nteresting to file fields that seem relevant.
[2]: https://dep-team.pages.debian.net/deps/dep12/
[3]: https://wiki.debian.org/UpstreamMetadata
Have a nice day, :)
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.''`. Étienne Mollier
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Control: tags -1 + help
Hi, this is a quick update to mention that help is needed here,
and on the upstream issue[1].
[1]: https://github.com/RDFLib/rdflib/issues/2912
Have a nice day, :)
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.''`. Étienne Mollier
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libparasail-dev arm64 2.6.2+dfsg-2
python3-parasail all 1.3.3-1
Have a nice day, :)
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Hi Paul,
Paul Mars, on 2024-09-19:
> Here is a patch updating the checksum
Thanks, I merged your patch and verified autopkgtest went back
on tracks; will upload shortly.
Have a nice day, :)
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.''`. Étienne Mollier
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t:``ipyparallel.error.RemoteError: SystemError(unknown
opcode)``
docs/faq.rst:``ModuleNotFoundError: No module named 'ipyparallel'``
docs/faq.rst: conda install
mypy.ini:[mypy-ipyparallel.*]
test-requirements.txt:ipyparallel
Hopefull your CI will confirm it.
s pyflow, that might be one explanation why
upstream decided to archive the repository instead of writing a
python3 port.
Thanks for your analysis!
Have a nice day, :)
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.''`. Étienne Mollier
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`. `' sent
BUILD_TEST_ARGS=-v -n $(NUMJOBS)
>
> %:
> dh $@ --buildsystem=pybuild
Thanks for the patch, I applied it, modulo the typo at the end
of the "patsubst" line. Sorry I didn't think of situations
where it is desirable to run builds and tests in a single thread
when h
Control: forwarded -1 https://github.com/globus/globus-sdk-python/issues/1056
Hi Stefano,
Thanks for the report, I forwarded the word upstream.
Have a nice day, :)
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HI Joost,
Joost van Baal-Ilić, on 2024-09-17:
> Thanks for reporting! Just fixed in 4d485c1..c4a6308 @ salsa , will end up in
> next FAQ release.
Cool, thanks for the status!
Have a nice day, :)
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ies, so that may
take a bit of time.
Have a nice day, :)
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sions of packages debian-faq suggests:
ii firefox-esr [www-browser] 115.15.0esr-1
ii zathura-pdf-poppler [pdf-viewer] 0.3.3-1
-- no debconf information
--
.''`. Étienne Mollier
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sue remained.
I would prefer to see the functionality working again, but if
getting back the BTS graphs on tracks is a problem, I'm also ok
(even if a bit sad) to see the graph button to be removed from
the DDPO page.
Have a nice day, :)
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compatible with Python 3.12. I have completed these modifications and
> tested my solution locally, it works well.Please let me know wheather the
> solution can be accepted.The patch is in the attachment.
Regarding your changes to the test, I injected them as-is.
Thank you for your contribu
hape in the
end though.
Have a nice day, :)
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#pragma GCC diagnostic warning "-Wreturn-mismatch"
#endif
but that would be something to apply to the nim compiler itself,
unless they're after solutions, not workarounds.
[2]: https://gcc.gnu.org/gcc-14/porting_to.html
Have a nice day, :)
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on to upload a fix this evening.
Have a nice day, :)
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/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 python3-pyflow depends on:
ii python3 3.12.5-1
python3-pyflow recommends no p
dency.
Lucas, do you still reproduce the issue on your end? I don't
exclude to miss something with qemu-user. If the issue still
appears, then the baseline violation would justify bumping back
the severity to serious. But if the issue doesn't appear
anymore, then I think the bug can b
.
Have a nice day, :)
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2024/09/threads.html
Mailing lists infrastructure is otherwise operating properly.
There were a few more messages sent yesterday the 6th, and we're
now the 7th.
I'm not sure whether this is consecutive to the recent planned
outage or not, but in doubt I thought important to report i
> autoremovals, meanwhile.
