import: Add Bioconductor importer and updater.
* guix/import/cran.scm (%bioconductor-updater, latest-bioconductor-release, bioconductor-package?): New procedures. (cran->guix-package): Support repositories other than CRAN. (%bioconductor-url, %bioconductor-svn-url): New variables. (description->package): Update signature to distinguish between packages from different repositories. (latest-release): Rename procedure ... (latest-cran-release): ... to this. (cran-package?): Do not assume all R packages are available on CRAN. * tests/cran.scm: Update tests. * guix/scripts/import/cran.scm: Add "--archive" option and default to CRAN. * guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater". * doc/guix.texi: Document Bioconductor importer and updater.
This commit is contained in:
Ricardo Wurmus
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4c3d2b2a8f
commit
d0bd632f89
@ -4279,11 +4279,12 @@ guix import cpan Acme::Boolean
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@item cran
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@cindex CRAN
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@cindex Bioconductor
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Import meta-data from @uref{http://cran.r-project.org/, CRAN}, the
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central repository for the @uref{http://r-project.org, GNU@tie{}R
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statistical and graphical environment}.
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Information is extracted from the package's DESCRIPTION file.
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Information is extracted from the package's @code{DESCRIPTION} file.
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The command command below imports meta-data for the @code{Cairo}
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R package:
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@ -4292,6 +4293,21 @@ R package:
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guix import cran Cairo
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@end example
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When @code{--archive=bioconductor} is added, meta-data is imported from
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@uref{http://www.bioconductor.org/, Bioconductor}, a repository of R
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packages for for the analysis and comprehension of high-throughput
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genomic data in bioinformatics.
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Information is extracted from a package's @code{DESCRIPTION} file
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published on the web interface of the Bioconductor SVN repository.
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The command command below imports meta-data for the @code{GenomicRanges}
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R package:
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@example
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guix import cran --archive=bioconductor GenomicRanges
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@end example
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@item nix
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Import meta-data from a local copy of the source of the
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@uref{http://nixos.org/nixpkgs/, Nixpkgs distribution}@footnote{This
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@ -4490,6 +4506,8 @@ the updater for GNOME packages;
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the updater for @uref{http://elpa.gnu.org/, ELPA} packages;
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@item cran
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the updater for @uref{http://cran.r-project.org/, CRAN} packages;
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@item bioconductor
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the updater for @uref{http://www.bioconductor.org/, Bioconductor} R packages;
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@item pypi
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the updater for @uref{https://pypi.python.org, PyPI} packages.
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@end table
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@ -29,12 +29,14 @@
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#:use-module (guix base32)
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#:use-module ((guix download) #:select (download-to-store))
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#:use-module (guix import utils)
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#:use-module ((guix build-system r) #:select (cran-uri))
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#:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri))
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#:use-module (guix upstream)
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#:use-module (guix packages)
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#:use-module (gnu packages)
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#:export (cran->guix-package
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%cran-updater))
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bioconductor->guix-package
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%cran-updater
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%bioconductor-updater))
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;;; Commentary:
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;;;
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@ -108,6 +110,15 @@ package definition."
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`((,type (,'quasiquote ,(format-inputs package-inputs)))))))
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(define %cran-url "http://cran.r-project.org/web/packages/")
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(define %bioconductor-url "http://bioconductor.org/packages/")
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;; The latest Bioconductor release is 3.2. Bioconductor packages should be
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;; updated together.
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(define %bioconductor-svn-url
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(string-append "https://readonly:readonly@"
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"hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/"
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"madman/Rpacks/"))
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(define (fetch-description base-url name)
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"Return an alist of the contents of the DESCRIPTION file for the R package
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@ -136,24 +147,31 @@ empty list when the FIELD cannot be found."
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(string-any char-set:whitespace item)))
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(map string-trim-both items))))))
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(define (description->package meta)
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"Return the `package' s-expression for a CRAN package from the alist META,
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which was derived from the R package's DESCRIPTION file."
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(define (description->package repository meta)
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"Return the `package' s-expression for an R package published on REPOSITORY
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from the alist META, which was derived from the R package's DESCRIPTION file."
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(define (guix-name name)
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(if (string-prefix? "r-" name)
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(string-downcase name)
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(string-append "r-" (string-downcase name))))
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(let* ((name (assoc-ref meta "Package"))
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(let* ((base-url (case repository
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((cran) %cran-url)
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((bioconductor) %bioconductor-url)))
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(uri-helper (case repository
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((cran) cran-uri)
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((bioconductor) bioconductor-uri)))
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(name (assoc-ref meta "Package"))
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(synopsis (assoc-ref meta "Title"))
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(version (assoc-ref meta "Version"))
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(license (string->license (assoc-ref meta "License")))
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;; Some packages have multiple home pages. Some have none.
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(home-page (match (listify meta "URL")
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((url rest ...) url)
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(_ (string-append %cran-url name))))
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(source-url (match (cran-uri name version)
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(_ (string-append base-url name))))
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(source-url (match (uri-helper name version)
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((url rest ...) url)
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((? string? url) url)
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(_ #f)))
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(tarball (with-store store (download-to-store store source-url)))
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(sysdepends (map string-downcase (listify meta "SystemRequirements")))
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@ -167,26 +185,32 @@ which was derived from the R package's DESCRIPTION file."
