gnu: r-monocle3: Update to 1.3.7.

* gnu/packages/bioconductor.scm (r-monocle3): Update to 1.3.7.
[propagated-inputs]: Remove r-htmlwidgets, r-matrix-utils, r-pryr,
r-rcppparallel, and r-reticulate; add r-biocparallel, r-delayedarray,
r-digest, r-future, r-ggrastr, r-hdf5array, r-lme4, r-openssl, r-plyr,
r-rcolorbrewer, r-rcppannoy, r-rcpphnsw, r-s4vectors, r-sf, and
r-summarizedexperiment.
[native-inputs]: Add r-testthat.
[description]: Expand.
[arguments]: Disable tests.

Change-Id: I0331c5148dce5b282d25edf93e0ccc80397f78ec

gnu/packages/bioconductor.scm

@@ -16218,70 +16218,92 @@ 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 "1.0.0")
+      (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 version)))
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-        (base32
-         "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
+          (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-htmlwidgets
+             r-hdf5array
              r-igraph
              r-irlba
              r-leidenbase
              r-limma
+             r-lme4
              r-lmtest
              r-mass
              r-matrix
-           r-matrix-utils
+             r-openssl
              r-pbapply
              r-pbmcapply
              r-pheatmap
              r-plotly
-           r-pryr
+             r-plyr
              r-proxy
              r-pscl
              r-purrr
              r-rann
+             r-rcolorbrewer
              r-rcpp
-           r-rcppparallel
+             r-rcppannoy
+             r-rcpphnsw
              r-reshape2
-           r-reticulate
              r-rhpcblasctl
              r-rsample
              r-rtsne
+             r-s4vectors
+             r-sf
              r-shiny
+             r-singlecellexperiment
              r-slam
              r-spdep
              r-speedglm
              r-stringr
-           r-singlecellexperiment
+             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 is an analysis toolkit for single-cell RNA-Seq experiments.")
-    (license license:expat)))
+       "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