guix_mirror_bot pushed a commit to branch r-team
in repository guix.
commit 0dde77a0b375e283a763c3481b615bcdcf90ef04
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Tue Nov 25 13:33:54 2025 +0100
gnu: r-screpertoire: Update to 2.5.8.
* gnu/packages/bioconductor.scm (r-screpertoire): Update to 2.5.8.
[propagated-inputs]: Remove r-assertthat, r-cubature, r-plyr, r-reshape2,
r-stringdist,
r-stringr, r-truncdist, and r-vgam; add r-immapex and r-matrix.
[native-inputs]: Remove r-devtools, r-seurat, r-vdiffr, and r-withr.
[arguments]: Adjust phase 'delete-bad-tests.
Change-Id: Ic8e9aaacf3d397e881aab2b73585df098567b3f5
---
gnu/packages/bioconductor.scm | 50 +++++++++++++++++++------------------------
1 file changed, 22 insertions(+), 28 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 46138203ea..45c9cf8550 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13563,13 +13563,13 @@ different experiment.")
(define-public r-screpertoire
(package
(name "r-screpertoire")
- (version "2.4.0")
+ (version "2.5.8")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scRepertoire" version))
(sha256
- (base32 "1lywcwh7zbjnfad2lxma5xxq33ah0kai65nxahls0lfk0j4xibyw"))))
+ (base32 "0ijycpmaivcqqmdc90h5jx8rcwg9112pl2mdpms1hgvww70x3s6w"))))
(properties
'((upstream-name . "scRepertoire")))
(build-system r-build-system)
@@ -13580,54 +13580,48 @@ different experiment.")
(add-after 'unpack 'disable-bad-tests
(lambda _
;; These attempt to connect to the Internet.
- (substitute* "tests/testthat/test-clonalCluster.R"
- ((".*clonalCluster works.*" m)
- (string-append m "skip('guix')\n")))
- (substitute* "tests/testthat/test-loadContigs.R"
- ((".*loadContigs.*works.*" m)
+ (substitute* "tests/testthat/test-getContigDoublets.R"
+ ((".*getContigDoublets works for no doublets.*" m)
+ (string-append m "skip('guix')\n"))
+ ((".*getContigDoublets works for inputs with doublets.*" m)
(string-append m "skip('guix')\n")))
(substitute* "tests/testthat/test-combineContigs.R"
((".*combineBCR works.*" m)
- (string-append m "skip('guix')\n")));
- ;; Small, Rare, and None are not included in the data.
- (substitute* "tests/testthat/test-utils.R"
- ((".*filteringNA.*works.*" m)
+ (string-append m "skip('guix')\n")))
+ (substitute* "tests/testthat/test-loadContigs.R"
+ ((".*loadContigs correctly auto-detects and processes various
formats.*" m)
+ (string-append m "skip('guix')\n"))
+ ((".*loadContigs correctly processes various formats from
URL.*" m)
+ (string-append m "skip('guix')\n")))
+ ;; These fail with: Unknown property set: 'kideraFactors'.
+ (substitute* "tests/testthat/test-positionalProperty.R"
+ ((".*positionalProperty: Output structure is correct.*" m)
+ (string-append m "skip('guix')\n"))
+ ((".*positionalProperty: ggplot object is correctly formed.*" m)
(string-append m "skip('guix')\n"))))))))
(propagated-inputs
- (list r-assertthat
- r-cubature
- r-dplyr
+ (list r-dplyr
r-evmix
r-ggalluvial
r-ggdendro
r-ggplot2
r-ggraph
r-igraph
+ r-immapex
r-inext
r-lifecycle
- r-plyr
+ r-matrix
r-purrr
r-quantreg
r-rcpp
- r-reshape2
r-rjson
r-rlang
r-s4vectors
r-seuratobject
r-singlecellexperiment
- r-stringdist
- r-stringr
r-summarizedexperiment
- r-tidygraph
- r-truncdist
- r-vgam))
- (native-inputs (list r-devtools
- r-knitr
- r-seurat
- r-spelling
- r-testthat
- r-vdiffr
- r-withr))
+ r-tidygraph))
+ (native-inputs (list r-knitr r-spelling r-testthat))
(home-page "https://bioconductor.org/packages/scRepertoire";)
(synopsis "Toolkit for single-cell immune receptor profiling")
(description
