argtable2-13/tests/test_file.c @@ -21,6 +21,7 @@ #include "../src/argtable2.h" #include +#include /* for memory leak debugging */ #ifdef DMALLOC signature.asc Description: PGP signature
Bug#1066663: marked as pending in dazzdb
Control: tag -1 pending Hello, Bug #103 in dazzdb reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/dazzdb/-/commit/6fe639ca615c146de96937acc2c5122addd74a15 fix-declaration.patch: new: fix build failure. The patch appends the missing declarations for vasprintf(3). Closes: #103 (this message was generated automatically) -- Greetings https://bugs.debian.org/103
Bug#1066485: [Debian-med-packaging] Bug#1066485: volpack: diff for NMU version 1.0b3-9.1
Hi Andrey, Andrey Rakhmatullin, on 2024-03-17: > I've prepared an NMU for volpack (versioned as 1.0b3-9.1) and > uploaded it to DELAYED/4. Please feel free to tell me if I > should delay it longer. Thank you for helping out with tackling these bugs, I reviewed through your changes, with which I agree, and inlined them in the VCS, so they will be preserved on further uploads. Please feel even free to reduce the delay to 0, if you like. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/4, please excuse my verbosity `-on air: Jean-Luc Ponty - Upon The Wings Of Music signature.asc Description: PGP signature
Bug#1066485: marked as pending in volpack
Control: tag -1 pending Hello, Bug #1066485 in volpack reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/volpack/-/commit/d85b54d6fb0c06207759da3510e70c218b8c7fa8 Fix FTBFS with -Werror=implicit-function-declaration Closes: #1066485 Signed-off-by: Étienne Mollier (this message was generated automatically) -- Greetings https://bugs.debian.org/1066485
Bug#1066326: marked as pending in codonw
Control: tag -1 pending Hello, Bug #1066326 in codonw reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/codonw/-/commit/5fbba98d10658ec9d77cff7bb0743b1e38d5d3c6 remove-gets.patch: new: replace gets by fgets. Closes: #1066326 (this message was generated automatically) -- Greetings https://bugs.debian.org/1066326
Bug#1067035: apache2-bin: rebuild for the 64-bit time_t migration is uninstallable
Hi Simon, Simon McVittie, on 2024-03-17: > I believe the attached patches should fix this (untested). After fixing > this in apr-util, apache2 will need a binNMU (or a re-upload). Thanks for your patches, I confirm they resolve the dependency issue after a rebuild of apache2. libaprutil164 without 't' is no more present in the dependencies. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1067035: apache2-bin: rebuild for the 64-bit time_t migration is uninstallable
Package: apache2-bin Version: 2.4.58-1+b2 Severity: serious Justification: uninstallable Dear Maintainer, Attempting to upgrade apache2-bin from rebuild 2.4.58-1+b1 to the rebuild 2.4.58-1+b2 leads to the following error: $ sudo apt upgrade apache2-bin Reading package lists... Done Building dependency tree... Done Reading state information... Done Calculating upgrade... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: apache2-bin : Depends: libaprutil164 (>= 1.2.7+dfsg) but it is not installable E: Broken packages libaprutil164 (note the missing 't' for "t64") is not available in unstable. The dependency looks typoed and duplicated, as libaprutil1t64 (>= 1.6.0) is also present as needed in the Depends field, Otherwise, have a nice Sunday, :) Étienne. -- Package-specific info: -- System Information: Debian Release: trixie/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.7.9-amd64 (SMP w/12 CPU threads; PREEMPT) Locale: LANG=C.UTF-8, LC_CTYPE=C.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 Versions of packages apache2-bin depends on: ii libapr1t64 [libapr1] 1.7.2-3.2 ii libaprutil1-dbd-sqlite3 1.6.3-1.1+b1 ii libaprutil1-ldap 1.6.3-1.1+b1 ii libaprutil1t64 [libaprutil1] 1.6.3-1.1+b1 ii libbrotli11.1.0-2+b3 ii libc6 2.37-15.1 ii libcrypt1 1:4.4.36-4 ii libcurl4t64 [libcurl4]8.6.0-4 ii libjansson4 2.14-2+b2 ii libldap-2.5-0 2.5.16+dfsg-2 ii liblua5.3-0 5.3.6-2+b2 ii libnghttp2-14 1.59.0-1+b1 ii libpcre2-8-0 10.42-4+b1 ii libssl3t64 [libssl3] 3.1.5-1.1 ii libxml2 2.9.14+dfsg-1.3+b2 ii perl 5.38.2-3.2 ii zlib1g1:1.3.dfsg-3.1 apache2-bin recommends no packages. Versions of packages apache2-bin suggests: pn apache2-doc pn apache2-suexec-pristine | apache2-suexec-custom ii firefox-esr [www-browser]115.8.0esr-1+b1 ii lynx [www-browser] 2.9.0rel.0-2+b1 ii surf [www-browser] 2.1+git20221016-6+b1 ii w3m [www-browser]0.5.3+git20230121-2+b3 Versions of packages apache2 depends on: ii apache2-data 2.4.58-1 ii apache2-utils2.4.58-1+b1 ii init-system-helpers 1.66 ii media-types 10.1.0 ii perl 5.38.2-3.2 ii procps 2:4.0.4-4 Versions of packages apache2 recommends: ii ssl-cert 1.1.2 Versions of packages apache2 suggests: pn apache2-doc pn apache2-suexec-pristine | apache2-suexec-custom ii firefox-esr [www-browser]115.8.0esr-1+b1 ii lynx [www-browser] 2.9.0rel.0-2+b1 ii surf [www-browser] 2.1+git20221016-6+b1 ii w3m [www-browser]0.5.3+git20230121-2+b3 Versions of packages apache2-bin is related to: ii apache2 2.4.58-1+b1 ii apache2-bin 2.4.58-1+b1 -- no debconf information -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/4, please excuse my verbosity `-on air: Antony Kalugin - Key signature.asc Description: PGP signature
Bug#1066595: marked as pending in phylip
Control: tag -1 pending Hello, Bug #1066595 in phylip reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/phylip/-/commit/2d8182d9e4cd2ec150e0238d77ba0629c06c37dc fix-declarations.patch: new: fix a build failure. Closes: #1066595 (this message was generated automatically) -- Greetings https://bugs.debian.org/1066595
Bug#1066559: marked as pending in dialign-t
Control: tag -1 pending Hello, Bug #1066559 in dialign-t reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/dialign-t/-/commit/642d951ce54b6c26ca2eba7054d7f214399c5457 fix-declarations.patch: new: fix build failures. Closes: #1066559 (this message was generated automatically) -- Greetings https://bugs.debian.org/1066559
Bug#1066659: marked as pending in dialign
Control: tag -1 pending Hello, Bug #1066659 in dialign reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/dialign/-/commit/f4c663c1457be3e103cdc94dff2196d60d9f3a22 fix-declarations.patch: new: fix build failure. Closes: #1066659 (this message was generated automatically) -- Greetings https://bugs.debian.org/1066659
Bug#1066478: marked as pending in readseq
Control: tag -1 pending Hello, Bug #1066478 in readseq reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/readseq/-/commit/2d13ad1bade77b6fdd4a55d229f8fc6cfc071255 fix-gets.patch: new: replace gets by fgets. Closes: #1066478 (this message was generated automatically) -- Greetings https://bugs.debian.org/1066478
Bug#1066363: marked as pending in seqprep
