diff options
| -rw-r--r-- | doc/guix.texi | 20 | ||||
| -rw-r--r-- | guix/import/cran.scm | 103 | ||||
| -rw-r--r-- | guix/scripts/import/cran.scm | 9 | ||||
| -rw-r--r-- | guix/scripts/refresh.scm | 1 | ||||
| -rw-r--r-- | tests/cran.scm | 2 |
5 files changed, 112 insertions, 23 deletions
diff --git a/doc/guix.texi b/doc/guix.texi index a3d751a296..2a97516084 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -4279,11 +4279,12 @@ guix import cpan Acme::Boolean @item cran @cindex CRAN +@cindex Bioconductor Import meta-data from @uref{http://cran.r-project.org/, CRAN}, the central repository for the @uref{http://r-project.org, GNU@tie{}R statistical and graphical environment}. -Information is extracted from the package's DESCRIPTION file. +Information is extracted from the package's @code{DESCRIPTION} file. The command command below imports meta-data for the @code{Cairo} R package: @@ -4292,6 +4293,21 @@ R package: guix import cran Cairo @end example +When @code{--archive=bioconductor} is added, meta-data is imported from +@uref{http://www.bioconductor.org/, Bioconductor}, a repository of R +packages for for the analysis and comprehension of high-throughput +genomic data in bioinformatics. + +Information is extracted from a package's @code{DESCRIPTION} file +published on the web interface of the Bioconductor SVN repository. + +The command command below imports meta-data for the @code{GenomicRanges} +R package: + +@example +guix import cran --archive=bioconductor GenomicRanges +@end example + @item nix Import meta-data from a local copy of the source of the @uref{http://nixos.org/nixpkgs/, Nixpkgs distribution}@footnote{This @@ -4490,6 +4506,8 @@ the updater for GNOME packages; the updater for @uref{http://elpa.gnu.org/, ELPA} packages; @item cran the updater for @uref{http://cran.r-project.org/, CRAN} packages; +@item bioconductor +the updater for @uref{http://www.bioconductor.org/, Bioconductor} R packages; @item pypi the updater for @uref{https://pypi.python.org, PyPI} packages. @end table diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 1c30da89c7..f36e9482cf 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -29,12 +29,14 @@ #:use-module (guix base32) #:use-module ((guix download) #:select (download-to-store)) #:use-module (guix import utils) - #:use-module ((guix build-system r) #:select (cran-uri)) + #:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri)) #:use-module (guix upstream) #:use-module (guix packages) #:use-module (gnu packages) #:export (cran->guix-package - %cran-updater)) + bioconductor->guix-package + %cran-updater + %bioconductor-updater)) ;;; Commentary: ;;; @@ -108,6 +110,15 @@ package definition." `((,type (,'quasiquote ,(format-inputs package-inputs))))))) (define %cran-url "http://cran.r-project.org/web/packages/") +(define %bioconductor-url "http://bioconductor.org/packages/") + +;; The latest Bioconductor release is 3.2. Bioconductor packages should be +;; updated together. +(define %bioconductor-svn-url + (string-append "https://readonly:readonly@" + "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/" + "madman/Rpacks/")) + (define (fetch-description base-url name) "Return an alist of the contents of the DESCRIPTION file for the R package @@ -136,24 +147,31 @@ empty list when the FIELD cannot be found." (string-any char-set:whitespace item))) (map string-trim-both items)))))) -(define (description->package meta) - "Return the `package' s-expression for a CRAN package from the alist META, -which was derived from the R package's DESCRIPTION file." +(define (description->package repository meta) + "Return the `package' s-expression for an R package published on REPOSITORY +from the alist META, which was derived from the R package's DESCRIPTION file." (define (guix-name name) (if (string-prefix? "r-" name) (string-downcase name) (string-append "r-" (string-downcase name)))) - (let* ((name (assoc-ref meta "Package")) + (let* ((base-url (case repository + ((cran) %cran-url) + ((bioconductor) %bioconductor-url))) + (uri-helper (case repository + ((cran) cran-uri) + ((bioconductor) bioconductor-uri))) + (name (assoc-ref meta "Package")) (synopsis (assoc-ref meta "Title")) (version (assoc-ref meta "Version")) (license (string->license (assoc-ref meta "License"))) ;; Some packages have multiple home pages. Some have none. (home-page (match (listify meta "URL") ((url rest ...) url) - (_ (string-append %cran-url name)))) - (source-url (match (cran-uri name version) + (_ (string-append base-url name)))) + (source-url (match (uri-helper name version) ((url rest ...) url) + ((? string? url) url) (_ #f))) (tarball (with-store store (download-to-store store source-url))) (sysdepends (map string-downcase (listify meta "SystemRequirements"))) @@ -167,26 +185,32 @@ which was derived from the R package's DESCRIPTION file." (version ,version) (source (origin (method url-fetch) - (uri (cran-uri ,name version)) + (uri (,(procedure-name uri-helper) ,name version)) (sha256 (base32 ,(bytevector->nix-base32-string (file-sha256 tarball)))))) - (properties ,`(,'quasiquote ((,'upstream-name . ,name)))) + ,@(if (not (equal? (string-append "r-" name) + (guix-name name))) + `((properties ,`(,'quasiquote ((,'upstream-name . ,name))))) + '()) (build-system r-build-system) ,@(maybe-inputs sysdepends) ,@(maybe-inputs propagate 'propagated-inputs) (home-page ,(if (string-null? home-page) - (string-append %cran-url name) + (string-append base-url name) home-page)) (synopsis ,synopsis) (description ,(beautify-description (assoc-ref meta "Description"))) (license ,license)))) -(define (cran->guix-package package-name) - "Fetch the metadata for PACKAGE-NAME from cran.r-project.org, and return the -`package' s-expression corresponding to that package, or #f on failure." - (let ((module-meta (fetch-description %cran-url package-name))) - (and=> module-meta description->package))) +(define* (cran->guix-package package-name #:optional (repo 'cran)) + "Fetch the metadata for PACKAGE-NAME from REPO and return the `package' +s-expression corresponding to that package, or #f on failure." + (let* ((url (case repo + ((cran) %cran-url) + ((bioconductor) %bioconductor-svn-url))) + (module-meta (fetch-description url package-name))) + (and=> module-meta (cut description->package repo <>)))) ;;; @@ -212,7 +236,7 @@ which was derived from the R package's DESCRIPTION file." (_ #f))) (_ #f))))) -(define (latest-release package) +(define (latest-cran-release package) "Return an <upstream-source> for the latest release of PACKAGE." (define upstream-name @@ -229,16 +253,55 @@ which was derived from the R package's DESCRIPTION file." (version version) (urls (cran-uri upstream-name version)))))) +(define (latest-bioconductor-release package) + "Return an <upstream-source> for the latest release of PACKAGE." + + (define upstream-name + (package->upstream-name (specification->package package))) + + (define meta + (fetch-description %bioconductor-svn-url upstream-name)) + + (and meta + (let ((version (assoc-ref meta "Version"))) + ;; Bioconductor does not provide signatures. + (upstream-source + (package package) + (version version) + (urls (bioconductor-uri upstream-name version)))))) + (define (cran-package? package) "Return true if PACKAGE is an R package from CRAN." - ;; Assume all R packages are available on CRAN. - (string-prefix? "r-" (package-name package))) + (and (string-prefix? "r-" (package-name package)) + (match (and=> (package-source package) origin-uri) + ((? string? uri) + (string-prefix? "mirror://cran" uri)) + ((? list? uris) + (any (cut string-prefix? "mirror://cran" <>) uris)) + (_ #f)))) + +(define (bioconductor-package? package) + "Return true if PACKAGE is an R package from Bioconductor." + (and (string-prefix? "r-" (package-name package)) + (match (and=> (package-source package) origin-uri) + ((? string? uri) + (string-prefix? "http://bioconductor.org" uri)) + ((? list? uris) + (any (cut string-prefix? "http://bioconductor.org" <>) uris)) + (_ #f)))) (define %cran-updater (upstream-updater (name 'cran) (description "Updater for CRAN packages") (pred cran-package?) - (latest latest-release))) + (latest latest-cran-release))) + +(define %bioconductor-updater + (upstream-updater + (name 'bioconductor) + (description "Updater for Bioconductor packages") + (pred bioconductor-package?) + (latest latest-bioconductor-release))) ;;; cran.scm ends here diff --git a/guix/scripts/import/cran.scm b/guix/scripts/import/cran.scm index 8d001ac494..ace1123b90 100644 --- a/guix/scripts/import/cran.scm +++ b/guix/scripts/import/cran.scm @@ -42,6 +42,8 @@ (display (_ "Usage: guix import cran PACKAGE-NAME Import and convert the CRAN package for PACKAGE-NAME.\n")) (display (_ " + -a, --archive=ARCHIVE specify the archive repository")) + (display (_ " -h, --help display this help and exit")) (display (_ " -V, --version display version information and exit")) @@ -57,6 +59,10 @@ Import and convert the CRAN package for PACKAGE-NAME.\n")) (option '(#\V "version") #f #f (lambda args (show-version-and-exit "guix import cran"))) + (option '(#\a "archive") #t #f + (lambda (opt name arg result) + (alist-cons 'repo (string->symbol arg) + (alist-delete 'repo result)))) %standard-import-options)) @@ -82,7 +88,8 @@ Import and convert the CRAN package for PACKAGE-NAME.\n")) (reverse opts)))) (match args ((package-name) - (let ((sexp (cran->guix-package package-name))) + (let ((sexp (cran->guix-package package-name + (or (assoc-ref opts 'repo) 'cran)))) (unless sexp (leave (_ "failed to download description for package '~a'~%") package-name)) diff --git a/guix/scripts/refresh.scm b/guix/scripts/refresh.scm index a5834d12cc..f9e3f31a03 100644 --- a/guix/scripts/refresh.scm +++ b/guix/scripts/refresh.scm @@ -195,6 +195,7 @@ unavailable optional dependencies such as Guile-JSON." %gnome-updater %elpa-updater %cran-updater + %bioconductor-updater ((guix import pypi) => %pypi-updater))) (define (lookup-updater name) diff --git a/tests/cran.scm b/tests/cran.scm index 0a4a2fdd8f..e4f22353bd 100644 --- a/tests/cran.scm +++ b/tests/cran.scm @@ -107,7 +107,7 @@ Date/Publication: 2015-07-14 14:15:16 ("mirror://cran/src/contrib/My-Example_1.2.3.tar.gz" "source") (_ (error "Unexpected URL: " url)))))))) - (match ((@@ (guix import cran) description->package) description-alist) + (match ((@@ (guix import cran) description->package) 'cran description-alist) (('package ('name "r-my-example") ('version "1.2.3") |