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| author | Ben Woodcroft <donttrustben@gmail.com> | 2016-06-16 22:35:08 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-06-21 21:29:17 +1000 |
| commit | 7b3df1e56ea2346211e3ee5d52e197d3a2e674ca (patch) | |
| tree | b7caba0c7950e07ecb74bd8083b75f2242d835d0 | |
| parent | 0846620803685bd35675ebcb4bfcff806c21c990 (diff) | |
| download | patches-7b3df1e56ea2346211e3ee5d52e197d3a2e674ca.tar patches-7b3df1e56ea2346211e3ee5d52e197d3a2e674ca.tar.gz | |
gnu: Add r-vegan.
* gnu/packages/bioinformatics.scm (r-vegan): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
1 files changed, 51 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2ac6e34652..91b40fa20c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3815,6 +3815,57 @@ data in the form of VCF files.") ;; at https://vcftools.github.io/license.html (license license:lgpl3))) +(define-public r-vegan + (package + (name "r-vegan") + (version "2.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "vegan" version)) + (sha256 + (base32 + "10cygzkyg2m0y054ygivqxrkvqz792qsg6bmbdfzaqq37qv4wc7z")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'revert-test-deletion + ;; The distributed sources do not include tests with the CRAN + ;; package. Here we revert the commit + ;; `591d0e8ba1deaaf82445474ec6619c0b43db4e63' which deletes these + ;; tests. There are plans to not delete tests in future as + ;; documented at https://github.com/vegandevs/vegan/issues/181. + (lambda* (#:key inputs #:allow-other-keys) + (zero? + (system* "patch" "-R" "-p1" "-i" + (assoc-ref inputs "r-vegan-delete-tests-patch")))))))) + (native-inputs + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr) + ("r-vegan-delete-tests-patch" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/vegandevs/vegan/commit/" + "591d0e8ba1deaaf82445474ec6619c0b43db4e63.patch")) + (sha256 + (base32 + "0b1bi7y4jjdl3ph721vm9apm51dr2z9piwvhy4355sf2b4kyyj5a")))))) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-lattice" ,r-lattice) + ("r-mgcv" ,r-mgcv) + ("r-permute" ,r-permute))) + (home-page "https://cran.r-project.org/web/packages/vegan") + (synopsis "Functions for community ecology") + (description + "The vegan package provides tools for descriptive community ecology. It +has most basic functions of diversity analysis, community ordination and +dissimilarity analysis. Most of its multivariate tools can be used for other +data types as well.") + (license license:gpl2+))) + (define-public vsearch (package (name "vsearch") |