Control: tag -1 pending Hello, Bug #1066363 in seqprep reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/seqprep/-/commit/bd38f750ddab564da9f7371d96ac6930461c4b77 fix-declarations.patch: new: fix ftbfs. Closes: #1066363 (this message was generated automatically) -- Greetings https://bugs.debian.org/1066363
Bug#1066633: marked as pending in poa
Control: tag -1 pending Hello, Bug #1066633 in poa reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/poa/-/commit/321a813c57dcfaf6c8937bf5d4976da90af08c69 fix-declaration.patch: new: fix missing declarations. Closes: #1066633 (this message was generated automatically) -- Greetings https://bugs.debian.org/1066633
Bug#1066534: marked as pending in daligner
Control: tag -1 pending Hello, Bug #1066534 in daligner reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/daligner/-/commit/3043c218631b8dc8d36a05feddd54d3e6f5c9359 fix-missing-include.patch: new: fix ftbfs with dpkg. Closes: #1066534 (this message was generated automatically) -- Greetings https://bugs.debian.org/1066534
Bug#1065976: python-levenshtein: FTBFS on arm{el,hf}: Levenshtein/_levenshtein.c:749:15: error: implicit declaration of function ‘PyUnicode_AS_UNICODE’; did you mean ‘PyUnicode_AsUCS4’? [-Werror=impli
Hi, Sebastian Ramacher, on 2024-03-10: > Levenshtein/_levenshtein.c:749:15: error: implicit declaration of function > ‘PyUnicode_AS_UNICODE’; did you mean ‘PyUnicode_AsUCS4’? > [-Werror=implicit-function-declaration] > 749 | string1 = PyUnicode_AS_UNICODE(arg1); This looks to be a duplicate of an initial ftbfs issue I looked up this morning. Ultimately it would be fixed by the latest upstream version of python-levenshtein, but for this to be doable, rapidfuzz-cpp needs to make it to the archive first. Julian pushed rapidfuzz-cpp some time ago to the New queue, thanks! Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/4, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1064147: ftbfs: test failures affecting Bio.SeqIO.SeqXmlIO
Control: severity -1 normal I reduce the severity. The version 1.83+dfsg-1 recently uploaded skips the affected tests, due to lack of better options. I leave the issue open in case someone comes up with a more appropriate way to resolve this, but the situation is not serious anymore. -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `-on air: Fates Warning - From The Rooftops signature.asc Description: PGP signature
Bug#1064147: ftbfs: test failures affecting Bio.SeqIO.SeqXmlIO
So, following discutions with upstream, and quite some investigation, this turned out to be caused by the migration of expat from version 2.5 to 2.6. The newer version looks to have had to introduce breaking changes in order to be able to fix a security vulnerability. When looking into expat migration excuses[1], I noted that there were also test failures affecting Python's xml module[2]. Then, I had a lookup at open CPython issues, which suggest a change to address the build failure has landed[3] and will be ready for upcoming interpreter versions. That being said, looking closely at the patch, it seems the direction taken was to adjust the test suite to ignore the affected cases. There don't seem to have been any changes to the core logic of the xml module. This suggests it may be necessary to skip the affected tests, at least for now. Those are only two failures among dozens of tests, which suggest the SeqXmlIO is in otherwise mostly working conditions. [1]: https://qa.debian.org/excuses.php?package=expat [2]: https://ci.debian.net/packages/p/python3.12/testing/amd64/43764480/ [3]: https://github.com/python/cpython/pull/115289/files Now pondering a version that has a chance to migrate, -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: Genesis - Turn It on Again signature.asc Description: PGP signature
Bug#1063403: marked as pending in eegdev
Control: tag -1 pending Hello, Bug #1063403 in eegdev reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/eegdev/-/commit/847b8fa882207c8a6c2e442800b23c97628999fb d/rules: also update dh_installdocs call. This avoids shipping /usr/share/doc/libeegdev0/changelog* in the other binary packages of eegdev. Closes: #1063403 Signed-off-by: Étienne Mollier (this message was generated automatically) -- Greetings https://bugs.debian.org/1063403
Bug#1065765: marked as pending in libmems
Control: tag -1 pending Hello, Bug #1065765 in libmems reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/libmems/-/commit/e943912ae14a66d0c36754f607566b98078481af fix-system.patch: new: fix build failure on arm. Closes: #1065765 (this message was generated automatically) -- Greetings https://bugs.debian.org/1065765
Bug#1062403: marked as done (freecontact: NMU diff for 64-bit time_t transition)
From mwhud...@debian.org: > This has been uploaded now, but unfortunately I forgot to include the bug > number in the changelog. Apologies. No worries, I happen to trip on this carpet from time to time. NMU is acknowledged in the VCS, thanks for the work on the 64-bit time_t transition! Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1062757: [Debian-med-packaging] Bug#1062757: odil: NMU diff for 64-bit time_t transition
Benjamin Drung, on 2024-02-29: > Please find attached a final version of this patch for the time_t > transition. This patch is being uploaded to unstable. NMU acknowledged, thanks! :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1062525: [Debian-med-packaging] Bug#1062525: eegdev: NMU diff for 64-bit time_t transition
mwhud...@fastmail.fm, on 2024-02-28: > Please find attached a final version of this patch for the time_t > transition. This patch is being uploaded to unstable. Thanks Michael, your NMU is inlined in Salsa. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1062316: libgkarrays: NMU diff for 64-bit time_t transition
Benjamin Drung, on 2024-02-29: > On Wed, 28 Feb 2024 20:12:53 +0100 =?utf-8?Q?=C3=89tienne?= Mollier > wrote: > > Benjamin Drung, on 2024-02-28: > > > Please find attached a final version of this patch for the time_t > > > transition. This patch is being uploaded to unstable. > > > > NMU acknowledged, thank you! :) > > The upload was rejected, because the the version number 2.1.0+dfsg-4.1 > was used for the experimental upload. So I had to bump the version > number to 2.1.0+dfsg-4.2. Thanks for the notice, I updated the VCS tree accordingly. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1064147: ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO
Control: forwarded -1 https://github.com/biopython/biopython/issues/4640 Control: tags -1 + sid Control: tags -1 - testing I'm dry on even pinpointing what change is causing Biopython 1.81 to fail those tests, maybe upstream will have a better idea. If nothing, there remains the option to skip the affected tests and reduce the bug severity, but this is not ideal. We'll see how things go, -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1061208: Please upgrade to llvm-toolchain-17
