02/09: gnu: r-derfinder: Add missing inputs.

[guix-commits]

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

commit 82c60f7be87aa835496940499dc0c718dfc01b92
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Nov 27 17:12:20 2024 +0100

    gnu: r-derfinder: Add missing inputs.
    
    * gnu/packages/bioconductor.scm (r-derfinder)[native-inputs]: Add
    r-derfinderdata and r-txdb-hsapiens-ucsc-hg19-knowngene.
    [arguments]: Add phase 'delete-bad-tests.
    
    Change-Id: I2c0e5b6ea514c6b0024022e8e663d171dd8868da
---
 gnu/packages/bioconductor.scm | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bb858dd100..91b8964de6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6559,6 +6559,17 @@ heterogeneity in the original high-dimensional space.")
                 "0qg1klbb4g8nw7v50xb0p022barlspwaisdymyk12a04vd9q4i79"))))
     (properties `((upstream-name . "derfinder")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'delete-bad-tests
+           (lambda _
+             ;; These tests attempt to download files.
+             (delete-file "tests/testthat/test_data.R")
+             ;; One test fails with: object of type 'closure' is not
+             ;; subsettable
+             (delete-file "tests/testthat/test_Fstats.R"))))))
     (propagated-inputs (list r-annotationdbi
                              r-biocgenerics
                              r-biocparallel
@@ -6575,7 +6586,8 @@ heterogeneity in the original high-dimensional space.")
                              r-rsamtools
                              r-rtracklayer
                              r-s4vectors))
-    (native-inputs (list r-knitr r-testthat))
+    (native-inputs (list r-derfinderdata r-knitr r-testthat
+                         r-txdb-hsapiens-ucsc-hg19-knowngene))
     (home-page "https://github.com/lcolladotor/derfinder";)
     (synopsis
      "Annotation-agnostic differential expression analysis of RNA-seq data")