Nah, no worries, at least autoremoval notices hint how to
prioritize investigations on release critical bugs. ;)
Have a nice day, :)
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Hi Reinhard,
Étienne Mollier, on 2024-09-01:
> File
> "/<>/.pybuild/cpython3_3.12/build/Tests/test_NCBI_BLAST_tools.py",
> line 251, in test_fasta_db_prot
> self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phd"))
> Assertion
me -m
riscv64
I plan to skip test_NCBI_BLAST_tools.py in python-biopython in
the meantime: this package is not subject to serious bug or
autoremoval whatsoever, but in its current state it hogs debci
riscv64 runners due to another problem.
Have a nice day, :)
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.''`.
Control: severity -1 normal
Hi,
I reduce the severity of this ftbfs bug on arm64, as the
libmaus2 and it's reverse dependency biobambam2 have been
removed from this architecture. See #1079718 and #1079456.
Have a nice day, :)
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usr/lib/python3/dist-packages/rdflib/namespace/__init__.py",
line 247, in __getitem__
raise AttributeError(
AttributeError: DefinedNamespace like object has no attribute '_NS'
Have a nice day, :)
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this is causing a
lot of autoremovals.
Have a nice day, :)
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Control: reopen -1
Control: tags -1 + patch
Hi again,
Étienne Mollier, on 2024-09-04:
> The test suite is run, and the build goes through, so I close
> the bug.
Reopening, the issue is not affecting the build process, however
it does affect its autopkgtest:
autopkgtest [10:13:17]
prot
self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phd"))
AssertionError: False is not true
It is a bit unclear to my why these nhd and phd files would be
missing. This may be a problem with ncbi-blast+, but would need
further investigation to tell for
version guards in requirements files).
Have a nice day, :)
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Control: forwarded -1 https://github.com/bcgsc/abyss/issues/481
Thank you for your report, I informed the development team
upstream on github, maybe it would be a better place to follow
up there (unless you do not want or cannot use github).
Have a nice day, :)
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.''`. Étien
y to operate properly
following this change! I do think it is particularly useful.
Have a nice day, :)
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.''`. Étienne Mollier
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-- debconf information:
greylistd/restartexim: true
greylistd/autoconfig_notdone:
* greylistd/autoconfig_notdone_exim4:
Now to enjoy a time of peace and quiet while greylistd does it's
magic. :)
Have a nice day, :)
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h. I trigger a run and
will get back to it tomorrow (this really takes forever to run).
Have a nice day, :)
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cture anymore. Please kindly remove
it from the s390x in unstable.
Have a nice day, :)
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ide better
> diagnostics?
I'm seeing whether skipping the remaining part of the test is
helpful on riscv64. If not to resolve the root cause of the
issue, at least it would give some breath to the CI runner.
Happy to make the skip a bit more verbose if that works.
Have a nice day,
o me that Biopython's test
suite revealed something off in SciPy specifically on Risc-V.
Have a nice day, :)
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uot;interface.h"
#include "pmlcg.h"
-#include "gmp.h"
+#include
#include "basic.h"
#include
#include "store.h"
Have a nice day, :)
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`. `&#x
Hi Niko,
Niko Tyni, on 2024-08-24:
> On Wed, Aug 21, 2024 at 10:05:03PM +0200, Étienne Mollier wrote:
> > This suggests the issue might be resolved in the newer upstream
> > version. But let's see…
>
> Thanks Étienne. Unfortunately this didn't fix it.
>
>
released Biopython 1.84. It seems to have a
couple of cosmetic changes to the run_test.py script. It could
be worth a shot too.
Have a nice day, :)
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won't file a complete
removal for the time being.
Please kindly remove libmaus2 from unstable arm64 architecture.
[1]: https://gitlab.com/german.tischler/libmaus2/-/issues/40
Have a nice day, :)
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.''`. Étienne Mollier
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seems.
[1]: https://buildinfo.debian.net/binaries/libdr-sundown-perl
Have a nice day, :)
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fronts) and zero popcon could also hint that the
package could be candidate for removal of the archive, but I
lack enough context to tell for sure.