Hi Christian, Christian Kastner, on 2024-02-26: > Hi Sebastian, > > writing to you as you bumped the severity to 'serious': could the rT > please give us an extension on the autoremoval for this particular bug. If that helps, the autoremoval timer is reset each time the RC critical bug triggering the autoremoval is updated, e.g. when reporting an evolution of the situation in a new comment. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1064147: ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO
Source: python-biopython Version: 1.81+dfsg-3 Severity: serious Tags: ftbfs Justification: ftbfs While trying to pinpoint the root cause of test failures in the packaging attempt of Biopython 1.83, I eventually realized that the version 1.81 of Biopython is also affected by the same issues. The relevant part of the test log looks like: == ERROR: test_embl7 (test_SeqIO.TestSeqIO.test_embl7) -- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 3388, in test_embl7 self.perform_test( File "/<>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 626, in perform_test self.check_simple_write_read( File "/<>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 363, in check_simple_write_read records2 = list(SeqIO.parse(handle=handle, format=fmt)) File "/<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py", line 72, in __next__ return next(self.records) ^^ File "/<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 447, in iterate parser.close() File "/usr/lib/python3.11/xml/sax/expatreader.py", line 240, in close self.feed(b"", isFinal=True) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed self._parser.Parse(data, isFinal) File "../Modules/pyexpat.c", line 416, in StartElement File "/usr/lib/python3.11/xml/sax/expatreader.py", line 369, in start_element_ns self._cont_handler.startElementNS(pair, None, File "/<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 163, in startEntryFieldElement return self.startPropertyElement(attrs) File "/<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 339, in startPropertyElement record = self.records[-1] IndexError: list index out of range == ERROR: test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) -- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 2785, in test_genbank8 self.perform_test( File "/<>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 626, in perform_test self.check_simple_write_read( File "/<>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 363, in check_simple_write_read records2 = list(SeqIO.parse(handle=handle, format=fmt)) File "/<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py", line 72, in __next__ return next(self.records) ^^ File "/<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 447, in iterate parser.close() File "/usr/lib/python3.11/xml/sax/expatreader.py", line 240, in close self.feed(b"", isFinal=True) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed self._parser.Parse(data, isFinal) File "../Modules/pyexpat.c", line 416, in StartElement File "/usr/lib/python3.11/xml/sax/expatreader.py", line 369, in start_element_ns self._cont_handler.startElementNS(pair, None, File "/<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 163, in startEntryFieldElement return self.startPropertyElement(attrs) File "/<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 339, in startPropertyElement record = self.records[-1] IndexError: list index out of range I haven't checked but I heavily suspect that this is causing also autopkgtest failures. For information, -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/0, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1044079: augur 24 still ftbfs against pandas 2.1.4
Control: reopen -1 I must have mistaken something about pandas versions when uploading augur 24.0.0, because the error is still there and is now causing ftbfs again with at least pandas 2.1.4. This is still the same error in the same test: self = capsys = <_pytest.capture.CaptureFixture object at 0x7fc3d81d59d0> def test_fix_dates(self, capsys): full_date = "4-5-2020" > assert parse.fix_dates(full_date) == "2020-05-04" tests/test_parse.py:14: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ d = '4-5-2020', dayfirst = True def fix_dates(d, dayfirst=True): ''' attempt to parse a date string using pandas date parser. If ambiguous, the argument 'dayfirst' determines whether month or day is assumed to be the first field. Incomplete dates will be padded with XX. On failure to parse the date, the function will return the input. ''' try: from pandas.core.tools.datetimes import parsing > results = parsing.parse_time_string(d, dayfirst=dayfirst) E AttributeError: module 'pandas._libs.tslibs.parsing' has no attribute 'parse_time_string' Too bad things looked promising, -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/3, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1062344: [Debian-med-packaging] Bug#1062344: htslib: NMU diff for 64-bit time_t transition
Hi Graham, Thanks for your (and the others) titan work on moving this transition forward. \o/ > diff -Nru htslib-1.18+ds/debian/changelog htslib-1.18+ds/debian/changelog > --- htslib-1.18+ds/debian/changelog 2023-11-07 18:46:30.0 + > +++ htslib-1.18+ds/debian/changelog 2024-02-01 05:58:50.0 + > @@ -1,3 +1,10 @@ > +htslib (1.18+ds-1.1) experimental; urgency=medium ^^^ There is an htslib 1.19 upload lingering in experimental, that I did some time ago to make sure I was not throwing entropy to too many reverse dependencies. I'm afraid it might have voided your NMU. Would it be more helpful to adjust the patch to the newer htslib version, or do you prefer the 1.19 to be reverted for now until the time_t 64-bit transition goes through? I may be able to upload myself if you're busy somewhere else, I'm just unsure of the way forward. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/5, please excuse my verbosity `-on air: Agusa - Under bar himmel signature.asc Description: PGP signature
Bug#1060965: q2-feature-classifier: FTBFS due to qiime AttributeError: module 'bibtexparser' has no attribute 'bparser'
Control: reassign -1 src:qiime 2022.11.1-2 Control: affects -1 + q2-feature-classifier Control: merge -1 1060987 This is another manifestation of #1060987, this time affecting q2-feature-classifier: > /usr/lib/python3/dist-packages/qiime2/core/cite.py:26: in load > parser = bp.bparser.BibTexParser() > E AttributeError: module 'bibtexparser' has no attribute 'bparser' Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1060987: q2cli: FTBFS: AttributeError: module 'bibtexparser' has no attribute 'bparser'
