39/56: gnu: r-sgseq: Add missing inputs.

[guix-commits]

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

commit d0ed65a2db7e575c2edf950d097ad81d77084923
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Nov 26 11:43:29 2024 +0100

    gnu: r-sgseq: Add missing inputs.
    
    * gnu/packages/bioconductor.scm (r-sgseq)[native-inputs]: Add
    r-bsgenome-hsapiens-ucsc-hg19.
    [arguments]: Add phase 'delete-bad-tests.
    
    Change-Id: I5ff9e2af754700e5ba70ad7bdd1be5ec952946a3
---
 gnu/packages/bioconductor.scm | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9acf6c3cde..372996019b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -18967,6 +18967,14 @@ alignment tool.")
          "1xchrzd384wzm81vzrcixyzn3mgnd343cp544yvfzfn2vxr4y1ij"))))
     (properties `((upstream-name . "SGSeq")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'delete-bad-tests
+           (lambda _
+             ;; This test attempts to download a data file.
+             (delete-file "inst/unitTests/test_predictVariantEffects.R"))))))
     (propagated-inputs
      (list r-annotationdbi
            r-biocgenerics
@@ -18983,7 +18991,7 @@ alignment tool.")
            r-s4vectors
            r-summarizedexperiment))
     (native-inputs
-     (list r-knitr r-runit))
+     (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-runit))
     (home-page "https://bioconductor.org/packages/SGSeq/";)
     (synopsis "Splice event prediction and quantification from RNA-seq data")
     (description