Your message dated Wed, 13 May 2026 12:36:12 +0000
with message-id <[email protected]>
and subject line Bug#1131058: fixed in insilicoseq 2.0.1-3
has caused the Debian Bug report #1131058,
regarding insilicoseq: autopkgtest regression with NumPy 2.4
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.
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--
1131058: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1131058
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: insilicoseq
Version: 2.0.1-2
Severity: important
User: [email protected]
Usertags: numpy2.4
Dear maintainer,
According to https://ci.debian.net data, your package insilicoseq has an
autopkgtest regression with numpy.
The following architectures failed: amd64, arm64.
Hopefully relevant excerpt from
https://ci.debian.net/packages/i/insilicoseq/unstable/amd64/69506600/
follows:
86s test/test_bam.py::test_to_model FAILED [
23%]
88s test/test_modeller.py::test_kde_qualities FAILED [
65%]
88s =================================== FAILURES
===================================
88s E numpy.linalg.LinAlgError: 1-th leading minor of the array is
not positive definite
88s E numpy.linalg.LinAlgError: The data appears to lie in a
lower-dimensional subspace of the space in which it is expressed. This has
resulted in a singular data covariance matrix, which cannot be treated using
the algorithms implemented in `gaussian_kde`. Consider performing principal
component analysis / dimensionality reduction and using `gaussian_kde` with the
transformed data.
88s > except np.linalg.linalg.LinAlgError:
88s E AttributeError: module 'numpy.linalg' has no attribute
'linalg'
88s E numpy.linalg.LinAlgError: 1-th leading minor of the array is
not positive definite
88s E numpy.linalg.LinAlgError: The data appears to lie in a
lower-dimensional subspace of the space in which it is expressed. This has
resulted in a singular data covariance matrix, which cannot be treated using
the algorithms implemented in `gaussian_kde`. Consider performing principal
component analysis / dimensionality reduction and using `gaussian_kde` with the
transformed data.
88s > except np.linalg.linalg.LinAlgError:
88s E AttributeError: module 'numpy.linalg' has no attribute
'linalg'
88s FAILED test/test_bam.py::test_to_model - AttributeError: module
'numpy.linalg...
88s FAILED test/test_modeller.py::test_kde_qualities - AttributeError: module
'nu...
88s ============= 2 failed, 43 passed, 1 skipped, 7 warnings in 2.63s
==============
89s run-unit-test FAIL non-zero exit status 1
89s run-unit-test FAIL non-zero exit status 1
--- End Message ---
--- Begin Message ---
Source: insilicoseq
Source-Version: 2.0.1-3
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
insilicoseq, 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 insilicoseq 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, 13 May 2026 13:45:15 +0200
Source: insilicoseq
Binary: insilicoseq
Architecture: source all
Version: 2.0.1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
insilicoseq - sequencing simulator producing realistic Illumina reads
Closes: 1131058
Changes:
insilicoseq (2.0.1-3) unstable; urgency=medium
.
* Team upload.
* Fix build with numpy 2.4
Closes: #1131058
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Remove Priority field (cme)
* debputy lint --auto-fix (routine-update)
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Files:
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6b8b1600e4f71fc3c31e9d0f2771f7f0 5780 science optional
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insilicoseq_2.0.1-3_all.deb
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