Control: reassign -1 src:qiime/2022.11.1-2 Control: retitle -1 qiime: FTBFS: AttributeError: module 'bibtexparser' has no attribute 'bparser' Control: affects -1 + q2cli This looks to be the main issue: > /usr/lib/python3/dist-packages/qiime2/core/cite.py:26: in load > parser = bp.bparser.BibTexParser() > E AttributeError: module 'bibtexparser' has no attribute 'bparser' Since update of bibtexparser to 2.0.0b, the bparser has been either removed or not reimplemented yet. The documentation exposed in the bibtexparser source code gives little clue how to migrate from that particular situation. Quick lookup at contemporary qiime source code[1] shows the invocation is still around as of today, so an upstream version bump won't help yet. Maybe an option could be to avoid attemting to apply the bibtex parser customization when the bparser does not exist anymore? I'm not entirely confident on the side effects downstream. Only other option I can think of would be to wait and see how the bibtexparser v2.0.0 release will behave if there are planned changes on the parser or unicode customizations front. [1]: https://github.com/qiime2/qiime2/blob/dev/qiime2/core/cite.py Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/3, please excuse my verbosity `-on air: Fish - Little Man What Now? signature.asc Description: PGP signature
Bug#1060973: python-pbcore: FTBFS
Control: tags -1 + unreproducible moreinfo Hi Lucas, I got information from Andreas Tille that the build failure is not reproducible in his environment. Actually I did give it a go myself, and the build went through for me as well. The build log is available on the people's server[1]. Actually, looking closely, I'm not sure why the build works in normal times: the build environment does not look to embed python3-pip packages in both cases, so in my case, pip may not be called in the first place. [1]: https://people.debian.org/~emollier/logs/python-pbcore/python-pbcore_amd64-2024-01-18T18:13:24Z.build.xz Thanks for your quality assessment work, this is very useful to catch issues! Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/4, please excuse my verbosity `-on air: Flying Colors - Peaceful Harbor (Live) signature.asc Description: PGP signature
Bug#1060205: castxml: BD-Uninstallable: castxml build-depends on missing: libclang-17-dev:mips64el
Hi Andreas, Andreas Tille, on 2024-01-09: > Am Sun, Jan 07, 2024 at 09:05:10PM +0100 schrieb Étienne Mollier: > > Thanks for the heads up, I'm afraid this is a bit out of hands > > right now. According to bug entries #1059465 and #1056116, > > llvm-toolchain-16 and -17 fail to build on mips64el at the > > moment. Also, the llvm-toolchain-15 is not planned to ship with > > trixie if I trust #1058812. > > Wouldn't it make sense to ask ftpmaster for removal of the binary > castxml:mips64el? It may be a bit early to tell: I saw llvm-toolchain-17 upload today, so maybe its maintainers are up to something. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: Spheric Universe Experience - Moonlight signature.asc Description: PGP signature
Bug#1060176: [Debian-med-packaging] Bug#1060176: dipy: FTBFS on ppc64el: FAILED dipy/segment/tests/test_mrf.py::test_icm_square - AssertionError
Control: tags -1 + fixed-upstream pending Good day, I am working on bumping dipy version to 1.8.0 for some time, and in the light of my ppc64el build attempt, the new upstream version did not fail to build from source. I'm hopeful that the upcoming upload is going to fix this for sure. That was a qemu build, and I'm not at risk of flaky test issue, but crossing fingers. Have a nice one, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: The Inner Road - Dark Door signature.asc Description: PGP signature
Bug#1060205: castxml: BD-Uninstallable: castxml build-depends on missing: libclang-17-dev:mips64el
Control: block -1 by #1056116 Hi Sebastian, > castxml build-depends on missing: > - libclang-17-dev:mips64el Thanks for the heads up, I'm afraid this is a bit out of hands right now. According to bug entries #1059465 and #1056116, llvm-toolchain-16 and -17 fail to build on mips64el at the moment. Also, the llvm-toolchain-15 is not planned to ship with trixie if I trust #1058812. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/0, please excuse my verbosity `-on air: Apple Pie - Letters Of A Deadman - Part III - … signature.asc Description: PGP signature
Bug#1059650: marked as pending in libsbml
Control: tag -1 pending Hello, Bug #1059650 in libsbml reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/libsbml/-/commit/c04371a65f0823ab8ad298c0d741f0e308faac8c d/control: X-Python3-Version: 3.11 (==) While this change is not ideal, because of the upcoming necessary upload to bring python3.12 support when it becomes the default, it is a short term fix to move the python3.12 migration forward. Closes: #1059650 (this message was generated automatically) -- Greetings https://bugs.debian.org/1059650
Bug#1056089: marked as pending in autodock-vina
Control: tag -1 pending Hello, Bug #1056089 in autodock-vina reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/autodock-vina/-/commit/9c5e791a0082163c3fcd96c2b4e7c282ecd66be5 boost1.83.patch: new: fix ftbfs with boost 1.83. Closes: #1056089 Thanks: jalegido (this message was generated automatically) -- Greetings https://bugs.debian.org/1056089
Bug#1058790: marked as pending in mayavi2
Control: tag -1 pending Hello, Bug #1058790 in mayavi2 reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/python-team/packages/mayavi2/-/commit/ecd9bc059dfb7bd0406e15f218917bebd3ff8e56 traitsui-8.patch: fix missing traitsui.qt4.editor. Closes: #1058790 (this message was generated automatically) -- Greetings https://bugs.debian.org/1058790
Bug#1058790: mayavi2: autopkgtest failure in pysurfer since python-traitsui 8
Source: mayavi2
Version: 4.8.1-1
Severity: serious
Justification: autopkgtest failure in reverse dependecy
Tags: patch upstream fixed-upstream
Affects: pysurfer
Forwarded: https://github.com/enthought/mayavi/pull/1255
Dear Maintainer,
Since introduction of python3-traitsui 8, pysurfer is failing
its autopkgtest suite with errors like[1]:
ERRORS
_ ERROR collecting tests/test_utils.py
_
ImportError while importing test module
'/tmp/autopkgtest.pQ5bOG/autopkgtest_tmp/tests/test_utils.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_utils.py:9: in
from surfer import utils
/usr/lib/python3/dist-packages/surfer/__init__.py:1: in
from .viz import Brain, TimeViewer # noqa
/usr/lib/python3/dist-packages/surfer/viz.py:17: in
from mayavi.core.ui.api import SceneEditor
/usr/lib/python3/dist-packages/mayavi/core/ui/api.py:4: in
from tvtk.pyface.scene_editor import SceneEditor
/usr/lib/python3/dist-packages/tvtk/pyface/scene_editor.py:12: in
SceneEditor = toolkit_object('scene_editor:SceneEditor')
/usr/lib/python3/dist-packages/pyface/base_toolkit.py:127: in __call__
module = import_module(mname, package)
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3/dist-packages/tvtk/pyface/ui/qt4/scene_editor.py:16:
in
from traitsui.qt4.editor import Editor
E ModuleNotFoundError: No module named 'traitsui.qt4.editor'
[1]: https://ci.debian.net/packages/p/pysurfer/unstable/amd64/39514398/
They look to stem from mayavi2 trying to make use of an old way
of loading the editor module, now called traitsui.qt.editor.
