From e3a87d770f8be330259ef92348e0cf0a392bb24d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 1 Jun 2018 23:03:31 +0200
Subject: [PATCH 001/117] self: Improve backtraces for 'imported-files'.

* guix/self.scm (imported-files): Pass #:env-vars.
---
 guix/self.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/guix/self.scm b/guix/self.scm
index 3503fbda43..1b2a73e8f7 100644
--- a/guix/self.scm
+++ b/guix/self.scm
@@ -502,7 +502,8 @@ (define build
   ;; 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
                            #:optional

From 8031b3fa3c01d084a557b53b72e9bf1bcd99aa1a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sat, 2 Jun 2018 00:02:23 +0200
Subject: [PATCH 002/117] self: 'compiled-files' builds the given list of
 files.

* guix/self.scm (compiled-files): Add 'module-files' parameter.
[build]: 'process-directory' now honors MODULE-FILES instead of
building any '.scm' file it sees.
(scheme-node): Adjust accordingly.
---
 guix/self.scm | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/guix/self.scm b/guix/self.scm
index 1b2a73e8f7..bf5b1be1f3 100644
--- a/guix/self.scm
+++ b/guix/self.scm
@@ -171,7 +171,8 @@ (define* (scheme-node name modules #:optional (dependencies '())
          (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
@@ -505,7 +506,7 @@ (define build
                              #: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 '())
@@ -513,6 +514,9 @@ (define* (compiled-modules name module-tree modules
                            (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
@@ -543,16 +547,13 @@ (define (report-compilation file total completed)
                     (* 100. (/ completed total)) total)
             (force-output))
 
-          (define (process-directory directory output)
-            (let ((files  (find-files directory "\\.scm$"))
-                  (prefix (+ 1 (string-length directory))))
-              ;; Hide compilation warnings.
-              (parameterize ((current-warning-port (%make-void-port "w")))
-                (compile-files directory #$output
-                               (map (cut string-drop <> prefix) files)
-                               #:workers (parallel-job-count)
-                               #:report-load report-load
-                               #:report-compilation report-compilation))))
+          (define (process-directory directory files output)
+            ;; Hide compilation warnings.
+            (parameterize ((current-warning-port (%make-void-port "w")))
+              (compile-files directory #$output files
+                             #:workers (parallel-job-count)
+                             #:report-load report-load
+                             #:report-compilation report-compilation)))
 
           (setvbuf (current-output-port) _IONBF)
           (setvbuf (current-error-port) _IONBF)
@@ -580,7 +581,7 @@ (define (process-directory directory output)
 
           (mkdir #$output)
           (chdir #+module-tree)
-          (process-directory "." #$output)
+          (process-directory "." '#+module-files #$output)
           (newline))))
 
   (computed-file name build

From 1458f768c1049812166228b8526128b199518e50 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sat, 2 Jun 2018 00:04:39 +0200
Subject: [PATCH 003/117] self: Include gnu/build/* in the result.

Previously, modules like gnu/build/cross-toolchain.scm or
gnu/build/svg.scm were missing from the result.

* guix/self.scm (compiled-guix)[*system-modules*]: Add gnu/build/* to
 #:extra-files.
(imported-files)[same-target?]: New procedure.
[build]: Call 'delete-duplicates' on FILES.
---
 guix/self.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/guix/self.scm b/guix/self.scm
index bf5b1be1f3..a24e9c6147 100644
--- a/guix/self.scm
+++ b/guix/self.scm
@@ -314,7 +314,12 @@ (define *system-modules*
                        *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))
 
@@ -482,6 +487,11 @@ (define %nix-instantiate       ;for (guix import snix)
 (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)))
@@ -498,7 +508,7 @@ (define build
                        ;; 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

From d5452aa201a2f297e503658576ee99a7c070787c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Sat, 2 Jun 2018 12:54:16 +0200
Subject: [PATCH 004/117] gnu: emacs-elfeed: Update to 3.0.0.

* gnu/packages/emacs.scm (emacs-elfeed): Update to 3.0.0.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 4aafb7355e..7694d2410b 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -4170,7 +4170,7 @@ (define-public emacs-projectile
 (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/"
@@ -4178,7 +4178,7 @@ (define-public emacs-elfeed
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1fd1mx0q1qb9vgdzls5ppxfriyid48blg8smgjspiazp7kxakzxv"))))
+                "1wkdrxr6zzqb48czqqv34l87bx8aqjk1739ddqg933aqh241kfvn"))))
     (build-system emacs-build-system)
     (arguments
      `(#:tests? #t

From d22546cf80696719cfb76aec2ffdf44863be3fbc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 1 Jun 2018 17:10:48 +0200
Subject: [PATCH 005/117] gnu: r-minimal: Update to 3.5.0.

