diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2024-11-29 14:34:34 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-12-03 16:59:58 +0100 |
| commit | 79989a9f537157c7dc276d27d6c56339445f5388 (patch) | |
| tree | 376621ab94bf5ad349f243f5d6f7b7e707475d0e /gnu/packages/bioinformatics.scm | |
| parent | 1c559a129c0c62fb1a52235965198557695e0790 (diff) | |
gnu: r-cytoexplorer: Add missing inputs.
* gnu/packages/bioinformatics.scm (r-cytoexplorer)[native-inputs]: Drop
labels; add r-cytoexplorerdata, r-mockery, and r-testthat.
[arguments]: Add phase 'skip-bad-tests.
Change-Id: I5060b1ae4ad42ae122a46db018f10910340985d6
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 53 |
1 files changed, 40 insertions, 13 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7e8c9f7aed..e40ddd5a49 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -18285,6 +18285,31 @@ is then merged.") (list #:phases '(modify-phases %standard-phases + (add-after 'unpack 'skip-bad-tests + (lambda _ + ;; These tests fail. Some fail because of unimportant + ;; differences in printed messages. + (with-directory-excursion "tests/testthat/" + (substitute* "test-cyto_channels-helpers.R" + (("^test_that.*cyto_channels_restrict.*" m) + (string-append m "skip('guix')"))) + (substitute* "test-cyto_gate_helpers.R" + (("^test_that.*cyto_gate_rename.*" m) + (string-append m "skip('guix')")) + (("^test_that.*cyto_gate_remove.*" m) + (string-append m "skip('guix')"))) + (substitute* "test-cyto_helpers.R" + (("^test_that.*cyto_compensate.*" m) + (string-append m "skip('guix')")) + (("^test_that.*cyto_empty.*" m) + (string-append m "skip('guix')")) + (("^test_that.*cyto_group_by.*" m) + (string-append m "skip('guix')"))) + (substitute* "test-cyto_spillover_spread_compute.R" + (("^test_that.*cyto_spillover_spread_compute internal reference.*" m) + (string-append m "skip('guix')")) + (("^test_that.*cyto_spillover_spread_compute universal reference.*" m) + (string-append m "skip('guix')")))))) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "docs/articles/CytoExploreR_files/" @@ -18317,19 +18342,21 @@ is then merged.") r-umap r-visnetwork)) (native-inputs - `(("esbuild" ,esbuild) - ("r-knitr" ,r-knitr) - ("js-vis" - ,(let ((version "4.20.1")) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/almende/vis") - (commit (string-append "v" version)))) - (file-name (git-file-name "js-vis" version)) - (sha256 - (base32 - "09ldcqzzki5c0jlwas5992qjffqxnx6j5sl703qccfw7rg1hn469"))))))) + (list esbuild + r-cytoexplorerdata + r-knitr + r-mockery + r-testthat + (let ((version "4.20.1")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/almende/vis") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-vis" version)) + (sha256 + (base32 + "09ldcqzzki5c0jlwas5992qjffqxnx6j5sl703qccfw7rg1hn469")))))) (home-page "https://github.com/DillonHammill/CytoExploreR") (synopsis "Interactive analysis of cytometry data") (description |