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

1 files changed, 86 insertions, 64 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3408ebebac..e95713792c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16218,70 +16218,92 @@ user-defined and/or data-driven sets of hypotheses.")
       (license license:gpl3))))
 
 (define-public r-monocle3
-  (package
-    (name "r-monocle3")
-    (version "1.0.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/cole-trapnell-lab/monocle3")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     (list r-assertthat
-           r-batchelor
-           r-biobase
-           r-biocgenerics
-           r-delayedmatrixstats
-           r-dplyr
-           r-ggplot2
-           r-ggrepel
-           r-grr
-           r-htmlwidgets
-           r-igraph
-           r-irlba
-           r-leidenbase
-           r-limma
-           r-lmtest
-           r-mass
-           r-matrix
-           r-matrix-utils
-           r-pbapply
-           r-pbmcapply
-           r-pheatmap
-           r-plotly
-           r-pryr
-           r-proxy
-           r-pscl
-           r-purrr
-           r-rann
-           r-rcpp
-           r-rcppparallel
-           r-reshape2
-           r-reticulate
-           r-rhpcblasctl
-           r-rsample
-           r-rtsne
-           r-shiny
-           r-slam
-           r-spdep
-           r-speedglm
-           r-stringr
-           r-singlecellexperiment
-           r-tibble
-           r-tidyr
-           r-uwot
-           r-viridis))
-    (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)))
+  (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