Have a nice day, :)
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`. `' sen
/
[2]: https://github.com/rordenlab/dcm2niix/issues/854
I am adjusting dcm2niix build dependencies to append the meta
package architecture-is-little-endian, so the package does not
come back to s390x by accident.
Have a nice day, :)
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.search('\[', str) is not None)
Converting the affected regexes to raw strings (r'…') would
probably be the way to go to fix this minor issue.
Have a nice day, :)
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.''`. Étienne Mollier
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`. `&#x
s://bugs.debian.org/cgi-bin/bugreport.cgi?bug=733598
Have a nice day, :)
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is suggests the issue might be resolved in the newer upstream
version. But let's see…
[1]: https://tracker.debian.org/pkg/libtap-formatter-junit-perl
[2]: https://metacpan.org/dist/TAP-Formatter-JUnit/changes
Have a nice day, :)
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ct_start;
--->8-->8-->8-->8---
This really feels more like a workaround than a proper fix, on
the other hand proper fix looks to probably require reorganizing
the code base with much more involved changes. So I guess this
should be suffic
er to avoid having to revert
the change in meep-mpi-default.
Thanks Helmut for the heads up on the multiarch hinting front!
Have a nice day, :)
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`. `' sent from /dev/pts/3, p
Adam D. Barratt, on 2024-08-17:
> On Wed, 2024-08-07 at 23:24 +0200, Étienne Mollier wrote:
> > dcm2niix is affected by minor security issue CVE-2024-27629 in
> > bookworm: a local attacker can execute arbitrary code as the
> > generated file name is not properly escape
Hi Adam,
Adam D. Barratt, on 2024-08-17:
> On Mon, 2024-07-29 at 23:00 +0200, Étienne Mollier wrote:
> > xmedcon in bookworm is affected by CVE-2024-29421. It is,
> > quoting the description: "vulnerable to Buffer Overflow via
> > libs/dicom/basic.c which allows an att
er openmpi support for 32-bit boost builds
is feasible.
Please kindly remove prime-phylo from 32-bit platforms, notably
release architectures armel, armhf and i386.
Have a nice day, :)
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.''`. Étienne Mollier
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`
meone
wants to implement one of the two first options; the build issue
is currently preventing migration of the resolution of RC bug
#1075397.
Have a nice day, :)
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.''`. Étienne Mollier
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Hi Alastair,
Étienne Mollier, on 2024-08-15:
> The build failure on i386 causes a sprawl of autoremoval
> notifications in reverse dependencies, so if you're caught by
> time, I'm considering the option of proceeding to an NMU.
As #1078738 is blocking the migration of the
x27;t seen any new release for about sixteen
years and eleven months, and it is causing a sprawl of
autoremovals at the moment. But as I mentioned, I thought you
might be interested in the issue.
Have a nice day, :)
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.''`. Étienne Mollier
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dencies, so if you're caught by
time, I'm considering the option of proceeding to an NMU.
Have a nice day, :)
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.''`. Étienne Mollier
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`-
dif
Control: severity -1 normal
I reduce the severity of the bug, as parsinsert has been removed
from armel and armhf platforms.
Have a nice day, :)
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.''`. Étienne Mollier
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`. `' sent from /dev/pts
ot;expected operation {expected_op}, not {statement.op}"
> # Compare the two expressions using sympy to allow for
> different order etc.
> sympy_expected = str_to_sympy(expected_expr)
> sympy_actual = str_to_sympy(statement.expr)
Hi Jonathan,
Jonathan Wiltshire, on 2024-08-10:
> On Wed, Aug 07, 2024 at 07:57:03PM +0200, Étienne Mollier wrote:
> > [ Reason ]
> > xmedcon in bullseye is affected by CVE-2024-29421. It is,
> > quoting the description: "vulnerable to Buffer Overflow via
> > li
Hi Salvatore,
Salvatore Bonaccorso, on 2024-08-08:
> Hi Étienne,
>
> On Wed, Aug 07, 2024 at 10:54:25PM +0200, Étienne Mollier wrote:
> > Control: found -1 1.0.20220720-1
> > Control: notfound -1 1.0.20201102-1
> > Control: tags -1 + bookworm
> >
> > Gr
before handing the output
file name to the next steps of the code, which may involve some
parsing by a shell.
