[R-pkg-team] Bug#970038: r-cran-seurat: dependency is missing (hdf5r)

[Lucas Kanashiro]

Source: r-cran-seurat
Version: 3.2.0-1
Severity: important

Dear Maintainer,

r-cran-remotes has not migrated to testing because of a regression detected by autopkgtest:

https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-seurat/6977467/log.gz

This is the important part:

── 1. Error: (unknown) (@test_load_10X.R#34)  ──────────────────────────────────
Please install hdf5r to read HDF5 files
Backtrace:
 1. Seurat::Load10X_Spatial(data.dir = "../testdata/visium")
 2. Seurat::Read10X_h5(...)

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 392 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
1. Error: (unknown) (@test_load_10X.R#34)


After some digging I noticed that the main change in version 3.2 is "Support for analysis and visualization of spatially resolved datasets", and the Seurat::Load10X_Spatial and Seurat::Read10X_h5 pre-processing functions depend on the hdf5r R package. AFAICS this new dependency it is not available in the archive. So in order to enable this feature the hdf5r package is needed. As soon as we have this package in the archive it should be added as a test and runtime dependency.

Cheers!

-- 
Lucas Kanashiro