17/17: gnu: r-cytoexplorer: Add missing inputs.

[guix-commits]

rekado pushed a commit to branch r-team
in repository guix.

commit cb9dd7f0d4ec34540c87f555ada01650e38cb69e
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Nov 29 14:34:34 2024 +0100

    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
---
 gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++----------
 1 file changed, 40 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index be26003a86..f89f849a07 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -18210,6 +18210,31 @@ 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/"
@@ -18242,19 +18267,21 @@ 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