diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2023-04-28 17:59:48 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-04-29 20:27:17 +0200 |
| commit | 52e738d3462a7c35aa9fc12cc97a76ae2bc05b70 (patch) | |
| tree | 83536c9368adcab19678a08db01aaaed1bd46ef4 /gnu/packages/bioconductor.scm | |
| parent | 2bf6f659c490de0832ef8bcdf6fef56544d7bbe4 (diff) | |
gnu: r-debcam: Update to 1.18.0.
* gnu/packages/bioconductor.scm (r-debcam): Update to 1.18.0.
[source]: Delete bundled Java archives.
[arguments]: Add phase 'build-jar; add phase 'strip-jar-timestamps; do a fake
installation and disable tests due to a regression in R 4.3.0.
[inputs]: Replace openjdk with icedtea:jdk; add java-pj.
[native-inputs]: Add zip.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 48 |
1 files changed, 43 insertions, 5 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7439538a9e..9c00fbfa24 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -59,7 +59,7 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages web) #:use-module (gnu packages xml) - #:use-module (srfi srfi-1)) + #:use-module ((srfi srfi-1) #:hide (zip))) ;;; Annotations @@ -4341,16 +4341,53 @@ set analyses, and can deal with repeated or longitudinal data.") (define-public r-debcam (package (name "r-debcam") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "debCAM" version)) (sha256 (base32 - "09dm861adbxdy3ncfdxq46wjr4hpn56c66n64xm9gwzkzsrxyc2a")))) + "11vqfkyd3fklc8fhn850kklph8x4pmwclb9xbqji4i21222m89hh")) + (snippet + '(for-each delete-file + '("inst/java/CornerDetect.jar" + "inst/java/lib/pj20150107.jar"))))) (properties `((upstream-name . "debCAM"))) (build-system r-build-system) - (inputs (list openjdk)) + (arguments + (list + ;; XXX: since the upgrade to R 4.3.0 this package takes too long to be + ;; loaded. + #:tests? #false + #:configure-flags '(list "--fake") + #:modules + '((guix build r-build-system) + ((guix build ant-build-system) #:prefix ant:) + (guix build utils)) + #:imported-modules + `((guix build ant-build-system) + ,@%r-build-system-modules) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'build-jar + (lambda* (#:key inputs #:allow-other-keys) + (install-file + (search-input-file inputs "/share/java/pj20150107.jar") + "inst/java/lib") + (with-directory-excursion "java" + (mkdir "build") + (invoke "javac" "-d" "./build" + "-cp" "../inst/java/lib/pj20150107.jar" + "CornerDetectTopN.java" + "FixSizedPriorityQueue.java") + (with-directory-excursion "build" + (apply invoke "jar" "cvf" "../../inst/java/CornerDetect.jar" + (find-files ".")))))) + (add-after 'install 'strip-jar-timestamps + (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))) + (inputs + (list (list icedtea "jdk") + java-pj)) (propagated-inputs (list r-apcluster r-biobase @@ -4363,7 +4400,8 @@ set analyses, and can deal with repeated or longitudinal data.") r-pcapp r-rjava r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-knitr zip)) (home-page "https://bioconductor.org/packages/debCAM") (synopsis "Deconvolution by convex analysis of mixtures") (description |