Upstream prepared the a patch[2] to upcoming versions of
mayavi2, but it is not there yet.
[2]: https://github.com/enthought/mayavi/pull/1255
I have verified the patch fixes the autopkgtest regression in
pysurfer, and did not raise any obvious issues in mayavi2. I'm
considering providing a team upload to resolve this particular
issue.
Have a nice day, :)
--
.''`. Étienne Mollier
: :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/7, please excuse my verbosity
`-on air: K2 - Storm at Sunset
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Bug#1058252: marked as pending in pynn
Control: tag -1 pending Hello, Bug #1058252 in pynn reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/pynn/-/commit/ea997cc5c80af982868d15c07a3076f76c1d2b6d python3.12.patch: new: fix test with python3.12. Closes: #1058252 (this message was generated automatically) -- Greetings https://bugs.debian.org/1058252
Bug#1058252: marked as pending in pynn
Control: tag -1 pending Hello, Bug #1058252 in pynn reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/pynn/-/commit/ea997cc5c80af982868d15c07a3076f76c1d2b6d python3.12.patch: new: fix test with python3.12. Closes: #1058252 (this message was generated automatically) -- Greetings https://bugs.debian.org/1058252
Bug#1058220: marked as pending in q2-sample-classifier
Control: tag -1 pending Hello, Bug #1058220 in q2-sample-classifier reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/446dfe546dd9004b38f4dd9fa9c6ad126240f666 python3.12.patch: new: port versioneer.py. Closes: #1058220 (this message was generated automatically) -- Greetings https://bugs.debian.org/1058220
Bug#1058334: marked as pending in python-ete3
Control: tag -1 pending Hello, Bug #1058334 in python-ete3 reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/python-ete3/-/commit/11f450737651b73905a5eed6ac1e36824e9a4cc9 python3.12.patch: new: fix test failures. Closes: #1058334 (this message was generated automatically) -- Greetings https://bugs.debian.org/1058334
Bug#1058394: augur: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13
Control: reassign -1 src:pyfastx 2.0.2-1 Control: affects -1 src:augur > > /usr/lib/python3.12/importlib/__init__.py:90: in import_module > > return _bootstrap._gcd_import(name[level:], package, level) > > tests/test_align.py:16: in > > from augur import align > > augur/__init__.py:15: in > > from .io.print import print_err > > augur/io/__init__.py:6: in > > from .metadata import read_metadata # noqa: F401 > > augur/io/metadata.py:5: in > > import pyfastx > > E ModuleNotFoundError: No module named 'pyfastx' These test failures stem from pyfastx lacking Python 3.12 due to missing cython shared objects rebuild for that python3 version. I'm checking whether other packages are affected. Have a nice day, :) -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/5, please excuse my verbosity `-on air: Arch/Matheos - Neurotically Wired signature.asc Description: PGP signature
Bug#1055669: marked as pending in bcftools
Control: tag -1 pending Hello, Bug #1055669 in bcftools reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/bcftools/-/commit/cc9b561acb4c6f577954b5534857f42674e7e361 fix-bus-error-armhf.patch: new: fix Bus errors. Thanks: Rob Davies Closes: #1055669 (this message was generated automatically) -- Greetings https://bugs.debian.org/1055669
Bug#1055414: marked as pending in bedtools
Control: tag -1 pending Hello, Bug #1055414 in bedtools reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/bedtools/-/commit/c246f48850287ee4309d2a0590096e8b56827524 d/rules: use sse for floating point calculations. This fixes bedtools "intersect" test failures during build time. This change is brought for consistency with htslib's own settings. While this is an architecture baseline violation, the alternative is no htslib support at all for the i386 distribution, since it fails its own test suite with anything else than sse for floating point calculations. Closes: #1055414 (this message was generated automatically) -- Greetings https://bugs.debian.org/1055414
Bug#1055414: patch for bedtools FTBFS on i386 with "intersect" tool failure
Control: tags -1 + patch The below patch fixes the test failure. There is a catch though in that I think it introduces a baseline violation on i386, but similar change was already needed in htslib to fix #942580. I'm not sure what to make of that for now. --- a/debian/rules +++ b/debian/rules @@ -6,7 +6,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all include /usr/share/dpkg/default.mk ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386)) - export DEB_CXXFLAGS_MAINT_APPEND=-ffloat-store + export DEB_CXXFLAGS_MAINT_APPEND=-msse -mfpmath=sse endif %: -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/5, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1055669: bcftools: test_vcf_merge failures on armhf: Bus error
Source: bcftools Version: 1.18-1 Severity: serious Tags: ftbfs Justification: ftbfs Control: forwarded -1 https://github.com/samtools/bcftools/issues/2036 Dear Maintainer, bcftools currently ftbfs on armhf due to multiple test_vcf_merge failures with Bus error[1]. I already informed upstream[2]. This bug is mostly to keep track of the issue on Debian side and eventually comment on possible Debian specific workarounds. For the context, there are 44 failure looking typically like: test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -0 /tmp/YVqRgiAYOP/merge.a.vcf.gz /tmp/YVqRgiAYOP/merge.b.vcf.gz /tmp/YVqRgiAYOP/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ Non-zero status 1 Failed to read from standard input: unknown file type .. failed ... [1]: https://buildd.debian.org/status/fetch.php?pkg=bcftools=armhf=1.18-1=1699434189=1 [2]: https://github.com/samtools/bcftools/issues/2036 For information, -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: Silent Voices - Humancradlegrave signature.asc Description: PGP signature
Bug#1055414: bedtools: FTBFS on i386: "intersect" tool failure
Source: bedtools Version: 2.31.0+dfsg-1 Severity: serious Tags: ftbfs Justification: ftbfs Dear Maintainer, While making a routine metadata update on a Debian patch against bedtools, Salsa CI caught a build failure on i386[1] which I could reproduce multiple times in sid and in testing with the unmodified version of the package. [1]: https://salsa.debian.org/med-team/bedtools/-/jobs/4891166 The relevant part of the build log shows the following differences in the test suite of the "intersect" tool: intersect.t22.p...0a1 > chr1 0 30 one_block_one_exon_30bp 40 - 0 30 0,0,0 1 30, 0, chr1 0 100 exon1 1 + 30 fail intersect.t22.q...1a2 > chr1 80 110 one_block_one_exon_20bp 40 - 80 110 0,0,0 1 30, 0, chr1 0 100 exon1 1 + 20 fail The tests are started from test/intersect/test-intersect.sh. I'm not sure what change caused the build failure to appear. The issue is not affecting amd64, nor armhf, which suggest something very i386 specific. I have not checked closely the other CPU architectures yet. The relevant upstream change that introduced this code begins to date back from quite some time ago[2] and the package builds with -ffloat-store for a while, so this may be caused by a dependency, or a compiler change. [2]: https://github.com/arq5x/bedtools2/commit/9d22ccb24f258553b0eff31e689b09563227331b Hope this helps pinpointing what's up, Étienne. -- System Information: Debian Release: trixie/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.5.0-3-amd64 (SMP w/12 CPU threads; PREEMPT) Locale: LANG=C.UTF-8, LC_CTYPE=C.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 -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/7, please excuse my verbosity `-on air: Condition Red - Let It All Come Out signature.asc Description: PGP signature
