From 86ea888ceb9b4a9f4269bd1d94d44998d19ea8d4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 31 Mar 2026 14:09:31 +0200
Subject: [PATCH] gnu: r-biomformat: Update to 1.38.3.

* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.38.3.
[arguments]: Remove phase 'testthat-compatibility.
[propagated-inputs]: Remove r-plyr.

Change-Id: I67e973b606f8135b0c4ef0dbf2d29229d87522a4
---
 gnu/packages/bioconductor.scm | 16 +++-------------
 1 file changed, 3 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7b79a971c1..4422cca11f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -28451,28 +28451,18 @@ separate published packages.")
 (define-public r-biomformat
   (package
     (name "r-biomformat")
-    (version "1.38.0")
+    (version "1.38.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomformat" version))
        (sha256
         (base32
-         "1ydcgifdrgg48y7qxg0gw30h332y3yk3k3n17fajkv58mlvyx1yc"))))
+         "0b0w0mfx448ph8fla3nb4i50mvpnv498kxip7rnh14xwas9rhdd7"))))
     (properties `((upstream-name . "biomformat")))
     (build-system r-build-system)
-    (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-IO.R"
-               (("is_true\\(\\)") "expect_true")
-               (("is_false\\(\\)") "expect_false")))))))
     (propagated-inputs
-     (list r-jsonlite r-matrix r-plyr r-rhdf5))
+     (list r-jsonlite r-matrix r-rhdf5))
     (native-inputs (list r-knitr r-testthat))
     (home-page "https://github.com/joey711/biomformat/")
     (synopsis "Interface package for the BIOM file format")