From 8bf5832379202f940bce2cc9673fd2db5da855a2 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Wed, 15 Jul 2026 14:42:52 +0200
Subject: gnu: Remove r-monocle3.

* gnu/packages/bioconductor.scm (r-monocle3): Delete variable.
---
 gnu/packages/bioconductor.scm | 88 -------------------------------------------
 1 file changed, 88 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5ee2636a1c6..3c5ec9f77c5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -18299,94 +18299,6 @@ testing context, sansSouci provides statistical guarantees on possibly
 user-defined and/or data-driven sets of hypotheses.")
       (license license:gpl3))))
 
-(define-public r-monocle3
-  (let ((commit "98402ed0c10cac020524bebbb9300614a799f6d1")
-        (revision "1"))
-    (package
-      (name "r-monocle3")
-      (version (git-version "1.3.7" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/cole-trapnell-lab/monocle3")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "1qs4qcdz9hcq966qcr7xvkpx3ri8g1n5psfwik09m7ngzpdd1r5q"))))
-      (properties `((upstream-name . "monocle3")))
-      (build-system r-build-system)
-      ;; FIXME Tests are apparently broken.  30 of them fail with accuracy
-      ;; errors.
-      (arguments (list #:tests? #false))
-      (propagated-inputs
-       (list r-assertthat
-             r-batchelor
-             r-biobase
-             r-biocgenerics
-             r-biocparallel
-             r-delayedarray
-             r-delayedmatrixstats
-             r-digest
-             r-dplyr
-             r-future
-             r-ggplot2
-             r-ggrastr
-             r-ggrepel
-             r-grr
-             r-hdf5array
-             r-igraph
-             r-irlba
-             r-leidenbase
-             r-limma
-             r-lme4
-             r-lmtest
-             r-mass
-             r-matrix
-             r-openssl
-             r-pbapply
-             r-pbmcapply
-             r-pheatmap
-             r-plotly
-             r-plyr
-             r-proxy
-             r-pscl
-             r-purrr
-             r-rann
-             r-rcolorbrewer
-             r-rcpp
-             r-rcppannoy
-             r-rcpphnsw
-             r-reshape2
-             r-rhpcblasctl
-             r-rsample
-             r-rtsne
-             r-s4vectors
-             r-sf
-             r-shiny
-             r-singlecellexperiment
-             r-slam
-             r-spdep
-             r-speedglm
-             r-stringr
-             r-summarizedexperiment
-             r-tibble
-             r-tidyr
-             r-uwot
-             r-viridis))
-      (native-inputs (list r-knitr r-testthat))
-      (home-page "https://github.com/cole-trapnell-lab/monocle3")
-      (synopsis "Analysis toolkit for single-cell RNA-Seq data")
-      (description
-       "Monocle 3 performs clustering, differential expression and trajectory
-analysis for single-cell expression experiments.  It orders individual cells
-according to progress through a biological process, without knowing ahead of
-time which genes define progress through that process.  Monocle 3 also
-performs differential expression analysis, clustering, visualization, and
-other useful tasks on single-cell expression data.  It is designed to work
-with RNA-Seq data, but could be used with other types as well.")
-      (license license:expat))))
-
 (define-public r-noiseq
   (package
     (name "r-noiseq")
-- 
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