Bug#1054818: marked as pending in neo
Control: tag -1 pending Hello, Bug #1054818 in neo reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/neo/-/commit/826230c99abb73b30ee83cf19a2466b6ecc393ee d/clean: add trailing "/" to directories. Closes: #1054818 (this message was generated automatically) -- Greetings https://bugs.debian.org/1054818
Bug#1051325: marked as pending in sortmerna
Control: tag -1 pending Hello, Bug #1051325 in sortmerna reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/sortmerna/-/commit/60576c41b798914b9655c20f3a80b50e9dfd75ec concurrentqueue.h.patch: update concurrentqueue.h location. Closes: #1051325 (this message was generated automatically) -- Greetings https://bugs.debian.org/1051325
Bug#1051325: [Debian-med-packaging] Bug#1051325: sortmerna: FTBFS: concurrentqueue.h: No such file or directory
Control: tags -1 + confirmed Hi László, László Böszörményi, on 2023-09-06: > /build/sortmerna-4.3.6/include/readsqueue.hpp:49:12: fatal error: > concurrentqueue/concurrentqueue.h: No such file or directory >49 | # include > |^~~ […] > It seems the mentioned header moved to > /usr/include/concurrentqueue/moodycamel/concurrentqueue.h ; please > update your package. Thanks for the report and the hint, I'm looking at this. Have a nice day, :) -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: Marillion - Angelina signature.asc Description: PGP signature
Bug#1037846: marked as pending in rocm-smi-lib
Control: tag -1 pending Hello, Bug #1037846 in rocm-smi-lib reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/rocm-team/rocm-smi-lib/-/commit/3d23c4b1243b4577c48a21c0910aa7987d009a2d d/*.symbols*: update symbols table for gcc 13. Closes: #1037846 Closes: #1042134 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037846
Bug#1042134: marked as pending in rocm-smi-lib
Control: tag -1 pending Hello, Bug #1042134 in rocm-smi-lib reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/rocm-team/rocm-smi-lib/-/commit/3d23c4b1243b4577c48a21c0910aa7987d009a2d d/*.symbols*: update symbols table for gcc 13. Closes: #1037846 Closes: #1042134 (this message was generated automatically) -- Greetings https://bugs.debian.org/1042134
Bug#1050557: marked as pending in abyss
Control: tag -1 pending Hello, Bug #1050557 in abyss reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/abyss/-/commit/6b436c46ac14f056dec7d35f7ed70f0caeb277b0 d/rules: build with -Wno-error=dangling-reference. This fixes build failures with gcc 13. Closes: #1050557 (this message was generated automatically) -- Greetings https://bugs.debian.org/1050557
Bug#1050557: [Debian-med-packaging] Bug#1050557: abyss: FTBFS: error: possibly dangling reference to a temporary [-Werror=dangling-reference]
Control: tags -1 + confirmed Hi Aurélien, Aurelien Jarno, on 2023-08-26: > | GfaIO.h:182:27: error: possibly dangling reference to a temporary > [-Werror=dangling-reference] Thank you for your report, this seems to be one of those cases where the newly introduced warnings in gcc 13 are getting possibly overzealous. I did reproduce the crash on my end and consider making the warning non-fatal for the time being. This will solve the build failure on amd64, riscv64, and all the other architectures which were otherwise working with this package. Have a nice day, :) -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: Sieges Even - Unbreakable signature.asc Description: PGP signature
Bug#1042046: marked as pending in pyranges
Control: tag -1 pending Hello, Bug #1042046 in pyranges reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/pyranges/-/commit/051023b667ecae2f1ae9832b6652cda88a17f729 healthcheck-all.patch: new: fix test failure. The test failure seems to be caused by a call to an obsoleted method in a decorator describing the properties of the affected test. Closes: #1042046 (this message was generated automatically) -- Greetings https://bugs.debian.org/1042046
Bug#1042053: marked as pending in nipy
Control: tag -1 pending Hello, Bug #1042053 in nipy reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/nipy/-/commit/df190faf39b387bb4f89ca4454b7e408e256f1bb nibabel5.1.0.patch: new: resolve test failures. These test failures are related to the introduction of the newer nibabel version in Debian, which deprecates a couple of functions, resulting in some build time test errors in nipy. Closes: #1042053 (this message was generated automatically) -- Greetings https://bugs.debian.org/1042053
Bug#1042146: gatb-core: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file
This symbol tracking issue in gatb-core seems to be an uncaught regression on introduction of gcc-13: last upload dates back from before change of compiler, and reverse dependencies do not show autopkgtest regressions. I'll update symbols files appropriately. Have a nice day, :) -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/0, please excuse my verbosity `-on air: Galahad - Seas Of Change signature.asc Description: PGP signature
Bug#1042146: marked as pending in gatb-core
Control: tag -1 pending Hello, Bug #1042146 in gatb-core reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/gatb-core/-/commit/761a4aa775f4f376aaba2eea06ea9b5a6bc18c5b d/*.symbols*: update table. Marking several symbols leaked by the compiler as optional fixes build failures with gcc-13 and enables link time optimizations. Closes: #1042146 Closes: #1015412 (this message was generated automatically) -- Greetings https://bugs.debian.org/1042146
Bug#1037750: marked as pending in libxdf
Control: tag -1 pending Hello, Bug #1037750 in libxdf reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/libxdf/-/commit/425bec96e9c09ae899353fb676e062295a640568 gcc-13.patch: new: fix build failure with gcc-13. Closes: #1037750 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037750
Bug#1041451: gmap: FTBFS on all !amd64 archs
