From 1ec0fb5d1809fea8a8cde1b55923914236c50e3d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 27 Nov 2025 07:23:02 +0100
Subject: [PATCH] gnu: r-abaenrichment: Adjust for testthat compatibility.

* gnu/packages/bioconductor.scm (r-abaenrichment)[arguments]: Add phase
'testthat-compatibility.

Change-Id: I532339067402d2465b793bb16f6b137c425170ff
---
 gnu/packages/bioconductor.scm | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f9074d00a4548b416482fcad6cc53d5255875ba0..346198385058813b5f02de5fd7376aa3db807fbd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -20273,6 +20273,19 @@ annotations and ontologies.")
         (base32
          "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
     (properties `((upstream-name . "ABAEnrichment")))
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; These deprecated procedures have been removed in testthat.
+         (add-after 'unpack 'testthat-compatibility
+           (lambda _
+             (substitute* '("tests/testthat/test_0load_by_name.R"
+                            "tests/testthat/test_aba_enrich.R"
+                            "tests/testthat/test_detect_identifier.R"
+                            "tests/testthat/test_get_superstructures.R")
+               (("is_true\\(\\)") "expect_true")
+               (("is_false\\(\\)") "expect_false")))))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-abadata