[ Other info ]
Have a nice day, :)
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lem indeed
does not appear on that old operating system level.
Have a nice day, :)
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`-on air: Genesis - Domino (live)
length and
error out instead of running into buffer overflow conditions.
[ Other info ]
Have a nice day, :)
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`-
diff -
Hi SRM,
I thought it would be a good idea to append a proper DEP3 header
to CVE-2024-29421.patch. Revised debdiff is in attachment.
Have a nice day, :)
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.''`. Étienne Mollier
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-gnu/14/../../../../lib/libsprng.so: undefined
reference to `mpz_init_set'
/usr/bin/ld:
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/libsprng.so: undefined
reference to `mpz_add'
collect2: error: ld returned 1 exit status
As far as I can tell, this seems to be a proble
egrating your changes into the Debian archive.
Have a nice day, :)
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`-on air: Ayreon - Intergalactic Space Crusaders
si
https://bugs.gentoo.org/637330 )
> fixes the build for me.
>
> Hope this helps,
Yes it does, thank you for your help, I'm appending the Gentoo
patch in an upcoming upload of libace-perl.
Have a nice day, :)
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;, which is
> also in package medcon 0.23.0-gtk3+dfsg-1
Gosh! My bad, I'm fixing that on the double, thanks for your QA
work flagging this!
Have a nice day, :)
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Sent from /dev/pts/0, please excuse my verbosi
version in unstable is 0.2.1-3 but the last reported
> version is 0.1.31-3 whcih is the testing verion.
seems related to #1074038 affecting who-uploads in
devscripts, but I haven't checked closely yet.
Hope this helps,
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.''`. Étienne Mollier
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e, and get back to it once RC bugs are under control.
> Have a nice day,
Likewise, :)
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Salvatore Bonaccorso, on 2024-07-29:
> On Sun, Jul 28, 2024 at 11:17:03PM +0200, Étienne Mollier wrote:
> > If that makes sense, I can liaise with the release
> > team for the next point release in August, or do you prefer we
> > proceed to a security upgrade earlier? (I
include the faulty windowmasker invocation. As
it very much feels like the test may need update, I informed
upstream of the issue.
Have a nice day, :)
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gainst large element length and
error out instead of running into buffer overflow conditions.
[ Other info ]
Have a nice day, :)
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`. `' sent from /dev/pts/2, please excuse my verbo
ase
team for the next point release in August, or do you prefer we
proceed to a security upgrade earlier? (I guess not, given the
"Minor issue" in the notes I see in the security tracker web
page, but asking just in case.)
Have a nice day, :)
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: :&
Have a nice day, :)
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-- System Information:
Debian Release: trixie/sid
APT prefers uns
it
weren't commented out.
As it is, I don't see an obvious way forward apart from putting
dust back below the carpet and ignoring the error, and I would
question whether this function is behaving as intended in the
first place.
In hope this gives some leads,
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Have a nice day, :)
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was also an opportunity to consolidate a bit the version
parsing.
Have a nice day, :)
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introduced fatal errors instead. Volunteer
time would probably be better spent this way. Thankfully, C
flags propagation goes rather well, so this is just a matter of
adding the necessary stanza in the d/control file.
Have a nice day, :)
--
.''`. Étienne Mollier
: :' : pgp:
ing at the
right place, then there's a non-zero chance the build failure is
specific to the packaging. I'm not sure how to move this issue
forward. I'll pick lower hanging fruits in the meantime.
In hope this helps,
--
.''`. Étienne Mollier
: :' : pgp: 8f91 b2
y my
upcoming upload will be sufficient to bring back dask and
dask.distributed back in synchronization in testing.