Hi, The relevant part of the error message shows that the generic fully scalar gmap.nosimd executable is never built for any cpu architecture: Note: /<>/build/src/gmap.avx2 does not exist. For faster speed, may want to compile package on an AVX2 machine Note: /<>/build/src/gmap.sse42 does not exist. For faster speed, may want to compile package on an SSE4.2 machine Note: /<>/build/src/gmap.sse41 does not exist. For faster speed, may want to compile package on an SSE4.1 machine Note: /<>/build/src/gmap.ssse3 does not exist. For faster speed, may want to compile package on an SSSE3 machine Note: /<>/build/src/gmap.sse2 does not exist. For faster speed, may want to compile package on an SSE2 machine Note: /<>/build/src/gmap.nosimd does not exist. For faster speed, may want to compile package on an non-SIMD machine Error: appropriate GMAP version not found Looking into src/Makefile.am, indeed they seem disabled upstream for the current gmap versions: # intersect-uint2.c requires SIMD #bin_PROGRAMS += gmap.nosimd #bin_PROGRAMS += gmapl.nosimd #bin_PROGRAMS += gsnap.nosimd #bin_PROGRAMS += gsnapl.nosimd My quick attempts to bring the necessary support in the aforementioned intersect-uint2.c file were not very fruitful so far. Something in there looks to prevent use of simde. Anyways, in hope this helps further investigations, -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/4, please excuse my verbosity `- signature.asc Description: PGP signature
Bug#1037816: marked as pending in parsinsert
Control: tag -1 pending Hello, Bug #1037816 in parsinsert reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/parsinsert/-/commit/cdb1ed695c967874b4fdb9732841c5bbd8d8edb7 d/rules: drop compiler optimization to -O1. This used to be done only on a handful of cpu architectures in the past, but since gcc-13, precision errors also affect amd64. Closes: #1037816 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037816
Bug#1037718: marked as pending in libbpp-phyl
Control: tag -1 pending Hello, Bug #1037718 in libbpp-phyl reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/libbpp-phyl/-/commit/38f671626f6ec730aa6efe9b7b46af5226fdc012 d/*.symbols*: mark some gcc specific symbols as optional. Closes: #1037718 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037718
Bug#1037689: marked as pending in hhsuite
Control: tag -1 pending Hello, Bug #1037689 in hhsuite reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/hhsuite/-/commit/5538ace5c83d75ccf3bd22ef8cfa74cf9bfd819e gcc-13.patch: new: fix ftbfs with gcc 13. Closes: #1037689 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037689
Bug#1037662: marked as pending in flye
Control: tag -1 pending Hello, Bug #1037662 in flye reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/flye/-/commit/b50fc2b3b4393d39136ea6cd9d2063ac089613b2 gcc-13.patch: new: fix ftbfs with gcc-13. Closes: #1037662 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037662
Bug#1037817: marked as pending in phyx
Control: tag -1 pending Hello, Bug #1037817 in phyx reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/phyx/-/commit/203d3d14a39bccf797ae712cde57ae73283ee1bd deoptimize.patch: new: fix ftbfs with gcc-13. This disables building phyx with -ffast-math. Closes: #1037817 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037817
Bug#1037655: marked as pending in filtlong
Control: tag -1 pending Hello, Bug #1037655 in filtlong reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/filtlong/-/commit/be6173ef06dbd6bb29f239d652c24bec31813bd6 gcc-13.patch: new: fix ftbfs with gcc-13. Closes: #1037655 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037655
Bug#1042119: FTBFS: igraph.h:31:10: fatal error: igraph_version.h: No such file or directory
Control: tags -1 + pending There is a change pending upload in python-leidenalg to fix this RC bug. However, the newer python-leidenalg will need introduction of the new package libleidenalg, still pending packaging. So this is a bit on hold for the moment. Cheers, :) -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/5, please excuse my verbosity `-on air: Mr. Sirius - Eternal Jealousy (single version) signature.asc Description: PGP signature
Bug#1037879: marked as pending in unifrac-tools
Control: tag -1 pending Hello, Bug #1037879 in unifrac-tools reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/unifrac-tools/-/commit/a14968b435dfb0814cfb01bf67282b613210d5ad gcc-13.patch: new: fix build failures with gcc-13 Closes: #1037879 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037879
Bug#1037746: marked as pending in vbz-compression
Control: tag -1 pending Hello, Bug #1037746 in vbz-compression reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/libvbz-hdf-plugin/-/commit/bbb470883ceece8fe5925d8212353b09954bde6f gcc-13.patch: new: fix build failures with gcc 13. Closes: #1037746 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037746
Bug#1037715: marked as pending in libatomicqueue
Control: tag -1 pending Hello, Bug #1037715 in libatomicqueue reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/libatomic-queue/-/commit/bb61075a753d52a90a10e51ca0aa2b8b1cb4f08e d/rules: build with -Wno-error=array-bounds. This works around gcc-13 bug [1], also Debian Bug#1041607. Closes: #1037715 [1]: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=110764 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037715
Bug#1037700: marked as pending in ivar
Control: tag -1 pending Hello, Bug #1037700 in ivar reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/ivar/-/commit/516c261c7cc2c7abfa1c77c9d70b714489e1a3db gcc-13.patch: add: fix ftbfs with gcc-13. Closes: #1037700 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037700
Bug#1041529: gqrx-sdr: unsatisfiable build dependencies
Source: gqrx-sdr Version: 2.15.9-1 Severity: serious Tags: ftbfs Justification: ftbfs Dear Maintainer, gqrx-sdr currently fails to build from source due to unsatisfiable build dependencies: # apt-get build-dep gqrx-sdr Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: builddeps:gqrx-sdr : Depends: libvolk2-dev but it is not installable E: Unable to correct problems, you have held broken packages. Upon further investigation, this looks to be caused by the collision between gnuradio-dev and libvolk2-dev, the former depending on libvolk-dev (unversioned) which in turn conflicts with libvolk2-dev: # apt-get install --dry-run gnuradio-dev libvolk2-dev Reading package lists... Done Building dependency tree... Done Reading state information... Done libvolk2-dev is already the newest version (2.5.2-3). Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: libvolk-dev : Breaks: libvolk2-dev but 2.5.2-3 is to be installed libvolk2-dev : Breaks: libvolk-dev but 3.0.0-2 is to be installed E: Unable to correct problems, you have held broken packages. Removing the build dependency on libvolk2-dev and relying on the libvolk-dev being pulled by gnuradio-dev looks to do the trick on my end. In hope this helps, Have a nice day, :) Étienne. -- System Information: Debian Release: trixie/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.3.0-2-amd64 (SMP w/12 CPU threads; PREEMPT) Locale: LANG=C.UTF-8, LC_CTYPE=C.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 -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/7, please excuse my verbosity `-on air: Kingcrow - Right Before signature.asc Description: PGP signature