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(version ,version)
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(source (origin
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(method url-fetch)
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(uri (cran-uri ,name version))
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(uri (,(procedure-name uri-helper) ,name version))
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(sha256
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(base32
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,(bytevector->nix-base32-string (file-sha256 tarball))))))
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(properties ,`(,'quasiquote ((,'upstream-name . ,name))))
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,@(if (not (equal? (string-append "r-" name)
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(guix-name name)))
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`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
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'())
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(build-system r-build-system)
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,@(maybe-inputs sysdepends)
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,@(maybe-inputs propagate 'propagated-inputs)
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(home-page ,(if (string-null? home-page)
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(string-append %cran-url name)
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(string-append base-url name)
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home-page))
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(synopsis ,synopsis)
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(description ,(beautify-description (assoc-ref meta "Description")))
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(license ,license))))
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(define (cran->guix-package package-name)
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"Fetch the metadata for PACKAGE-NAME from cran.r-project.org, and return the
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`package' s-expression corresponding to that package, or #f on failure."
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(let ((module-meta (fetch-description %cran-url package-name)))
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(and=> module-meta description->package)))
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(define* (cran->guix-package package-name #:optional (repo 'cran))
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"Fetch the metadata for PACKAGE-NAME from REPO and return the `package'
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s-expression corresponding to that package, or #f on failure."
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(let* ((url (case repo
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((cran) %cran-url)
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((bioconductor) %bioconductor-svn-url)))
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(module-meta (fetch-description url package-name)))
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(and=> module-meta (cut description->package repo <>))))
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;;;
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@ -212,7 +236,7 @@ which was derived from the R package's DESCRIPTION file."
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(_ #f)))
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(_ #f)))))
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(define (latest-release package)
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(define (latest-cran-release package)
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"Return an <upstream-source> for the latest release of PACKAGE."
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(define upstream-name
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@ -229,16 +253,55 @@ which was derived from the R package's DESCRIPTION file."
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(version version)
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(urls (cran-uri upstream-name version))))))
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(define (latest-bioconductor-release package)
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"Return an <upstream-source> for the latest release of PACKAGE."
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(define upstream-name
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(package->upstream-name (specification->package package)))
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(define meta
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(fetch-description %bioconductor-svn-url upstream-name))
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(and meta
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(let ((version (assoc-ref meta "Version")))
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;; Bioconductor does not provide signatures.
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(upstream-source
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(package package)
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(version version)
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(urls (bioconductor-uri upstream-name version))))))
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(define (cran-package? package)
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"Return true if PACKAGE is an R package from CRAN."
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;; Assume all R packages are available on CRAN.
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(string-prefix? "r-" (package-name package)))
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(and (string-prefix? "r-" (package-name package))
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(match (and=> (package-source package) origin-uri)
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((? string? uri)
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(string-prefix? "mirror://cran" uri))
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((? list? uris)
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(any (cut string-prefix? "mirror://cran" <>) uris))
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(_ #f))))
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(define (bioconductor-package? package)
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"Return true if PACKAGE is an R package from Bioconductor."
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(and (string-prefix? "r-" (package-name package))
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(match (and=> (package-source package) origin-uri)
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((? string? uri)
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(string-prefix? "http://bioconductor.org" uri))
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((? list? uris)
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(any (cut string-prefix? "http://bioconductor.org" <>) uris))
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(_ #f))))
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(define %cran-updater
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(upstream-updater
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(name 'cran)
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(description "Updater for CRAN packages")
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(pred cran-package?)
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(latest latest-release)))
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(latest latest-cran-release)))
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(define %bioconductor-updater
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(upstream-updater
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(name 'bioconductor)
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(description "Updater for Bioconductor packages")
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(pred bioconductor-package?)
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(latest latest-bioconductor-release)))
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;;; cran.scm ends here
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@ -41,6 +41,8 @@
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(define (show-help)
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(display (_ "Usage: guix import cran PACKAGE-NAME
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Import and convert the CRAN package for PACKAGE-NAME.\n"))
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(display (_ "
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-a, --archive=ARCHIVE specify the archive repository"))
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(display (_ "
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-h, --help display this help and exit"))
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(display (_ "
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@ -57,6 +59,10 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
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(option '(#\V "version") #f #f
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(lambda args
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(show-version-and-exit "guix import cran")))
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(option '(#\a "archive") #t #f
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(lambda (opt name arg result)
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(alist-cons 'repo (string->symbol arg)
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(alist-delete 'repo result))))
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%standard-import-options))
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@ -82,7 +88,8 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
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(reverse opts))))
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(match args
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((package-name)
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(let ((sexp (cran->guix-package package-name)))
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(let ((sexp (cran->guix-package package-name
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(or (assoc-ref opts 'repo) 'cran))))
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(unless sexp
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(leave (_ "failed to download description for package '~a'~%")
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package-name))
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@ -195,6 +195,7 @@ unavailable optional dependencies such as Guile-JSON."
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%gnome-updater
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%elpa-updater
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%cran-updater
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%bioconductor-updater
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((guix import pypi) => %pypi-updater)))
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(define (lookup-updater name)
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@ -107,7 +107,7 @@ Date/Publication: 2015-07-14 14:15:16
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("mirror://cran/src/contrib/My-Example_1.2.3.tar.gz"
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"source")
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(_ (error "Unexpected URL: " url))))))))
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(match ((@@ (guix import cran) description->package) description-alist)
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(match ((@@ (guix import cran) description->package) 'cran description-alist)
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(('package
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('name "r-my-example")
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('version "1.2.3")
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