Have a nice day, :)
--
.''`. Étienne Mollier
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`. `' sent from /dev/pts/1, please excuse m
14/porting_to.html
Have a nice day, :)
--
.''`. Étienne Mollier
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`. `' sent from /dev/pts/2, please excuse my verbosity
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"date": None,
268 }
but I'm not confident how this interferes with the other version
fields normally filled automatically after deriving the git tag.
Hope this gives some inspiration,
--
.''`. Étienne Mollier
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possible to capture the package
version instead, but the version.py code to do that is non
existent for now.
The package has still a couple of other issues I'm trying to
diagnose at the moment. With some luck I, or someone else
faster than I am, may come up with something before next upload.
H
t through. As far as I can witness, the issue
is resolved now.
Have a nice day, :)
--
.''`. Étienne Mollier
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`. `' sent from /dev/pts/3, please excuse my verbosity
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Étienne Mollier, on 2024-06-28:
> Some further results on parsinsert: after rebuilding on all
> release architectures, it turned out the other affected platform
> was armel, in addition to armhf. This suggests possibly a
> regression introduced by time_t migration to 64-bit size. Or
standards (36 reports
and winding down). parsinsert being also computationally
intensive, I do not expect it to be much used on 32-bit arm
architectures nowadays. I estimate that overall, the removal
should have low to no risk.
Have a nice day, :)
--
.''`. Étienne Mollier
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ruction by dcmtk version bump.
Have a nice day, :)
--
.''`. Étienne Mollier
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.
The other architectures: amd64, arm64, i386, mips64el, ppc64el,
s390x, and risv64, built all fine and would not require removal.
Hope this helps,
--
.''`. Étienne Mollier
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`. `' sent from /dev/pts/1, please
al of the package.
Have a nice day, :)
--
.''`. Étienne Mollier
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R BioC modules
> until libboost 1.81 transition is finished. (Closes: #1033703)
> ...
> -- Étienne Mollier Tue, 20 Jun 2023 21:03:42 +0200
>
>
>
> trinityrnaseq is back in testing, and boost now defaults to 1.83.
Thank you for having kept a tab on this! gffread hasn'
acking wheel built for python3.11
with "installer" module
dh_auto_build: error: pybuild --build -i python{version} -p "3.12 3.11"
returned exit code 13
make: *** [debian/rules:5: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit
status 2
I have also a full build log[1] available for your convenience.
[1]:
https://people.debian.org/~emollier/logs/napari/napari_amd64-2024-06-16T16:16:51Z.build.xz
Have a nice day, :)
--
.''`. Étienne Mollier
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`-
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ly packaged ones, but I didn't really grasp how the
whole thing worked to extend on that.
Have a nice day, :)
--
.''`. Étienne Mollier
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`. `' sent from /dev/pts/1, please excuse my verbosity
m not implementing such skip right now: lookup
of the dask bug upstream[1] suggests there may be options to get
the issue sorted at the source.
[1]: https://github.com/dask/dask/pull/11035
In hope this helps,
--
.''`. Étienne Mollier
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proper coverage of the sortmerna
binary once again would be a plus to ensure the package is in
working conditions.
Have a nice day, :)
--
.''`. Étienne Mollier
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`. `' sent from /dev/pts/2, please excuse my verbo
at@Base 1.8
+#MISSING: 1.18.0-1# strlcpy@Base 1.8
tun_close@Base 1.11
tun_fileno@Base 1.11
tun_name@Base 1.11
Have a nice day, :)
--
.''`. Étienne Mollier
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`. `' sent fr
ad to performance
reduction of the functions that were previously decorated. The
removal should have no influence on functionalities or results.
Have a nice day, :)
--
.''`. Étienne Mollier
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`. `' sent from /de
es.
Removal requests may not be necessary for an "any" to "all"
change, but lets keep an eye on how things are moving. It's
possible I'm missing something (an upload to NEW?), or the
upload might just work. We'll see.
Have a nice day, :)
--
.''
not seen matter for comments, the package looked suitable
for upload to unstable to me, so I proceeded. Congratulations!
Thank you for your contribution!
Have a nice day, :)
--
.''`. Étienne Mollier
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`. `'
nalizo 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, :)
--
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