Bug#1037772: marked as pending in mash
Control: tag -1 pending Hello, Bug #1037772 in mash reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/mash/-/commit/4089b1a5a5c39201145ae812b269376cf37e70bd gcc-13.patch: new: fix ftbfs with gcc-13. Closes: #1037772 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037772
Bug#1037739: marked as pending in libseqlib
Control: tag -1 pending Hello, Bug #1037739 in libseqlib reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/libseqlib/-/commit/d358946f695abfb1232f12e5cfc00981ad5fea3f d/libseqlib2.symbols.amd64: update. Mark symbols optimized out by LTO as optional. This has the side effect of resolving build failures with Gcc 13. Closes: #1015520 Closes: #1037739 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037739
Bug#1037728: marked as pending in libgenome
Control: tag -1 pending Hello, Bug #1037728 in libgenome reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/libgenome/-/commit/41bd06fd143f86006d0dd8ad0259fe4c0bcc0e88 d/libgenome0.symbols.amd64: update. Mark symbols optimized out by LTO as optional. This has also the side effect of resolving build issues encountered with Gcc 13. Closes: #1015488 Closes: #1037728 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037728
Bug#1037708: marked as pending in kmc
Control: tag -1 pending Hello, Bug #1037708 in kmc reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/kmc/-/commit/f17330044d60a83b9b43f895407bebd7f7411808 gcc-13.patch: new: fix build failures with gcc-13. Closes: #1037708 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037708
Bug#1037738: marked as pending in libsecrecy
Control: tag -1 pending Hello, Bug #1037738 in libsecrecy reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/libsecrecy/-/commit/0a706c7c01cf00a6aa20fd64c13c34ded798c5e4 gcc-13.patch: add: fix ftbfs. Closes: #1037738 (this message was generated automatically) -- Greetings https://bugs.debian.org/1037738
Bug#1040776: marked as pending in python-biopython
Control: tag -1 pending Hello, Bug #1040776 in python-biopython reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/python-biopython/-/commit/f74f80414639e5c3204bf6db8848e2f2c70b9685 d/control: depend on python3-reportlab (>= 4.0.4-1~). Closes: #1040776 (this message was generated automatically) -- Greetings https://bugs.debian.org/1040776
Bug#1040776: marked as pending in python-biopython
Control: tag -1 pending Hello, Bug #1040776 in python-biopython reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/python-biopython/-/commit/f74f80414639e5c3204bf6db8848e2f2c70b9685 d/control: depend on python3-reportlab (>= 4.0.4-1~). Closes: #1040776 (this message was generated automatically) -- Greetings https://bugs.debian.org/1040776
Bug#1040776: [Debian-med-packaging] Bug#1040776: python-biopython: autopkgtest regression
Hi Adrian, Adrian Bunk, on 2023-07-10: > 580s ModuleNotFoundError: No module named 'reportlab.graphics._renderPM' Thanks for your report, migrations of biopython and reportlab seem to have gone entangled. I'll bump the version requirement of python3-reportlab to unlock the situation. Have a nice day, :) -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: Scale The Summit - Whales signature.asc Description: PGP signature
Bug#1033703: gffread: autopkgtest regression: test dependency not in testing
Trying to resolve the situation by removing dependency on trinityrnaseq-examples, I noticed that the autopkgtest setup now fails with a conflict over boost versions, pulled by the game of transitive dependencies: The following packages have unmet dependencies: libboost1.81-dev : Conflicts: libboost1.74-dev but 1.74.0+ds1-21 is to be installed I didn't manage to identify which packages cause this condition, though. Have a nice day, :) -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: John Arch - Cheyenne signature.asc Description: PGP signature
Bug#923824: marked as pending in libdancer2-plugin-database-perl
Control: tag -1 pending Hello, Bug #923824 in libdancer2-plugin-database-perl reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/perl-team/modules/packages/libdancer2-plugin-database-perl/-/commit/c40e2150ac2129d84869c6ae4b34fa3e0fdf9907 stabilize-test-database-connection.patch: new patch. Closes: #923824 (this message was generated automatically) -- Greetings https://bugs.debian.org/923824
Bug#1036743: [Debian-med-packaging] Bug#1036743: kleborate: debsums reports modified files after apt-get upgrade && apt-get dist-upgrade
I had difficulties reproducing the issue with piuparts, but I manage to reproduce the problem as I suspected, with the following upgrade path, most likely because of the inconsistent makeblastdb version between the one used for building kleborate in bookworm and the one "refreshed" during postinst by the one available in bullseye: 1. kleborate from bullseye - ncbi-blast+ from bullseye dpkg --verify raises no complaints 2. kleborate from bookworm - ncbi-blast+ from bullseye dpkg --verify starts complaining here! 3. kleborate from bookworm - ncbi-blast+ from bookworm dpkg --verify still complains! Upgrading on top of that with a package that only relies on postinst script (and prerm to manually cleanup the artifacts): 4. kleborate fixed - ncbi-blast+ from bookworm dpkg --verify raises no complaints The prerm change is important to ensure there are no leftovers during package removal and purge. The following upgrade path is also fixed: 2. kleborate fixed - ncbi-blast+ from bullseye dpkg --verify raises no complaints 3. kleborate fixed - ncbi-blast+ from bookworm dpkg --verify still raises no complaints I just pushed my changes on salsa and will upload shorly if CI tests do not raise anything else outstanding I would have missed otherwise. Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/3, please excuse my verbosity. signature.asc Description: PGP signature
Bug#1036743: [Debian-med-packaging] Bug#1036743: kleborate: debsums reports modified files after apt-get upgrade && apt-get dist-upgrade
Hi Andreas Tille, Andreas Tille, on 2023-05-25: > Am Thu, May 25, 2023 at 10:34:10AM +0200 schrieb Étienne Mollier: > > > > Installation of kleborate from sid and testing shown no issues. > > Installation of kleborate from bullseye on bullseye is okay too. > > Good. Maybe we should reflect in BTS that this bug is not relevant for > bookworm? The problem is there is a specific upgrade order which causes this bug to happen with the version provided in bookworm, so it does affect this one too, but this is fixable. I had difficulty to reproduce the issue reliably with piuparts but I have the manual steps. Stay tuned, details are in a draft email. Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity. signature.asc Description: PGP signature
