Your message dated Thu, 09 Jul 2026 18:00:11 +0000
with message-id <[email protected]>
and subject line Bug#1141283: fixed in iva 1.0.11+ds-7
has caused the Debian Bug report #1141283,
regarding iva: Autopkgtests fail: File "hiv_pcr_primers.fa" not found.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1141283: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1141283
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: iva
Version: 1.0.11+ds-6
Severity: serious
The following command failed with exit code 1
/usr/bin/iva --threads 1 --trimmomatic /usr/share/java/trimmomatic.jar
--pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out
The output was:
Error! File "hiv_pcr_primers.fa" not found. Cannot continue
Traceback (most recent call last):
File "/usr/bin/iva", line 184, in <module>
p1.start()
~~~~~~~~^^
File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
~~~~~~~~~~~^^^^^^
File "/usr/lib/python3.14/multiprocessing/context.py", line 230, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/usr/lib/python3.14/multiprocessing/context.py", line 306, in _Popen
return Popen(process_obj)
File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 35, in
__init__
super().__init__(process_obj)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line 20, in
__init__
self._launch(process_obj)
~~~~~~~~~~~~^^^^^^^^^^^^^
File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 51, in
_launch
self.sentinel, w = forkserver.connect_to_new_process(self._fds)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
File "/usr/lib/python3.14/multiprocessing/forkserver.py", line 106, in
connect_to_new_process
connection.answer_challenge(
~~~~~~~~~~~~~~~~~~~~~~~~~~~^
wrapped_client, self._forkserver_authkey)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.14/multiprocessing/connection.py", line 995, in
answer_challenge
message = connection.recv_bytes(256) # reject large message
File "/usr/lib/python3.14/multiprocessing/connection.py", line 226, in
recv_bytes
buf = self._recv_bytes(maxlength)
File "/usr/lib/python3.14/multiprocessing/connection.py", line 451, in
_recv_bytes
buf = self._recv(4)
File "/usr/lib/python3.14/multiprocessing/connection.py", line 416, in _recv
chunk = read(handle, to_read)
ConnectionResetError: [Errno 104] Connection reset by peer
-- System Information:
Debian Release: forky/sid
APT prefers unstable-debug
APT policy: (500, 'unstable-debug'), (500, 'unstable'), (500, 'testing'),
(101, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 7.0.13+deb14-amd64 (SMP w/16 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=ru_RU.UTF-8, LC_CTYPE=ru_RU.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 iva depends on:
ii default-jre-headless 2:1.25-77
pn fastaq <none>
pn kmc <none>
pn mummer <none>
ii perl 5.40.1-8
ii python3 3.13.9-3+b1
pn python3-networkx <none>
ii python3-numpy 1:2.4.6+ds-2
ii python3-packaging 26.2-2
pn python3-pysam <none>
pn samtools <none>
pn smalt <none>
Versions of packages iva recommends:
pn bioperl <none>
pn r-base-core <none>
pn trimmomatic <none>
iva suggests no packages.
--- End Message ---
--- Begin Message ---
Source: iva
Source-Version: 1.0.11+ds-7
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
iva, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated iva package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 08 Jul 2026 14:37:40 +0200
Source: iva
Binary: iva iva-examples
Architecture: source all amd64
Version: 1.0.11+ds-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
iva - iterative virus sequence assembler
iva-examples - iterative virus sequence assembler - test data
Closes: 1141283
Changes:
iva (1.0.11+ds-7) unstable; urgency=medium
.
[ Sascha Steinbiss ]
* Update the salsa-ci.yml file with the current Debian Med one.
.
[ Andreas Tille ]
* d/watch: version=5
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Remove Priority field (cme)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* Set upstream metadata fields: Repository.
* Separate iva-examples package containing test data
* Install autopkgtest as user example in docs as run-unit-test
* Adapt to forkserver in Python3.14
Closes: #1141283
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