Your message dated Sun, 07 Dec 2025 14:37:03 +0000
with message-id <[email protected]>
and subject line Bug#1111758: fixed in r-bioc-beachmat 2.22.0+ds-3~deb13u1
has caused the Debian Bug report #1111758,
regarding r-bioc-beachmat: autopkgtest regression:
isNamespaceLoaded("beachmat.hdf5") is not TRUE
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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--
1111758: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1111758
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: r-bioc-beachmat
Version: 2.22.0+ds-2
Severity: serious
User: [email protected]
Usertags: regression
Dear maintainer(s),
Your package has an autopkgtest, great. However, it fails. Can you
please investigate the situation and fix it? I copied some of the output
at the bottom of this report.
The release team has announced [1] that failing autopkgtest on amd64 and
arm64 are considered RC in testing.
More information about this bug and the reason for filing it can be
found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://lists.debian.org/debian-devel-announce/2019/07/msg00002.html
https://ci.debian.net/packages/r/r-bioc-beachmat/testing/amd64/63279645/
121s autopkgtest [01:08:56]: test pkg-r-autopkgtest:
[-----------------------
121s Test: Try to load the R library beachmat
121s
121s R version 4.5.1 (2025-06-13) -- "Great Square Root"
121s Copyright (C) 2025 The R Foundation for Statistical Computing
121s Platform: x86_64-pc-linux-gnu
121s
121s R is free software and comes with ABSOLUTELY NO WARRANTY.
121s You are welcome to redistribute it under certain conditions.
121s Type 'license()' or 'licence()' for distribution details.
121s
121s R is a collaborative project with many contributors.
121s Type 'contributors()' for more information and
121s 'citation()' on how to cite R or R packages in publications.
121s
121s Type 'demo()' for some demos, 'help()' for on-line help, or
121s 'help.start()' for an HTML browser interface to help.
121s Type 'q()' to quit R.
121s
121s > library('beachmat')
126s >
126s Test: Run tests for beachmat
126s Start: testthat.R
126s
126s R version 4.5.1 (2025-06-13) -- "Great Square Root"
126s Copyright (C) 2025 The R Foundation for Statistical Computing
126s Platform: x86_64-pc-linux-gnu
126s
126s R is free software and comes with ABSOLUTELY NO WARRANTY.
126s You are welcome to redistribute it under certain conditions.
126s Type 'license()' or 'licence()' for distribution details.
126s
126s R is a collaborative project with many contributors.
126s Type 'contributors()' for more information and
126s 'citation()' on how to cite R or R packages in publications.
126s
126s Type 'demo()' for some demos, 'help()' for on-line help, or
126s 'help.start()' for an HTML browser interface to help.
126s Type 'q()' to quit R.
126s
126s > library(testthat)
127s > library(beachmat)
131s > test_check("beachmat")
310s [ FAIL 1 | WARN 0 | SKIP 0 | PASS 17537 ]
310s
310s ══ Failed tests
════════════════════════════════════════════════════════════════
310s ── Failure ('test-initializeCpp-other.R:155:5'): initialization
works correctly with the HDF5Arrays ──
310s isNamespaceLoaded("beachmat.hdf5") is not TRUE
310s
310s `actual`: FALSE
310s `expected`: TRUE
310s
310s [ FAIL 1 | WARN 0 | SKIP 0 | PASS 17537 ]
311s Error: Test failures
311s Execution halted
312s autopkgtest [01:12:07]: test pkg-r-autopkgtest:
-----------------------]
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--- End Message ---
--- Begin Message ---
Source: r-bioc-beachmat
Source-Version: 2.22.0+ds-3~deb13u1
Done: Charles Plessy <[email protected]>
We believe that the bug you reported is fixed in the latest version of
r-bioc-beachmat, 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.
Charles Plessy <[email protected]> (supplier of updated r-bioc-beachmat 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: Sun, 14 Sep 2025 16:38:29 +0900
Source: r-bioc-beachmat
Architecture: source
Version: 2.22.0+ds-3~deb13u1
Distribution: trixie
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Charles Plessy <[email protected]>
Closes: 1111758
Changes:
r-bioc-beachmat (2.22.0+ds-3~deb13u1) trixie; urgency=medium
.
* Team upload.
.
[ Michael R. Crusoe ]
* Patch up part of a test that depends on the "beachmat.hdf5" R
package, which is not yet in Debian. Closes: #1111758
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