From 18c5a3b3246d49b89c235ed6ad287c543b159d59 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 29 Nov 2024 09:19:49 +0100
Subject: gnu: r-variantfiltering: Add missing inputs.

* gnu/packages/bioconductor.scm (r-variantfiltering)[native-inputs]: Add
r-biocstyle, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db, and
r-txdb-hsapiens-ucsc-hg19-knowngene.
[properties]: Tell updater to keep extra inputs.
[arguments]: Add phase 'delete-bad-tests; disable vignettes.

Change-Id: I23e78f1bd49b348719c6e03a116228b5657ae379
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ba33c4b405..48ac5ed1ac 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -21457,8 +21457,25 @@ provides methods for retrieving enriched pathways.")
         (base32
          "0839ljb4fh1qrjk1xm89q2hwnbbxi2slaw3l36dk8kmpifhqqi16"))))
     (properties
-     `((upstream-name . "VariantFiltering")))
+     `((upstream-name . "VariantFiltering")
+       (updater-extra-native-inputs
+        . ("r-biocstyle"
+           "r-bsgenome-hsapiens-1000genomes-hs37d5"
+           "r-org-hs-eg-db"
+           "r-txdb-hsapiens-ucsc-hg19-knowngene"))))
     (build-system r-build-system)
+    (arguments
+     (list
+      ;; Vignettes require an obscene amount of humongous annotation packages
+      ;; and *still* attempt to download additional files off the Internet.
+      ;; Enough is enough.
+      #:test-types '(list "tests")
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'delete-bad-tests
+           (lambda _
+             ;; One test tries to connect to a website.
+             (delete-file "inst/unitTests/test_location-methods.R"))))))
     (propagated-inputs
      (list r-annotationdbi
            r-biobase
@@ -21484,7 +21501,12 @@ provides methods for retrieving enriched pathways.")
            r-summarizedexperiment
            r-variantannotation
            r-xvector))
-    (native-inputs (list r-runit))
+    (native-inputs
+     (list r-biocstyle
+           r-bsgenome-hsapiens-1000genomes-hs37d5
+           r-org-hs-eg-db
+           r-runit
+           r-txdb-hsapiens-ucsc-hg19-knowngene))
     (home-page "https://github.com/rcastelo/VariantFiltering")
     (synopsis "Filtering of coding and non-coding genetic variants")
     (description
-- 
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