diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 31 |
1 files changed, 23 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 11d123b605..f1f6a3eb6d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> +;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -7580,13 +7581,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "07zljs2mfi8rf31g903f43v2f7767xbnflfrx9qjnmgf7bm039x0")))) + "0phadr67yb4l25x41a9wg4pjy1wbxlk14jhidhz6g5n4z6x45qbm")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7596,6 +7597,8 @@ ID and species. It is used by functions in the GenomeInfoDb package.") ("r-iranges" ,r-iranges) ("r-rcurl" ,r-rcurl) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GenomeInfoDb") (synopsis "Utilities for manipulating chromosome identifiers") (description @@ -7808,13 +7811,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.42.0") + (version "2.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0difh4dsccjzhpfkvajy2adh98ym9164gd6clnsnic6qr6sk86ss")))) + "0676s8aq9xj2pdrfk28kf5j69fmssn900k4vxrp11ghwjr8z24h7")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7827,6 +7830,8 @@ annotation data packages using SQLite data storage.") ("r-rappdirs" ,r-rappdirs) ("r-stringr" ,r-stringr) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/biomaRt") (synopsis "Interface to BioMart databases") (description @@ -13549,17 +13554,27 @@ allowing the insertion of arbitrary types into the tree.") (define-public python-intervaltree (package (name "python-intervaltree") - (version "2.1.0") + (version "3.0.2") (source (origin (method url-fetch) (uri (pypi-uri "intervaltree" version)) (sha256 (base32 - "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc")))) + "0wz234g6irlm4hivs2qzmnywk0ss06ckagwh15nflkyb3p462kyb")))) (build-system python-build-system) - ;; FIXME: error when collecting tests - (arguments '(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; pytest seems to have a check to make sure the user is testing + ;; their checked-out code and not an installed, potentially + ;; out-of-date copy. This is harmless here, since we just installed + ;; the package, so we disable the check to avoid skipping tests + ;; entirely. + (add-before 'check 'import-mismatch-error-workaround + (lambda _ + (setenv "PY_IGNORE_IMPORTMISMATCH" "1") + #t))))) (propagated-inputs `(("python-sortedcontainers" ,python-sortedcontainers))) (native-inputs |