[R-pkg-team] Bug#1111758: r-bioc-beachmat: autopkgtest regression: isNamespaceLoaded("beachmat.hdf5") is not TRUE

[Paul Gevers]

Source: r-bioc-beachmat
Version: 2.22.0+ds-2
Severity: serious
User: debian-ci at lists.debian.org
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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