diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fa84b19496..e5ba08a982 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7278,32 +7278,15 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-maaslin2
   (package
     (name "r-maaslin2")
-    (version "1.12.0")
+    (version "1.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Maaslin2" version))
        (sha256
-        (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89"))))
+        (base32 "05xha6y6ssf80l4xb7skbjafpqww2d85l4b6wn72r5djidyxxw6y"))))
     (properties `((upstream-name . "Maaslin2")))
     (build-system r-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'check 'remove-timestamps
-            (lambda _
-              (with-directory-excursion
-                  (string-append #$output "/site-library/Maaslin2/doc/demo_output/")
-                ;; Delete this log file with timestamps.
-                (delete-file "maaslin2.log")
-                ;; Replace PDF timestamps with an arbitrary fixed timestamp.
-                (with-fluids ((%default-port-encoding "ISO-8859-1"))
-                  (substitute* (find-files "." "\\.pdf$")
-                    (("/CreationDate \\(D:.*\\)")
-                     "/CreationDate (D:20230301143558)")
-                    (("/ModDate \\(D:.*\\)")
-                     "/ModDate (D:20230301143558)")))))))))
     (propagated-inputs
      (list r-biglm
            r-car
@@ -7320,14 +7303,12 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
            r-logging
            r-lpsymphony
            r-mass
-           r-mumin
            r-metagenomeseq
            r-optparse
            r-pbapply
            r-pcapp
            r-pheatmap
            r-pscl
-           r-rmarkdown
            r-robustbase
            r-vegan))
     (native-inputs (list r-knitr))