* gnu/packages/statistics.scm (r-with-tests): New variable derived from
r-minimal; update to 3.5.0.
[arguments]: Build recommended packages.
(r-minimal): Inherit from r-with-tests.
[arguments]: Disable recommended packages and tests.
---
 gnu/packages/statistics.scm | 29 ++++++++++++++++++++---------
 1 file changed, 20 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7d5c552a3e..7a6b674a1d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -113,10 +113,10 @@ (define-public pspp
 ;; 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")
-    (version "3.4.4")
+    (name "r-with-tests")
+    (version "3.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -124,7 +124,7 @@ (define-public r-minimal
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"))))
+                "0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -217,11 +217,9 @@ (define-public r-minimal
          (add-after 'build 'install-info
           (lambda _ (zero? (system* "make" "install-info")))))
        #:configure-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.
-         "--without-recommended-packages"
+       `(;; We build the recommended packages here, because they are needed in
+         ;; order to run the test suite.  We disable them in the r-minimal
+         ;; package.
          "--with-cairo"
          "--with-blas=-lopenblas"
          "--with-libpng"
@@ -292,6 +290,19 @@ (define-public r-minimal
 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")

From 2f5b3d8e90105b40695e33398b985c278410e5cf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:40:06 +0200
Subject: [PATCH 006/117] gnu: r-hpar: Update to 1.22.2.

* gnu/packages/bioconductor.scm (r-hpar): Update to 1.22.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 788e1e7def..5ae4fc1ac2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -64,14 +64,14 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm6
 (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")

From 72427c721dae18e8fc176c5bd29b3977ccab6dc3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:40:22 +0200
Subject: [PATCH 007/117] gnu: r-regioner: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-regioner): Update to 1.12.0.
[propagated-inputs]: Add r-s4vectors.
---
 gnu/packages/bioconductor.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5ae4fc1ac2..d1e39bc16c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -82,14 +82,14 @@ (define-public r-hpar
 (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 @@ (define-public r-regioner
        ("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

From 45bbccf4e7393822a547cdabfcbd8d7b963e1e88 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:40:51 +0200
Subject: [PATCH 008/117] gnu: r-diffbind: Update to 2.8.0.

* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.8.0.
[propagated-inputs]: Add r-genomicranges, r-ggplot2, and
r-summarizedexperiment.
---
 gnu/packages/bioconductor.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d1e39bc16c..5baf390fea 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -110,14 +110,14 @@ (define-public r-regioner
 (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
@@ -129,6 +129,8 @@ (define-public r-diffbind
        ("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)
@@ -139,6 +141,7 @@ (define-public r-diffbind
        ("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")

From 43734b47279b7e0d689297aff614b53b61495569 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:41:30 +0200
Subject: [PATCH 009/117] gnu: r-ripseeker: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5baf390fea..16b5e71452 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -155,14 +155,14 @@ (define-public r-diffbind
 (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

From f794e85daa8c401ab22b5bdacd897ccf9ea3b266 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:41:47 +0200
Subject: [PATCH 010/117] gnu: r-chippeakanno: Update to 3.14.0.

* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.0.
[propagated-inputs]: Add r-biostrings, r-delayedarray, r-genomicranges,
r-iranges, and r-s4vectors.
---
 gnu/packages/bioconductor.scm | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 16b5e71452..536349049c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -226,23 +226,27 @@ (define-public r-multtest
 (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)
@@ -254,6 +258,7 @@ (define-public r-chippeakanno
        ("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)

From 674870888323c54983cf6d7a4c3b387a7cb598d4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:42:34 +0200
Subject: [PATCH 011/117] gnu: r-marray: Update to 1.58.0.

* gnu/packages/bioconductor.scm (r-marray): Update to 1.58.0.
[propagated-inputs]: Remove r-biobase.
---
 gnu/packages/bioconductor.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 536349049c..443480c4bd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -281,16 +281,15 @@ (define-public r-chippeakanno
 (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

From 205df4a4cba69354f6a171a6de98a09ac5fcc170 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:42:55 +0200
Subject: [PATCH 012/117] gnu: r-cghbase: Update to 1.40.0.

* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.40.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 443480c4bd..a7dc553ec5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -300,12 +300,12 @@ (define-public r-marray
 (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

From 5c0df206cf2a553cfffb7fd61315673354de1680 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:43:06 +0200
Subject: [PATCH 013/117] gnu: r-cghcall: Update to 2.42.0.

* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a7dc553ec5..0235f100e2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -320,12 +320,12 @@ (define-public r-cghbase
 (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

From 81b0181b6f3dff9c4a9142c467528aaab7e5f95b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:43:18 +0200
Subject: [PATCH 014/117] gnu: r-qdnaseq: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.16.0.
[propagated-inputs]: Add r-biocparallel.
---
 gnu/packages/bioconductor.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0235f100e2..ed35b4c61a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -343,16 +343,17 @@ (define-public r-cghcall
 (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)

From 02be818044278cb5376f9ec53c68f12899bf43ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:43:41 +0200
Subject: [PATCH 015/117] gnu: r-annotate: Update to 1.58.0.

* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.58.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e0bfaac06e..632a74cea0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6149,14 +6149,14 @@ (define-public r-vegan
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.56.2")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "0ybg9k1s289h15nj1kp9821i1rsk1gkn8i8blplmk7gsgpbw1f42"))))
+         "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)

From 14e9235f0ceed6191a936c66dfe93b895ad6ef47 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:43:54 +0200
Subject: [PATCH 016/117] gnu: r-copynumber: Update to 1.20.0.

* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.20.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 632a74cea0..bdfe2c04a4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6176,13 +6176,13 @@ (define-public r-annotate
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx"))))
+                "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)

From 4d70c8c486ffc238f9bbe96a01de8e6c69165ad8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:44:06 +0200
Subject: [PATCH 017/117] gnu: r-geneplotter: Update to 1.58.0.

* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.58.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bdfe2c04a4..44fdd1f16f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6199,14 +6199,14 @@ (define-public r-copynumber
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma"))))
+         "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)

From 41657b15f4de4a403fe1fe6cf86c05b69602ceb3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:44:18 +0200
Subject: [PATCH 018/117] gnu: r-genefilter: Update to 1.62.0.

* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.62.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 44fdd1f16f..2df630dc37 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6224,14 +6224,14 @@ (define-public r-geneplotter
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7"))))
+         "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))

From 51c1f96ebc9e2198e4f4da92d0c91280f20e8bae Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:44:32 +0200
Subject: [PATCH 019/117] gnu: r-deseq2: Update to 1.20.0.

* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.20.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2df630dc37..31b93984f2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6251,14 +6251,14 @@ (define-public r-genefilter
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv"))))
+         "1wjnfpb41a9mmf9a22bz4zh7r1d4id50vpdc1mn5vfzrz7li9qik"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs

From 16da69b5e68d5103c245d686c8f0a61768a5f3e5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:45:25 +0200
Subject: [PATCH 020/117] gnu: r-dexseq: Update to 1.26.0.

* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.26.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 31b93984f2..8f2764ab96 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6288,14 +6288,14 @@ (define-public r-deseq2
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.24.4")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5"))))
+         "1mqb3mdxcsi3largsl7k27bvqrgps9ixv806xvmf29pw0xn05sg1"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs

From 5516db9e7004dc3f4e9647b370146dc9e8c51b3c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:45:36 +0200
Subject: [PATCH 021/117] gnu: r-annotationforge: Update to 1.22.0.

* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8f2764ab96..debba7529f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6331,14 +6331,14 @@ (define-public r-dexseq
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1"))))
+         "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)

From 9177ac2295845c51afeba13af3945ce54960d0a6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:45:49 +0200
Subject: [PATCH 022/117] gnu: r-rbgl: Update to 1.56.0.

* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.56.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index debba7529f..fca84dda4c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6361,14 +6361,14 @@ (define-public r-annotationforge
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7"))))
+         "0hj972mmqpyi5fx1rq33kysavdyz4nspi6gcffzi3rv339m0anhf"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs `(("r-graph" ,r-graph)))

From f1094f50a798bc8966533c193ed290e5724e3f2c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:46:02 +0200
Subject: [PATCH 023/117] gnu: r-gseabase: Update to 1.42.0.

* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.42.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fca84dda4c..b549c32d21 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6382,14 +6382,14 @@ (define-public r-rbgl
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.40.1")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz"))))
+         "11bv92svik399q677jv96b71i4bq68xxyxn1yijpdik2lq4hgl7a"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs

From d8410d6610e948efab2fbfe35289e8215098d686 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:46:14 +0200
Subject: [PATCH 024/117] gnu: r-category: Update to 2.46.0.

* gnu/packages/bioinformatics.scm (r-category): Update to 2.46.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b549c32d21..f2b5660298 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6409,14 +6409,14 @@ (define-public r-gseabase
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "0mkav04vbla0xfa0dssxdd0rjs589sxi83xklf5iq5hj3dm8y0i8"))))
+         "03wfqa8d1dgwsm327zl2mpkq7dq3mzhq12598qz3ylfhrwplbgx0"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs

From 9da8e275caab5831fc74d38406857af7c4bd78eb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:46:28 +0200
Subject: [PATCH 025/117] gnu: r-gostats: Update to 2.46.0.

* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.46.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f2b5660298..ac05329799 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6440,14 +6440,14 @@ (define-public r-category
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "04gqfdlx9fxf97qf0l28x4aaqvl10n6v58qiz5fiaw05sbj1pf1i"))))
+         "1i5mydz5d95w2k28qr9j01hmbnl2id55jq94jvcpcyp1pvinkdq0"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs

From eabe78facafcee9aa170f292f630e45df9955720 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:46:39 +0200
Subject: [PATCH 026/117] gnu: r-shortread: Update to 1.38.0.

* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.38.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ac05329799..2eac1d5208 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6471,14 +6471,14 @@ (define-public r-gostats
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.36.1")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m"))))
+         "038z3z7qaw5bpgjzy91sjkybsny6jwjjsrnnq4gdqdw9ss1qy1fb"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs

From 712fe39680bafa6f70688eb6e7b760d89ee2acbf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:46:51 +0200
Subject: [PATCH 027/117] gnu: r-systempiper: Update to 1.14.0.

* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.14.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2eac1d5208..afd89e5954 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6513,14 +6513,14 @@ (define-public r-shortread
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "11mj8pjq5vj25768vmagpzv74fvi3p3kdk5zdlznqyiaggri04cv"))))
+         "1550pd63mmky0vgkmpni7zf14kqz1741wv63nfaw29kcmhh3m5lm"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs

From 9370b8ee9f35e838fe63bdc8e5a26def3a072c35 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:47:04 +0200
Subject: [PATCH 028/117] gnu: r-grohmm: Update to 1.14.0.

* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.14.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index afd89e5954..8f5a8373a7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6559,14 +6559,14 @@ (define-public r-systempiper
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "0cjkj0ypyc4dfi9s8dh88kh6q4xlpnc0wal7njg4b4gqj0l2hva7"))))
+         "1kjb14apyly44qdlx2ld6gr69wlazd4mbhs58l35hir12aphgrzp"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs

From e5907a44e1fbb208f7250cae636d35e2dcf5c8c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:47:15 +0200
Subject: [PATCH 029/117] gnu: r-biocgenerics: Update to 0.26.0.

* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.26.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8f5a8373a7..28863c1c8b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6878,13 +6878,13 @@ (define-public r-acsnminer
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.24.0")
+    (version "0.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "03wxvhxyrhipbgcg83lqlfn7p9gbzzrnl48y0dq7303xgp232zai"))))
+                "19qxhy2cd3pykkhzbb5q3crgaxf65cpzf2mkfsz16gqhi8flj72p"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)

From 97af51ef40ea172324ee50d0a2c6dc9a099f8f9a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:47:27 +0200
Subject: [PATCH 030/117] gnu: r-biocinstaller: Update to 1.30.0.

* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.30.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 28863c1c8b..647d8226a3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6898,13 +6898,13 @@ (define-public r-biocgenerics
 (define-public r-biocinstaller
   (package
     (name "r-biocinstaller")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocInstaller" version))
               (sha256
                (base32
-                "19fga27bv6q9v5mpil74y76lahmnwvpg2h33rdx1r79nvljkd19d"))))
+                "1xg1gi1hf5vflp71ji21gnmr4kcjpx8a6c47cllpc7yqnjv5nfg0"))))
     (properties
      `((upstream-name . "BiocInstaller")))
     (build-system r-build-system)

From e5f52b692ae7f4542912f528939d5b82e5e543a9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:47:39 +0200
Subject: [PATCH 031/117] gnu: r-biocviews: Update to 1.48.0.

* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 647d8226a3..3e1881b21e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6917,13 +6917,13 @@ (define-public r-biocinstaller
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.46.0")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "09zyqj1kqc089lmh9sliy0acanx9zimcasvp71dsrg2bqm08r1md"))))
+                "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)

From dc6c168ac17e77c83224eaa408375ab957319386 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:47:54 +0200
Subject: [PATCH 032/117] gnu: r-biocstyle: Update to 2.8.2.

* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.8.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3e1881b21e..5f50dfb996 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6968,13 +6968,13 @@ (define-public r-bookdown
 (define-public r-biocstyle
   (package
    (name "r-biocstyle")
-   (version "2.6.1")
+   (version "2.8.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm"))))
+                "17m901ylz00w1a3nq5f910v55zixm1nr6rb3qrsbhqd94qzr0l2p"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)

From 3679a2fec44e11fb2e43c06e733e9e85c445f024 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:48:05 +0200
Subject: [PATCH 033/117] gnu: r-bioccheck: Update to 1.16.0.

* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.16.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5f50dfb996..3d5e719818 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6993,13 +6993,13 @@ (define-public r-biocstyle
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "1nzp8kgw13z9pgf885rplj6k37jcldfhbz0adqclxr2gq0yalmyx"))))
+                "1srp1g809f1nn0fyqknr7r6dq89bw1xpjvmygr7cw6ffknbc671s"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)

From 607acf3194a9458a3eced9349387e4a3fa262a52 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:48:17 +0200
Subject: [PATCH 034/117] gnu: r-dnacopy: Update to 1.54.0.

* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.54.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3d5e719818..b7e034ec04 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7084,13 +7084,13 @@ (define-public r-optparse
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.52.0")
+    (version "1.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DNAcopy" version))
               (sha256
                (base32
-                "127il5rlg1hzjlhwhs64x3nm18p00q1pd9ckb2b9ifl0rax95wai"))))
+                "03hfhmmc5y60r2gcgm367w2fr7qj115l74m9bp3h9qpn5yci0d8n"))))
     (properties
      `((upstream-name . "DNAcopy")))
     (build-system r-build-system)

From 33cd15fa8424d2822dcf95ac306f7ca6f8f14188 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:48:29 +0200
Subject: [PATCH 035/117] gnu: r-s4vectors: Update to 0.18.2.

* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b7e034ec04..41c7cdad32 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7106,13 +7106,13 @@ (define-public r-dnacopy
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.16.0")
+    (version "0.18.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "03s8vz33nl6mivjb7dbvj702dkypi340lji1sjban03fyyls0hw0"))))
+                "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)

From 8b44c28f5d55efbcf75f7353552431a6ea446bdf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:48:42 +0200
Subject: [PATCH 036/117] gnu: r-iranges: Update to 2.14.10.

* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.10.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 41c7cdad32..c5b55c4824 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7158,13 +7158,13 @@ (define-public r-seqinr
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.12.0")
+    (version "2.14.10")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "1vqczb9wlxsmpwpqig6j1dmiblcfpq6mgnq8qwzcrvddm4cp47m5"))))
+                "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)

From 953c8b18f88628289e6753a01c32db62dec4483f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:48:54 +0200
Subject: [PATCH 037/117] gnu: r-genomeinfodb: Update to 1.16.0.

* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.16.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c5b55c4824..09d06f178e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7210,13 +7210,13 @@ (define-public r-genomeinfodbdata
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1jhm0imkac4gvchbjxj408aakk39xdv2fyh818d3lk295bz6bnyp"))))
+                "0yhnqhaydmmq7ihmhj3rbal4afq5p993l2qqrd0n5wmbyg7glg2d"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)

From 4639025284808908d6b60deb2cd54ba64654a944 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:49:06 +0200
Subject: [PATCH 038/117] gnu: r-edger: Update to 3.22.2.

* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 09d06f178e..ad9aec8879 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7238,13 +7238,13 @@ (define-public r-genomeinfodb
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.20.9")
+    (version "3.22.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw"))))
+                "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs

From d358a5a0c1e2726384b0b4c2911c4ed6741fae7b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:49:17 +0200
Subject: [PATCH 039/117] gnu: r-variantannotation: Update to 1.26.0.

* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ad9aec8879..88e252b1f9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7266,13 +7266,13 @@ (define-public r-edger
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.24.5")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2"))))
+                "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs

From 0a465e5694068306d90e3d9634fbff9370720c99 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:49:31 +0200
Subject: [PATCH 040/117] gnu: r-limma: Update to 3.36.1.

* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 88e252b1f9..2680d170dc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7304,13 +7304,13 @@ (define-public r-variantannotation
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.34.9")
+    (version "3.36.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc"))))
+                "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")

From c2401d06c5ba1603de31e04ba955609514d42d27 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:49:44 +0200
Subject: [PATCH 041/117] gnu: r-xvector: Update to 0.20.0.

* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.20.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2680d170dc..4dfd8825a2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7323,13 +7323,13 @@ (define-public r-limma
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.18.0")
+    (version "0.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "1i4i3kdxr78lr1kcxq657p11ybi7kq10c8kyaqyh6gfc8i9rhvmk"))))
+                "1zjlhh9lsyhg0js1858csyw2389kbrzdqnqnha833wazkwxilp3f"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)

From e51afc63b7924f632722c691e3ef0808e70d38f1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:49:57 +0200
Subject: [PATCH 042/117] gnu: r-genomicranges: Update to 1.32.3.

* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4dfd8825a2..66b645e08b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7359,13 +7359,13 @@ (define-public r-xvector
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.30.3")
+    (version "1.32.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1"))))
+                "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)

From 6fd71f1b6a102da3258e6af7d0b5cc8bd297fc24 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:50:13 +0200
Subject: [PATCH 043/117] gnu: r-biobase: Update to 2.40.0.

* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.40.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 66b645e08b..862b6b98d7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7388,13 +7388,13 @@ (define-public r-genomicranges
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.38.0")
+    (version "2.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg"))))
+                "1iwds2a5ir29k19dbpynlc7nn836cw2gamchhgpi2jf2xar9m9jz"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)

From 77f66feee7821902965571be5ae6f43caa848147 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:50:34 +0200
Subject: [PATCH 044/117] gnu: r-annotationdbi: Update to 1.42.1.

* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.42.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 862b6b98d7..e5d0f02727 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7410,13 +7410,13 @@ (define-public r-biobase
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.40.0")
+    (version "1.42.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "1dh4qs1a757n640gs34lf6z2glc96nan86x0sqaw5csadl2rhnlc"))))
+                "0afkbzli08vq02r2pr9phrz3rxd6ilp1w7yw8y99nbjiz14f8b1c"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)

From 1763cba80ebf99d19faa0c02ef409bbf4a07d365 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:50:56 +0200
Subject: [PATCH 045/117] gnu: r-biomart: Update to 2.36.1.

* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.36.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e5d0f02727..0bccc6c443 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7437,13 +7437,13 @@ (define-public r-annotationdbi
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.34.2")
+    (version "2.36.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79"))))
+                "0b70s350ffc74v3xz5c3jpazr9zxdb7gjmjfj7aghlsrizrspill"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)

From e6eac58d4c01a999ab9503a1657503fb9643a35b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:51:12 +0200
Subject: [PATCH 046/117] gnu: r-biocparallel: Update to 1.14.1.

* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0bccc6c443..9caa32f690 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7470,13 +7470,13 @@ (define-public r-biomart
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.12.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd"))))
+                "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)

From 942655add1b2eeeac614133fe5019503f08bc885 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:51:35 +0200
Subject: [PATCH 047/117] gnu: r-biostrings: Update to 2.48.0.

* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.48.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9caa32f690..d921229529 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7495,13 +7495,13 @@ (define-public r-biocparallel
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.46.0")
+    (version "2.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk"))))
+                "118b490jk87ydigm6ln25ms4kskzkw0akmh77clzznhzpqnxsi6j"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)

From d2367a89ddea3640323570d3ec757d28709e1c71 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:51:57 +0200
Subject: [PATCH 048/117] gnu: r-rsamtools: Update to 1.32.0.

* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d921229529..ed38e4c41f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7521,13 +7521,13 @@ (define-public r-biostrings
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams"))))
+                "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)

From 82f593f3787d3bb0386376ab26fc7da1fa161344 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:52:17 +0200
Subject: [PATCH 049/117] gnu: r-delayedarray: Update to 0.6.0.

* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.0.
[propagated-inputs]: Add r-biocparallel.
---
 gnu/packages/bioinformatics.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ed38e4c41f..4d5fef5efc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7565,18 +7565,19 @@ (define-public r-rsamtools
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.4.1")
+    (version "0.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b"))))
+                "0n3w57cwy911q812wc8658y0v3xgpmg379sj98kfqdxa80z1mxdf"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
        ("r-s4vectors" ,r-s4vectors)
        ("r-iranges" ,r-iranges)
        ("r-matrixstats" ,r-matrixstats)))

From 9bf4110ea17dbe5214a8a2737abe826bb08479a7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:52:44 +0200
Subject: [PATCH 050/117] gnu: r-summarizedexperiment: Update to 1.10.1.

* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.10.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4d5fef5efc..169615181f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7596,13 +7596,13 @@ (define-public r-delayedarray
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.8.1")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh"))))
+                "0v3zxl9cqsv79ag5cnvzlhvgaz5cr8f4rn7flmwnwpqd508cznl1"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)

From 90102bd06bdc8755d4a38e0759d074606cace927 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:53:04 +0200
Subject: [PATCH 051/117] gnu: r-genomicalignments: Update to 1.16.0.

* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.16.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 169615181f..791c948877 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7627,13 +7627,13 @@ (define-public r-summarizedexperiment
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.14.2")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv"))))
+                "00pi2cnkkbj2023fg2x2cmglkdalwzy1vr3glsikwz7ix9yylcaw"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)

From a30df29768890caa1da8a682f455fb9435b73486 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:53:35 +0200
Subject: [PATCH 052/117] gnu: r-rtracklayer: Update to 1.40.2.

* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.2.
[native-inputs]: Add pkg-config.
---
 gnu/packages/bioinformatics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 791c948877..e803bbca2c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7660,13 +7660,13 @@ (define-public r-genomicalignments
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.38.3")
+    (version "1.40.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k"))))
+                "0l90jn4df3akxl0n1i9wvnbjqrzjc0d15r8vqr7b15q2117mrn5r"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7678,6 +7678,8 @@ (define-public r-rtracklayer
              (substitute* "NAMESPACE"
                (("import\\(zlibbioc\\)") ""))
              #t)))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (inputs
      `(("zlib" ,zlib)))
     (propagated-inputs

From b4ad4ec6b41598d09dde665a33a6ae9b2a51313a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:54:15 +0200
Subject: [PATCH 053/117] gnu: r-genomicfeatures: Update to 1.32.0.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.0.
[propagated-inputs]: Remove r-rmysql.
---
 gnu/packages/bioinformatics.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e803bbca2c..721a25f9fe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7707,13 +7707,13 @@ (define-public r-rtracklayer
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.30.3")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"))))
+                "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -7729,7 +7729,6 @@ (define-public r-genomicfeatures
        ("r-iranges" ,r-iranges)
        ("r-rcurl" ,r-rcurl)
        ("r-rsqlite" ,r-rsqlite)
-       ("r-rmysql" ,r-rmysql)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xvector" ,r-xvector)))

From 2f66fecd890320926159464ae79840767c79cb6a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:54:40 +0200
Subject: [PATCH 054/117] gnu: r-graph: Update to 1.58.0.

* gnu/packages/bioinformatics.scm (r-graph): Update to 1.58.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 721a25f9fe..56c56346bd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7772,13 +7772,13 @@ (define-public r-go-db
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.56.0")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1"))))
+                "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))

From f2eb2e453e8f64c84435dbdaac4229b95e338183 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:54:55 +0200
Subject: [PATCH 055/117] gnu: r-topgo: Update to 2.32.0.

* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.32.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 56c56346bd..a5b205c27b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7791,13 +7791,13 @@ (define-public r-graph
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.30.1")
+    (version "2.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x"))))
+                "05yxnkid8bgw9lkm90if9fg63djhgvbailfa3qsfqa5c0zjmixw1"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)

From 89ef133ebd1d0f31de4167a48356481e19fe003a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:55:10 +0200
Subject: [PATCH 056/117] gnu: r-bsgenome: Update to 1.48.0.

* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.48.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a5b205c27b..7318e16b35 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7824,13 +7824,13 @@ (define-public r-topgo
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.46.0")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq"))))
+                "1rk2piqq5dppkd51ln3r872d7ng3rvq98071mnd0xdv2xwnyn5g8"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)

From 25d1df5764c538b893251cb88e647c9757449517 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:55:26 +0200
Subject: [PATCH 057/117] gnu: r-impute: Update to 1.54.0.

