Merge branch 'master' into core-updates

gnu/packages/bioconductor.scm

@@ -64,14 +64,14 @@ objects.")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.20.0")
+    (version "1.22.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8"))))
+         "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/hpar/")
     (synopsis "Human Protein Atlas in R")
@@ -82,14 +82,14 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp"))))
+         "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -98,7 +98,8 @@ the Human Protein Atlas project.")
        ("r-bsgenome" ,r-bsgenome)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-iranges" ,r-iranges)))
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)))
     (home-page "https://bioconductor.org/packages/regioneR/")
     (synopsis "Association analysis of genomic regions")
     (description "This package offers a statistical framework based on
@@ -109,14 +110,14 @@ region sets and other genomic features.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "2.6.6")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp"))))
+         "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (inputs
@@ -128,6 +129,8 @@ region sets and other genomic features.")
        ("r-dplyr" ,r-dplyr)
        ("r-edger" ,r-edger)
        ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
        ("r-ggrepel" ,r-ggrepel)
        ("r-gplots" ,r-gplots)
        ("r-iranges" ,r-iranges)
@@ -138,6 +141,7 @@ region sets and other genomic features.")
        ("r-rcpp" ,r-rcpp)
        ("r-rsamtools" ,r-rsamtools)
        ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-systempiper" ,r-systempiper)
        ("r-zlibbioc" ,r-zlibbioc)))
     (home-page "http://bioconductor.org/packages/DiffBind")
@@ -151,14 +155,14 @@ occupancy (overlap) analysis and plotting functions.")
 (define-public r-ripseeker
   (package
     (name "r-ripseeker")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RIPSeeker" version))
        (sha256
         (base32
-         "0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y"))))
+         "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
     (properties `((upstream-name . "RIPSeeker")))
     (build-system r-build-system)
     (propagated-inputs
@@ -222,23 +226,27 @@ expressed genes in DNA microarray experiments.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.12.7")
+    (version "3.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04"))))
+         "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-delayedarray" ,r-delayedarray)
        ("r-go-db" ,r-go-db)
        ("r-biomart" ,r-biomart)
        ("r-bsgenome" ,r-bsgenome)
        ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
        ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-iranges" ,r-iranges)
        ("r-matrixstats" ,r-matrixstats)
        ("r-annotationdbi" ,r-annotationdbi)
        ("r-limma" ,r-limma)
@@ -250,6 +258,7 @@ expressed genes in DNA microarray experiments.")
        ("r-dbi" ,r-dbi)
        ("r-ensembldb" ,r-ensembldb)
        ("r-biobase" ,r-biobase)
+       ("r-s4vectors" ,r-s4vectors)
        ("r-seqinr" ,r-seqinr)
        ("r-idr" ,r-idr)
        ("r-genomicalignments" ,r-genomicalignments)
@@ -272,16 +281,15 @@ enrichedGO (addGeneIDs).")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.56.0")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic"))))
+               (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
+     `(("r-limma" ,r-limma)))
-       ("r-limma" ,r-limma)))
     (home-page "http://bioconductor.org/packages/marray")
     (synopsis "Exploratory analysis for two-color spotted microarray data")
     (description "This package contains class definitions for two-color spotted
@@ -292,12 +300,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.38.0")
+   (version "1.40.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm"))))
+             (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -312,12 +320,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.40.0")
+   (version "2.42.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch"))))
+             (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -335,16 +343,17 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy"))))
+               (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
+       ("r-biocparallel" ,r-biocparallel)
        ("r-cghbase" ,r-cghbase)
        ("r-cghcall" ,r-cghcall)
        ("r-dnacopy" ,r-dnacopy)

gnu/packages/emacs.scm

@@ -4188,7 +4188,7 @@ If you want to mark a folder manually as a project just create an empty
 (define-public emacs-elfeed
   (package
     (name "emacs-elfeed")
-    (version "2.3.0")
+    (version "3.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/skeeto/elfeed/archive/"
@@ -4196,7 +4196,7 @@ If you want to mark a folder manually as a project just create an empty
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1fd1mx0q1qb9vgdzls5ppxfriyid48blg8smgjspiazp7kxakzxv"))))
+                "1wkdrxr6zzqb48czqqv34l87bx8aqjk1739ddqg933aqh241kfvn"))))
     (build-system emacs-build-system)
     (arguments
      `(#:tests? #t

gnu/packages/graph.scm

@@ -155,14 +155,14 @@ model.")
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "1y9nyjffa9644jch0p2i3w302fmnyc2kb0c3z1f3d5zp1p4qmyqv"))))
+         "1037hzfxxcn46w6y88wm3kk2nixj0s8bk0hkmnshpxih3kmnvqby"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     ;; FIXME: Rgraphviz bundles the sources of an older variant of

gnu/packages/statistics.scm

@@ -113,10 +113,10 @@ be output in text, PostScript, PDF or HTML.")
 ;; Update this package together with the set of recommended packages: r-boot,
 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
-(define-public r-minimal
+(define r-with-tests
   (package
-    (name "r-minimal")
+    (name "r-with-tests")
-    (version "3.4.4")
+    (version "3.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -124,7 +124,7 @@ be output in text, PostScript, PDF or HTML.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"))))
+                "0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -217,11 +217,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
          (add-after 'build 'install-info
           (lambda _ (zero? (system* "make" "install-info")))))
        #:configure-flags
-       `(;; Do not build the recommended packages.  The build system creates
+       `(;; We build the recommended packages here, because they are needed in
-         ;; random temporary directories and embeds their names in some
+         ;; order to run the test suite.  We disable them in the r-minimal
-         ;; package files.  We build these packages with the r-build-system
+         ;; package.
-         ;; instead.
-         "--without-recommended-packages"
          "--with-cairo"
          "--with-blas=-lopenblas"
          "--with-libpng"
@@ -292,6 +290,19 @@ publication-quality data plots.  A large amount of 3rd-party packages are
 available, greatly increasing its breadth and scope.")
     (license license:gpl3+)))
 
