diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9f1913d87d5..cd5455a841b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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")