diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2025-01-22 08:51:06 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2025-01-22 08:52:22 +0100 |
| commit | 617c42ac30093205a2626ced22a09e34d014a19c (patch) | |
| tree | 6f1f65c21699adad8e25b4cf275b8dab41b67ec7 | |
| parent | b6b35e29665187345bb34a92b37466bfe25e8be3 (diff) | |
| download | guix-617c42ac30093205a2626ced22a09e34d014a19c.tar.gz guix-617c42ac30093205a2626ced22a09e34d014a19c.zip | |
gnu: r-voltron: Update to 0.2.0-2.bbd7abb.
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-2.bbd7abb.
[arguments]: Add phase 'do-not-use-conda.
[propagated-inputs]: Remove r-basilisk; add r-pizzarr and r-rhdf5.
Change-Id: I4c57c154c8bac41d056fadb936a109ca6310d8d6
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 32 |
1 files changed, 24 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2db69d1c17..2af6221dec 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -22212,8 +22212,8 @@ patterns.") (license license:gpl3)))) (define-public r-voltron - (let ((commit "9f9415c72e9347f578a166981842d33e43b0466d") - (revision "1")) + (let ((commit "bbd7abb72681ae6dc91cb2f8fe4f3ce3a246f56b") + (revision "2")) (package (name "r-voltron") (version (git-version "0.2.0" revision commit)) @@ -22225,14 +22225,29 @@ patterns.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0bvvpj96ix2ij6034dfrh7za1lvf73qxqsdvbs2wrpc931s18q32")))) + (base32 "1h5m2r2hdp73yqsz60wq1sf98dbsqpx155qlxbxnzvhc0l8hjshd")))) (properties `((upstream-name . "VoltRon"))) (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; By default VoltRon will use Basilisk, which uses Conda to set + ;; up a Python environment. We override the fallback default + ;; here. Users can still override the location of the Python + ;; interpreter with the option "voltron.python.path". + (add-after 'unpack 'do-not-use-conda + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "R/conversion.R" + (("return\\(NULL\\)") + (string-append "Sys.setenv(GUIX_PYTHONPATH=\"" + (getenv "GUIX_PYTHONPATH") + "\"); return(\"" + (search-input-file inputs "/bin/python3") + "\")")))))))) (inputs (list opencv - ;; These Python inputs would be fetched by Basilisk via Conda. - ;; We add these inputs in anticipation of an upstream change to - ;; allow for a Conda-free use of the package. + ;; These Python inputs are used via reticulate. python python-numpy python-pandas @@ -22245,8 +22260,7 @@ patterns.") python-tifffile python-zarr zlib)) - (propagated-inputs (list r-basilisk - r-data-table + (propagated-inputs (list r-data-table r-dplyr r-ebimage r-ggplot2 @@ -22257,6 +22271,7 @@ patterns.") r-irlba r-magick r-matrix + r-pizzarr r-rann r-rcdt r-rcpp @@ -22264,6 +22279,7 @@ patterns.") r-rcpparmadillo r-reshape2 r-reticulate + r-rhdf5 r-rjson r-rlang r-s4arrays |