guix_mirror_bot pushed a commit to branch master
in repository guix.
commit e817a66e7b5727078613b025c82b9c9633e3b2b0
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Fri Feb 20 11:10:58 2026 +0100
gnu: r-anndatar: Update to 1.0.1.
anndataR is now on Bioconductor.
* gnu/packages/bioinformatics.scm (r-anndatar): Move from here...
* gnu/packages/bioconductor.scm (r-anndatar): ...to here; update to 1.0.1.
[properties]: Remove updater-extra-native-inputs.
[inputs]: Add python-wrapper and python-anndata.
[native-inputs]: Add r-processx, r-s4vectors, r-seurat, r-spelling, and
r-withr; remove r-vctrs.
[propagated-inputs]: Add r-cli, r-lifecycle, r-purrr, r-reticulate, and
r-rlang.
Change-Id: I2410f00b33451c60d8b1657ac30a6c1b014e260d
---
gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 37 -------------------------------
2 files changed, 49 insertions(+), 37 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3856127ff4..7d25eb989c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -63,6 +63,7 @@
#:use-module (gnu packages ncurses)
#:use-module (gnu packages netpbm)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-science)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
@@ -4578,6 +4579,54 @@ Powerful interactive and dynamic figures generated by
animalcules enable users
to understand their data better and discover new insights.")
(license license:artistic2.0)))
+(define-public r-anndatar
+ (package
+ (name "r-anndatar")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "anndataR" version))
+ (sha256
+ (base32 "1vi9aqgdjy0nlbsk7628sz12jsxd9bfb79yxhh0ngijpxj9sxd4p"))))
+ (properties `((upstream-name . "anndataR")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'find-python
+ (lambda _
+ (setenv "RETICULATE_PYTHON" (which "python3")))))))
+ (propagated-inputs (list r-cli
+ r-lifecycle
+ r-matrix
+ r-purrr
+ r-r6
+ r-reticulate
+ r-rlang))
+ (inputs (list python-wrapper
+ python-anndata))
+ (native-inputs (list r-knitr
+ r-processx
+ r-rhdf5
+ r-s4vectors
+ r-seurat
+ r-seuratobject
+ r-singlecellexperiment
+ r-spelling
+ r-testthat
+ r-withr))
+ (home-page "https://anndatar.data-intuitive.com";)
+ (synopsis "AnnData interoperability in R")
+ (description
+ "This package aims to bring the power and flexibility of @code{AnnData}
+to the R ecosystem, allowing you to effortlessly manipulate and analyze your
+single-cell data. This package lets you work with backed h5ad and zarr files,
+directly access various slots (e.g. X, obs, var), or convert the data into
+@code{SingleCellExperiment} and Seurat objects.")
+ (license license:expat)))
+
(define-public r-annotationhubdata
(package
(name "r-annotationhubdata")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0dfb5869cb..92f3b49714 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -813,43 +813,6 @@ experiments for downstream dataset integration. It
improves conventional
usage of highly-variable genes for integration tasks.")
(license license:gpl3+))))
-(define-public r-anndatar
- (let ((commit "5c3eb7e498d0d9bf1c522ad66f4eb8ad277238b6")
- (revision "1"))
- (package
- (name "r-anndatar")
- (version (git-version "0.99.0" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/scverse/anndataR";)
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0sx87i8cb4p08ihgpgflxs0fhkr1kw6lxvky4w766rq7wqy41cgk"))))
- (properties
- '((upstream-name . "anndataR")
- (updater-extra-native-inputs . ("r-vctrs"))))
- (build-system r-build-system)
- (propagated-inputs (list r-matrix r-r6))
- (native-inputs
- (list r-knitr
- r-rhdf5
- r-seuratobject
- r-singlecellexperiment
- r-testthat
- r-vctrs))
- (home-page "https://github.com/scverse/anndataR";)
- (synopsis "AnnData interoperability in R")
- (description
- "This package aims to bring the power and flexibility of @code{AnnData}
-to the R ecosystem, allowing you to effortlessly manipulate and analyze your
-single-cell data. This package lets you work with backed h5ad and zarr files,
-directly access various slots (e.g. X, obs, var), or convert the data into
-@code{SingleCellExperiment} and Seurat objects.")
- (license license:expat))))
-
(define-public r-anpan
(let ((commit "efd4dc4874c418a43104ed3f418283d2451f0483")
(revision "1"))
