gnu: r-rliger: Update to 2.2.1.

* gnu/packages/cran.scm (r-rliger, r-liger): Move variable definitions from here...
* gnu/packages/bioconductor.scm (r-rliger, r-liger): ...to here; update to 2.2.1.
[source]: Update source URL; remove obsolete snippet.
[arguments]: Remove phases 'strip-jar-timestamps and 'build-java-part.
[native-inputs]: Remove icedtea, optimizer-src, unzip, and zip; add
r-circlize, r-complexheatmap, r-testthat, and r-viridis.
[propagated-inputs]: Remove r-cowplot, r-dosnow, r-fnn, r-foreach, r-ggrepel,
r-hmisc, r-ica, r-irlba, r-mclust, r-plyr, r-rann-l1, r-riverplot, and
r-rtsne; add r-cli, r-delayedarray, r-hdf5array, r-hdf5r, r-leidenalg, r-lifecycle,
r-magrittr, r-rann, r-rcppplanc, r-rcppprogress, r-rlang, r-s4vectors,
r-scales, and r-uwot.

Change-Id: I35bcdd94954f6fdf5aa641f9756c65a0efe1008e

2 files changed, 48 insertions, 99 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 35bc2018660..cb419001b50 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10738,6 +10738,54 @@ nucleotide sequence analysis.  The package is primarily useful to developers
 of other R packages who wish to make use of HTSlib.")
     (license license:lgpl2.0+)))
 
+(define-public r-rliger
+  (package
+    (name "r-rliger")
+    (version "2.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/welch-lab/liger")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1w849km9b347m56qwr5lr6ymdk7wv22hr224riscm0zrnx402yb3"))))
+    (properties `((upstream-name . "rliger")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-cli
+                             r-delayedarray
+                             r-dplyr
+                             r-ggplot2
+                             r-hdf5array
+                             r-hdf5r
+                             r-leidenalg
+                             r-lifecycle
+                             r-magrittr
+                             r-matrix
+                             r-patchwork
+                             r-rann
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-rcppplanc
+                             r-rcppprogress
+                             r-rlang
+                             r-s4vectors
+                             r-scales
+                             r-uwot))
+    (native-inputs
+     (list r-circlize r-complexheatmap r-knitr r-testthat r-viridis))
+    (home-page "https://github.com/welch-lab/liger")
+    (synopsis "Linked inference of genomic experimental relationships")
+    (description
+     "LIGER is a package for integrating and analyzing multiple single-cell
+datasets. It relies on integrative non-negative matrix factorization to
+identify shared and dataset-specific factors.")
+    (license license:gpl3)))
+
+(define-deprecated-package r-liger
+  r-rliger)
+
 (define-public r-rnbeads
   (package
     (name "r-rnbeads")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d0e6b9d7bad..0fdf3caee40 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -42575,105 +42575,6 @@ read and more reliable, since they follow the DNRY (do not repeat yourself)
 rule.")
     (license license:asl2.0)))
 
-(define-public r-rliger
-  (package
-    (name "r-rliger")
-    (version "0.4.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/MacoskoLab/liger")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
-       (modules '((guix build utils)))
-       (snippet
-        '(delete-file "inst/java/ModularityOptimizer.jar"))))
-    (build-system r-build-system)
-    (arguments
-     (list
-      #:modules '((guix build r-build-system)
-                  ((guix build ant-build-system) #:prefix ant:)
-                  (guix build utils))
-      #:imported-modules `((guix build ant-build-system)
-                           ,@%r-build-system-modules)
-      #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'delete-bad-tests
-           (lambda _
-             ;; One test fails with: could not find function "theme_bw"
-             (delete-file "tests/testthat/test_post_factorization.R")))
-         (add-after 'unpack 'build-java-part
-           (lambda* (#:key inputs #:allow-other-keys)
-             (invoke "unzip" (assoc-ref inputs "optimizer-src"))
-             (for-each (lambda (file) (invoke "javac" file))
-                       (find-files "." "\\.java$"))
-
-             ;; Create a simple manifest.
-             (mkdir-p "META-INF")
-             (with-output-to-file "META-INF/MANIFEST.MF"
-               (lambda _
-                 (display "\
-Manifest-Version: 1.0
-Main-Class: ModularityOptimizer\n")))
-
-             ;; It is important that the manifest appears first.
-             (apply invoke "jar" "cfm" "inst/java/ModularityOptimizer.jar"
-                    "META-INF/MANIFEST.MF"
-                    (find-files "." "\\.class$"))))
-         (add-after 'install 'strip-jar-timestamps
-           (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))
-    (propagated-inputs
-     (list r-cowplot
-           r-dosnow
-           r-dplyr
-           r-fnn
-           r-foreach
-           r-ggplot2
-           r-ggrepel
-           r-hmisc
-           r-ica
-           r-irlba
-           r-matrix
-           r-mclust
-           r-patchwork
-           r-plyr
-           r-rann-l1
-           r-rcpp
-           r-rcpparmadillo
-           r-riverplot
-           r-rtsne
-           r-snow))
-    (native-inputs
-     `(("jdk" ,icedtea "jdk")
-       ;; See https://github.com/MacoskoLab/liger/issues/96
-       ;; The optimizer is released under the Expat license.
-       ("optimizer-src"
-        ,(origin
-           (method url-fetch)
-           (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
-           (sha256
-            (base32
-             "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
-       ("unzip" ,unzip)
-       ("zip" ,zip)
-       ("r-knitr" ,r-knitr)           ;for vignettes
-       ("r-testthat" ,r-testthat)))
-    (home-page "https://github.com/MacoskoLab/liger")
-    (synopsis "Integrate and analyze multiple single-cell datasets")
-    (description
-     "LIGER is a package for integrating and analyzing multiple single-cell
-datasets, developed and maintained by the Macosko lab.  It relies on
-integrative non-negative matrix factorization to identify shared and
-dataset-specific factors.")
-    (license license:gpl3)))
-
-(define-deprecated-package r-liger
-  r-rliger)
-
 (define-public r-harmony
   (package
     (name "r-harmony")