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| author | Ricardo Wurmus <rekado@elephly.net> | 2026-04-02 16:04:04 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2026-04-28 09:43:17 +0200 |
| commit | e6cea80a08130f941b135d978e52b8aefbb01a3c (patch) | |
| tree | c15a3c214fb92304b49fa776815db6c6cc08bb9d /gnu | |
| parent | b1241b98376d0e79e64c35e29d0605292d484286 (diff) | |
gnu: r-zellkonverter: Enable tests by bypassing Conda.
* gnu/packages/bioconductor.scm (r-zellkonverter)[arguments]: Enable all tests
but one; add phase 'basilisk-configuration.
[inputs]: Add python-anndata, python-h5py, python-natsort, python-numpy,
python-pandas, python-scipy, and python-wrapper.
Change-Id: I4eb5e34ab540bdeea64f6b8629bb8f17d24c3663
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 26 |
1 files changed, 24 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d95c3bf8a7..64cee530c7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -64,6 +64,7 @@ #:use-module (gnu packages netpbm) #:use-module (gnu packages python) #:use-module (gnu packages python-science) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages protobuf) @@ -15536,8 +15537,22 @@ libraries for systems that do not have these available via other means.") (base32 "1si2g69l4scgkfrgas7fj6klj1rn1bcnch9panv564nyvkfrlmmv")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) - ;; This uses r-basilisk, which attempts to set up a Conda environment. - (arguments (list #:tests? #false)) + (arguments + (list + #:skipped-tests + ;; In this file code outside of any particular testthat test attempts to + ;; fetch data from gypsum.artifactdb.com. + '("test-write.R") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'basilisk-configuration + ;; This uses r-basilisk, which attempts to set up a Conda + ;; environment. We've patched basilisk to work without Conda when + ;; GUIX_BYPASS_BASILISK is set, so that's what we do here. + (lambda* (#:key inputs #:allow-other-keys) + (setenv "HOME" "/tmp") + (setenv "RETICULATE_PYTHON" (which "python3")) + (setenv "GUIX_BYPASS_BASILISK" "1")))))) (propagated-inputs (list r-basilisk r-cli @@ -15548,6 +15563,13 @@ libraries for systems that do not have these available via other means.") r-singlecellexperiment r-sparsearray r-summarizedexperiment)) + (inputs (list python-anndata + python-h5py + python-natsort + python-numpy + python-pandas + python-scipy + python-wrapper)) (native-inputs (list r-biocfilecache r-hdf5array r-knitr |