+(define-public r-minimal
+  (package (inherit r-with-tests)
+    (name "r-minimal")
+    (arguments
+     `(#:tests? #f
+       ,@(substitute-keyword-arguments (package-arguments r-with-tests)
+           ((#:configure-flags flags)
+            ;; Do not build the recommended packages.  The build system creates
+            ;; random temporary directories and embeds their names in some
+            ;; package files.  We build these packages with the r-build-system
+            ;; instead.
+            `(cons "--without-recommended-packages" ,flags)))))))
+
 (define-public rmath-standalone
   (package (inherit r-minimal)
     (name "rmath-standalone")
@@ -3522,13 +3533,13 @@ vignettes.")
 (define-public r-mvtnorm
   (package
     (name "r-mvtnorm")
-    (version "1.0-7")
+    (version "1.0-8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mvtnorm" version))
               (sha256
                (base32
-                "0f7hzflygdnbwvzadr3knhybhanwg7agqddclj6mhbvwqpgb0qyh"))))
+                "0la42lylb7cjrcrc285bn69bz9kyg556xw317iz139dp1yswl410"))))
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))

guix/import/cran.scm

@@ -128,9 +128,9 @@ package definition."
 (define %cran-url "http://cran.r-project.org/web/packages/")
 (define %bioconductor-url "https://bioconductor.org/packages/")
 
-;; The latest Bioconductor release is 3.6.  Bioconductor packages should be
+;; The latest Bioconductor release is 3.7.  Bioconductor packages should be
 ;; updated together.
-(define %bioconductor-version "3.6")
+(define %bioconductor-version "3.7")
 
 (define %bioconductor-packages-list-url
   (string-append "https://bioconductor.org/packages/"

guix/self.scm

@@ -171,7 +171,8 @@ must be present in the search path."
          (source (imported-files (string-append name "-source")
                                  (append module-files extra-files))))
     (node name modules source dependencies
-          (compiled-modules name source modules
+          (compiled-modules name source
+                            (map car module-files)
                             (map node-source dependencies)
                             (map node-compiled dependencies)
                             #:extensions extensions
@@ -313,7 +314,12 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
                        *extra-modules* *core-modules*)
                  #:extensions dependencies
                  #:extra-files
-                 (file-imports source "gnu/system/examples" (const #t))
+                 (append (file-imports source "gnu/system/examples"
+                                       (const #t))
+
+                         ;; Build-side code that we don't build.  Some of
+                         ;; these depend on guile-rsvg, the Shepherd, etc.
+                         (file-imports source "gnu/build" (const #t)))
                  #:guile-for-build
                  guile-for-build))
 
@@ -481,6 +487,11 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
 (define (imported-files name files)
   ;; This is a non-monadic, simplified version of 'imported-files' from (guix
   ;; gexp).
+  (define same-target?
+    (match-lambda*
+      (((file1 . _) (file2 . _))
+       (string=? file1 file2))))
+
   (define build
     (with-imported-modules (source-module-closure
                             '((guix build utils)))
@@ -497,14 +508,15 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
                        ;; symlinks, as this makes a difference for
                        ;; 'add-to-store'.
                        (copy-file store-path final-path)))
-                    '#$files))))
+                    '#$(delete-duplicates files same-target?)))))
 
   ;; We're just copying files around, no need to substitute or offload it.
   (computed-file name build
                  #:options '(#:local-build? #t
-                             #:substitutable? #f)))
+                             #:substitutable? #f
+                             #:env-vars (("COLUMNS" . "200")))))
 
-(define* (compiled-modules name module-tree modules
+(define* (compiled-modules name module-tree module-files
                            #:optional
                            (dependencies '())
                            (dependencies-compiled '())
@@ -512,6 +524,9 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
                            (extensions '())       ;full-blown Guile packages
                            parallel?
                            guile-for-build)
+  "Build all the MODULE-FILES from MODULE-TREE.  MODULE-FILES must be a list
+like '(\"guix/foo.scm\" \"gnu/bar.scm\") and MODULE-TREE is the directory
+containing MODULE-FILES and possibly other files as well."
   ;; This is a non-monadic, enhanced version of 'compiled-file' from (guix
   ;; gexp).
   (define build
@@ -542,16 +557,13 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
                     (* 100. (/ completed total)) total)
             (force-output))
 
-          (define (process-directory directory output)
+          (define (process-directory directory files output)
-            (let ((files  (find-files directory "\\.scm$"))
+            ;; Hide compilation warnings.
-                  (prefix (+ 1 (string-length directory))))
+            (parameterize ((current-warning-port (%make-void-port "w")))
-              ;; Hide compilation warnings.
+              (compile-files directory #$output files
-              (parameterize ((current-warning-port (%make-void-port "w")))
+                             #:workers (parallel-job-count)
-                (compile-files directory #$output
+                             #:report-load report-load
-                               (map (cut string-drop <> prefix) files)
+                             #:report-compilation report-compilation)))
-                               #:workers (parallel-job-count)
-                               #:report-load report-load
-                               #:report-compilation report-compilation))))
 
           (setvbuf (current-output-port) _IONBF)
           (setvbuf (current-error-port) _IONBF)
@@ -579,7 +591,7 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
 
           (mkdir #$output)
           (chdir #+module-tree)
-          (process-directory "." #$output)
+          (process-directory "." '#+module-files #$output)
           (newline))))
 
   (computed-file name build