From 2cd5b86b8cde9003234fd9c45f452d1e44eb107d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 1 Mar 2025 09:26:49 +0100
Subject: [PATCH] gnu: r-chippeakanno: Fix tests.

* gnu/packages/bioconductor.scm (r-chippeakanno)[properties]: Record
updater-extra-native-inputs.
[arguments]: Add phase 'disable-bad-tests.
[native-inputs]: Add r-seqinr.

Change-Id: I82a17cc5cacf693ce109697e5d2c3cbe1937a420
---
 gnu/packages/bioconductor.scm | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 240aa1f7e2e..55bbac5322f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15618,8 +15618,21 @@ determining dependencies between variables, code improvement suggestions.")
        (sha256
         (base32
          "0zzpmrni4la6d2zws8wxak51lnn9g2i9xbwj1f3micpyn1bxlsc9"))))
-    (properties `((upstream-name . "ChIPpeakAnno")))
+    (properties
+     '((upstream-name . "ChIPpeakAnno")
+       (updater-extra-native-inputs . ("r-seqinr"))))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'disable-bad-tests
+           (lambda _
+             ;; "sequence MT not found", but it's probably because it tries to
+             ;; access the Internet earlier
+             (substitute* "tests/testthat/test_getAllPeakSequence.R"
+               ((".*getAllPeakSequence works not correct.*" m)
+                (string-append m "skip('guix')\n"))))))))
     (propagated-inputs
      (list r-annotationdbi
            r-biocgenerics
@@ -15663,6 +15676,7 @@ determining dependencies between variables, code improvement suggestions.")
            r-org-ce-eg-db
            r-org-hs-eg-db
            r-reactome-db
+           r-seqinr
            r-testthat
            r-txdb-hsapiens-ucsc-hg38-knowngene))
     (home-page "https://bioconductor.org/packages/ChIPpeakAnno")