33/45: gnu: r-category: Add missing inputs.

[guix-commits]

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

commit 8ff783d52100ea30029312b0e597a274adc0d3a6
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Nov 27 15:43:22 2024 +0100

    gnu: r-category: Add missing inputs.
    
    * gnu/packages/bioconductor.scm (r-category)[arguments]: Add phase
    'delete-bad-tests; skip building vignettes.
    [native-inputs]: Add r-all, r-geneplotter, r-hgu95av2-db, r-karyoploter,
    r-keggrest, r-lattice, r-limma, r-org-sc-sgd-db, and r-rcolorbrewer.
    [properties]: Tell updater to ignore r-gostats.
    
    Change-Id: I186b7a92437a20f85960bd605ae25ed5c29bf5b2
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2d3cf7b323..96c91de376 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7999,8 +7999,20 @@ genome data packages and support for efficient SNP 
representation.")
        (sha256
         (base32
          "0s65rfk9sw02qdqk7jhbkjybx1sm0hq0impdcxyypxbg77db5wk2"))))
-    (properties `((upstream-name . "Category")))
+    (properties
+     `((upstream-name . "Category")
+       (updater-ignored-native-inputs . ("r-gostats"))))
     (build-system r-build-system)
+    (arguments
+     (list
+      ;; Vignettes attempt to connect to rest.kegg.jp.
+      #:test-types '(list "tests")
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'delete-bad-tests
+           (lambda _
+             ;; These tests need r-gostats, which depends on this package.
+             (delete-file "inst/UnitTests/hyperGTest_test.R"))))))
     (propagated-inputs
      (list r-annotate
            r-annotationdbi
@@ -8012,7 +8024,16 @@ genome data packages and support for efficient SNP 
representation.")
            r-gseabase
            r-matrix
            r-rbgl))
-    (native-inputs (list r-runit))
+    (native-inputs (list r-all
+                         r-geneplotter
+                         r-hgu95av2-db
+                         r-karyoploter
+                         r-keggrest
+                         r-lattice
+                         r-limma
+                         r-org-sc-sgd-db
+                         r-rcolorbrewer
+                         r-runit))
     (home-page "https://bioconductor.org/packages/Category";)
     (synopsis "Category analysis")
     (description