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gnu: r-omnipathr/devel: Update to 3.15.3.

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* gnu/packages/bioinformatics.scm (r-omnipathr/devel): Update to 3.15.3.
[propagated-inputs]: Add r-fs, r-httr2, r-lubridate, r-r-utils, r-rmarkdown,
r-rsqlite, r-sessioninfo, r-stringi, r-vctrs, r-xml, and r-zip; remove r-httr.

Change-Id: I062eda0ab64edf696d89c4527e353a72dd6c2aa0
This commit is contained in:
Ricardo Wurmus 2025-02-28 11:32:36 +01:00
parent 8814cd92f8
commit f438c38dce
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1 changed files with 61 additions and 53 deletions
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@ -18755,58 +18755,66 @@ Mixtures.")
;; Needed for r-liana ;; Needed for r-liana
(define-public r-omnipathr/devel (define-public r-omnipathr/devel
(let ((commit "679bb79e319af246a16968d27d64d8d6937a331a") (package
(revision "1")) (name "r-omnipathr")
(package (version "3.15.3")
(name "r-omnipathr") (source (origin
(version (git-version "3.5.5" revision commit)) (method git-fetch)
(source (origin (uri (git-reference
(method git-fetch) (url "https://github.com/saezlab/omnipathr")
(uri (git-reference (commit (string-append "v" version))))
(url "https://github.com/saezlab/omnipathr") (file-name (git-file-name name version))
(commit commit))) (sha256
(file-name (git-file-name name version)) (base32
(sha256 "0sq32s3v7q5w9zym54fm0ws1d1wnwyhczazyk9g722ydx2zvbls4"))))
(base32 (properties `((upstream-name . "OmnipathR")))
"10h6lyapyx4ik8r4kx5z2dly46jlf2v57caq4g6i0hzifyz2vgjq")))) (build-system r-build-system)
(properties `((upstream-name . "OmnipathR"))) (arguments
(build-system r-build-system) `(#:phases
(arguments (modify-phases %standard-phases
`(#:phases (add-after 'unpack 'set-HOME
(modify-phases %standard-phases (lambda _ (setenv "HOME" "/tmp"))))))
(add-after 'unpack 'set-HOME (propagated-inputs
(lambda _ (setenv "HOME" "/tmp")))))) (list r-checkmate
(propagated-inputs r-crayon
(list r-checkmate r-curl
r-crayon r-digest
r-curl r-dplyr
r-digest r-fs
r-dplyr r-httr2
r-httr r-igraph
r-igraph r-jsonlite
r-jsonlite r-later
r-later r-logger
r-logger r-lubridate
r-magrittr r-magrittr
r-progress r-progress
r-purrr r-purrr
r-rappdirs r-r-utils
r-readr r-rappdirs
r-readxl r-readr
r-rlang r-readxl
r-rvest r-rlang
r-stringr r-rmarkdown
r-tibble r-rsqlite
r-tidyr r-rvest
r-tidyselect r-sessioninfo
r-withr r-stringi
r-xml2 r-stringr
r-yaml)) r-tibble
(native-inputs (list r-knitr r-testthat)) r-tidyr
(home-page "https://github.com/saezlab/omnipathr") r-tidyselect
(synopsis "OmniPath web service client and more") r-vctrs
(description r-withr
"This package provides a client for the OmniPath web service and many r-xml
r-xml2
r-yaml
r-zip))
(native-inputs (list r-knitr r-testthat))
(home-page "https://github.com/saezlab/omnipathr")
(synopsis "OmniPath web service client and more")
(description
"This package provides a client for the OmniPath web service and many
other resources. It also includes functions to transform and pretty print other resources. It also includes functions to transform and pretty print
some of the downloaded data, functions to access a number of other resources some of the downloaded data, functions to access a number of other resources
such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to
@ -18816,7 +18824,7 @@ RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore,
OmnipathR features a close integration with the NicheNet method for ligand OmnipathR features a close integration with the NicheNet method for ligand
activity prediction from transcriptomics data, and its R implementation activity prediction from transcriptomics data, and its R implementation
@code{nichenetr}.") @code{nichenetr}.")
(license license:expat)))) (license license:expat)))
(define-public r-liana (define-public r-liana
(let ((commit "10d81773e0874de676eb106ce56e3cf9d4fe01d3") (let ((commit "10d81773e0874de676eb106ce56e3cf9d4fe01d3")