guix_mirror_bot pushed a commit to branch r-team
in repository guix.
commit 7df6626aea99108c563be4169958a80eb809b8b1
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Thu Mar 12 12:08:09 2026 +0100
gnu: r-rliger: Update to 2.2.1.
* gnu/packages/cran.scm (r-rliger, r-liger): Move variable definitions from
here...
* gnu/packages/bioinformatics.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
---
gnu/packages/bioinformatics.scm | 48 ++++++++++++++++++++
gnu/packages/cran.scm | 99 -----------------------------------------
2 files changed, 48 insertions(+), 99 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 09d99603e0..3dd3dca243 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1483,6 +1483,54 @@ high-throughput 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-scdesign2
(let ((commit "554f2c4b1a7ee6cc04969a287df9b3b77d7bb2fe")
(revision "1"))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d0e6b9d7ba..0fdf3caee4 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")
