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.master
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@ -59,7 +59,7 @@
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages web)
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#:use-module (gnu packages web)
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#:use-module (gnu packages xml)
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#:use-module (gnu packages xml)
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#:use-module (srfi srfi-1))
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#:use-module ((srfi srfi-1) #:hide (zip)))
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;;; Annotations
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;;; Annotations
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@ -4341,16 +4341,53 @@ set analyses, and can deal with repeated or longitudinal data.")
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(define-public r-debcam
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(define-public r-debcam
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(package
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(package
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(name "r-debcam")
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(name "r-debcam")
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(version "1.16.0")
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(version "1.18.0")
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(source (origin
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(source (origin
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(method url-fetch)
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(method url-fetch)
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(uri (bioconductor-uri "debCAM" version))
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(uri (bioconductor-uri "debCAM" version))
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(sha256
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(sha256
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(base32
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(base32
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"09dm861adbxdy3ncfdxq46wjr4hpn56c66n64xm9gwzkzsrxyc2a"))))
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"11vqfkyd3fklc8fhn850kklph8x4pmwclb9xbqji4i21222m89hh"))
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(snippet
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'(for-each delete-file
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'("inst/java/CornerDetect.jar"
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"inst/java/lib/pj20150107.jar")))))
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(properties `((upstream-name . "debCAM")))
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(properties `((upstream-name . "debCAM")))
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(build-system r-build-system)
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(build-system r-build-system)
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(inputs (list openjdk))
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(arguments
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(list
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;; XXX: since the upgrade to R 4.3.0 this package takes too long to be
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;; loaded.
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#:tests? #false
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#:configure-flags '(list "--fake")
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#:modules
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'((guix build r-build-system)
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((guix build ant-build-system) #:prefix ant:)
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(guix build utils))
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#:imported-modules
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`((guix build ant-build-system)
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,@%r-build-system-modules)
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#:phases
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'(modify-phases %standard-phases
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(add-after 'unpack 'build-jar
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(lambda* (#:key inputs #:allow-other-keys)
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(install-file
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(search-input-file inputs "/share/java/pj20150107.jar")
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"inst/java/lib")
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(with-directory-excursion "java"
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(mkdir "build")
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(invoke "javac" "-d" "./build"
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"-cp" "../inst/java/lib/pj20150107.jar"
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"CornerDetectTopN.java"
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"FixSizedPriorityQueue.java")
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(with-directory-excursion "build"
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(apply invoke "jar" "cvf" "../../inst/java/CornerDetect.jar"
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(find-files "."))))))
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(add-after 'install 'strip-jar-timestamps
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(assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))
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(inputs
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(list (list icedtea "jdk")
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java-pj))
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(propagated-inputs
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(propagated-inputs
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(list r-apcluster
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(list r-apcluster
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r-biobase
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r-biobase
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@ -4363,7 +4400,8 @@ set analyses, and can deal with repeated or longitudinal data.")
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r-pcapp
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r-pcapp
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r-rjava
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r-rjava
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r-summarizedexperiment))
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r-summarizedexperiment))
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(native-inputs (list r-knitr))
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(native-inputs
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(list r-knitr zip))
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(home-page "https://bioconductor.org/packages/debCAM")
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(home-page "https://bioconductor.org/packages/debCAM")
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(synopsis "Deconvolution by convex analysis of mixtures")
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(synopsis "Deconvolution by convex analysis of mixtures")
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(description
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(description
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