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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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GPG key ID: 197A5888235FACAC
1 changed files with 61 additions and 53 deletions
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gnu/packages/bioinformatics.scm
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@ -18755,58 +18755,66 @@ Mixtures.")
;; Needed for r-liana
(define-public r-omnipathr/devel
(let ((commit "679bb79e319af246a16968d27d64d8d6937a331a")
(revision "1"))
(package
(name "r-omnipathr")
(version (git-version "3.5.5" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/saezlab/omnipathr")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"10h6lyapyx4ik8r4kx5z2dly46jlf2v57caq4g6i0hzifyz2vgjq"))))
(properties `((upstream-name . "OmnipathR")))
(build-system r-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
(list r-checkmate
r-crayon
r-curl
r-digest
r-dplyr
r-httr
r-igraph
r-jsonlite
r-later
r-logger
r-magrittr
r-progress
r-purrr
r-rappdirs
r-readr
r-readxl
r-rlang
r-rvest
r-stringr
r-tibble
r-tidyr
r-tidyselect
r-withr
r-xml2
r-yaml))
(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
(package
(name "r-omnipathr")
(version "3.15.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/saezlab/omnipathr")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0sq32s3v7q5w9zym54fm0ws1d1wnwyhczazyk9g722ydx2zvbls4"))))
(properties `((upstream-name . "OmnipathR")))
(build-system r-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
(list r-checkmate
r-crayon
r-curl
r-digest
r-dplyr
r-fs
r-httr2
r-igraph
r-jsonlite
r-later
r-logger
r-lubridate
r-magrittr
r-progress
r-purrr
r-r-utils
r-rappdirs
r-readr
r-readxl
r-rlang
r-rmarkdown
r-rsqlite
r-rvest
r-sessioninfo
r-stringi
r-stringr
r-tibble
r-tidyr
r-tidyselect
r-vctrs
r-withr
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
some of the downloaded data, functions to access a number of other resources
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
activity prediction from transcriptomics data, and its R implementation
@code{nichenetr}.")
(license license:expat))))
(license license:expat)))
(define-public r-liana
(let ((commit "10d81773e0874de676eb106ce56e3cf9d4fe01d3")