Merge branch 'master' into core-updates

6 files changed, 112 insertions, 26 deletions

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/import/gem.scm b/guix/import/gem.scm
index 3c42052f1a..4b2a253130 100644
--- a/guix/import/gem.scm
+++ b/guix/import/gem.scm
@@ -77,7 +77,7 @@ the package."
             (bytevector-u8-set! bv i (read-byte i))
             (loop (1+ i)))))))
 
-(define (make-gem-sexp name version hash home-page description
+(define (make-gem-sexp name version hash home-page synopsis description
                        dependencies licenses)
   "Return the `package' s-expression for a Ruby package with the given NAME,
 VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
@@ -101,7 +101,7 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
                          (,'unquote
                           ,(string->symbol name))))
                      dependencies)))))
-     (synopsis ,description)    ; nothing better to use
+     (synopsis ,synopsis)
      (description ,description)
      (home-page ,home-page)
      (license ,(match licenses
@@ -117,6 +117,7 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
          (let ((name         (assoc-ref package "name"))
                (version      (assoc-ref package "version"))
                (hash         (assoc-ref package "sha"))
+               (synopsis     (assoc-ref package "info")) ; nothing better to use
                (description  (beautify-description
                               (assoc-ref package "info")))
                (home-page    (assoc-ref package "homepage_uri"))
@@ -129,5 +130,5 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
                                               "runtime")))
                (licenses     (map string->license
                                   (assoc-ref package "licenses"))))
-           (make-gem-sexp name version hash home-page
+           (make-gem-sexp name version hash home-page synopsis
                           description dependencies licenses)))))
diff --git a/guix/licenses.scm b/guix/licenses.scm
index 9ace7f543b..1def1acb3e 100644
--- a/guix/licenses.scm
+++ b/guix/licenses.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2012, 2013 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -49,7 +50,7 @@
             imlib2
             ipa
             lgpl2.0 lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3 lgpl3+
-            mpl1.1 mpl2.0
+            mpl1.0 mpl1.1 mpl2.0
             ms-pl
             ncsa
             openldap2.8 openssl
@@ -302,6 +303,11 @@ at URI, which may be a file:// URI pointing the package's tree."
            "https://www.gnu.org/licenses/lgpl.html"
            "https://www.gnu.org/licenses/license-list#LGPLv3"))
 
+(define mpl1.0
+  (license "MPL 1.0"
+           "http://www.mozilla.org/MPL/1.0/"
+           "https://www.gnu.org/licenses/license-list.html#MPL"))
+
 (define mpl1.1
   (license "MPL 1.1"
            "http://directory.fsf.org/wiki/License:MPLv1.1"
diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm
index 9193ad32b2..7ca2c6ebc8 100644
--- a/guix/scripts/build.scm
+++ b/guix/scripts/build.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Mark H Weaver <mhw@netris.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -153,6 +153,8 @@ options handled by 'set-build-options-from-command-line', and listed in
   (display (_ "
   -K, --keep-failed      keep build tree of failed builds"))
   (display (_ "
+  -k, --keep-going       keep going when some of the derivations fail"))
+  (display (_ "
   -n, --dry-run          do not build the derivations"))
   (display (_ "
       --fallback         fall back to building when the substituter fails"))
@@ -183,6 +185,7 @@ options handled by 'set-build-options-from-command-line', and listed in
   ;; TODO: Add more options.
   (set-build-options store
                      #:keep-failed? (assoc-ref opts 'keep-failed?)
+                     #:keep-going? (assoc-ref opts 'keep-going?)
                      #:rounds (assoc-ref opts 'rounds)
                      #:build-cores (or (assoc-ref opts 'cores) 0)
                      #:max-build-jobs (or (assoc-ref opts 'max-jobs) 1)
@@ -214,6 +217,11 @@ options handled by 'set-build-options-from-command-line', and listed in
                   (apply values
                          (alist-cons 'keep-failed? #t result)
                          rest)))
+        (option '(#\k "keep-going") #f #f
+                (lambda (opt name arg result . rest)
+                  (apply values
+                         (alist-cons 'keep-going? #t result)
+                         rest)))
         (option '("rounds") #t #f
                 (lambda (opt name arg result . rest)
                   (apply values
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)