* gnu/packages/bioinformatics.scm (r-impute): Update to 1.54.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7318e16b35..e7d191f27c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7885,13 +7885,13 @@ (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.52.0")
+    (version "1.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "0b8r4swvyx3cjcc2ky8yn0ncpzlbi1pgfsn3wpbjmhh7sqrffm2n"))))
+                "1d3cpfaqlq2gnb3hsc2yhxwkrnbd7m6ifif32yp0ya0jr5brl4hr"))))
     (inputs
      `(("gfortran" ,gfortran)))
     (build-system r-build-system)

From 5229cedf576bdd144ec6fc5d167fd18ae8fd98d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:55:39 +0200
Subject: [PATCH 058/117] gnu: r-seqpattern: Update to 1.12.0.

* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.12.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e7d191f27c..08a01dcb06 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7905,13 +7905,13 @@ (define-public r-impute
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "seqPattern" version))
               (sha256
                (base32
-                "1kcm5w83q7w0v0vs7nyp4gq5z86c6n6pqy9zmyyhxcrns7f597pm"))))
+                "0dw0yldfcf0ibvpqxlpx1ijnjf9lma47w9w22siszzhw09i0wp3w"))))
     (properties
      `((upstream-name . "seqPattern")))
     (build-system r-build-system)

From 17d35de73fce32dd1166d3786776bd3d0ba2044d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:56:00 +0200
Subject: [PATCH 059/117] gnu: r-genomation: Update to 1.12.0.

* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.12.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 08a01dcb06..ae1f3dd094 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7932,13 +7932,13 @@ (define-public r-seqpattern
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.11.3")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v"))))
+                "1vdmdyrq0n7pf8cvy2950v7hrcrcbd9zl4fg7dcmyly3iiwdyirp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)

From 8217c2d0bc680aeb9f4d65282b8431284258cf33 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:56:18 +0200
Subject: [PATCH 060/117] gnu: r-seqlogo: Update to 1.46.0.

* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.46.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ae1f3dd094..09ca946c72 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8110,14 +8110,14 @@ (define-public r-org-mm-eg-db
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqLogo" version))
        (sha256
         (base32
-         "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq"))))
+         "16xvqcdknix9vjm8mrixi6nyfsr45jm844jh1x90m8044lwrsic1"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/seqLogo")

From 7e6537e257245715a647dfecb87c9453438bc1df Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:56:34 +0200
Subject: [PATCH 061/117] gnu: r-motifrg: Update to 1.24.0.

* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.24.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 09ca946c72..8a5d9fddd6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8356,14 +8356,14 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3
 (define-public r-motifrg
   (package
     (name "r-motifrg")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifRG" version))
        (sha256
         (base32
-         "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44"))))
+         "0mxhyidkyd2zqahdbg69y20r550z78lvr1r3pbjymnwfg4hcfq1p"))))
     (properties `((upstream-name . "motifRG")))
     (build-system r-build-system)
     (propagated-inputs

From 2c480bb01231238765657916fddd7bea7bdf7b3d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:56:48 +0200
Subject: [PATCH 062/117] gnu: r-zlibbioc: Update to 1.26.0.

* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.26.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8a5d9fddd6..f4ea3d43a5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8408,13 +8408,13 @@ (define-public r-qtl
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "zlibbioc" version))
               (sha256
                (base32
-                "1zr9hbh55hglfpy15cpxwmddxblhyb0an15953l3rbhmlh2vpy92"))))
+                "1rwr0mci8a712q0isavi4jmhm94gwivc4nr8j7r4kw05flp4g7gz"))))
     (properties
      `((upstream-name . "zlibbioc")))
     (build-system r-build-system)

From 1a08bb8a177ff1b1cca363e5a8bccacf5111bb01 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:58:55 +0200
Subject: [PATCH 063/117] gnu: r-rhtslib: Update to 1.12.1.

* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.12.1.
[native-inputs]: Remove autoconf.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f4ea3d43a5..7755b28243 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8450,14 +8450,14 @@ (define-public r-r4rna
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "1.10.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j"))))
+         "16ywnb8cmr2xabd1i21b92rfziw7xfbv25yv16ipw617p41wa39z"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8465,7 +8465,7 @@ (define-public r-rhtslib
     (inputs
      `(("zlib" ,zlib)))
     (native-inputs
-     `(("autoconf" ,autoconf)))
+     `(("pkg-config" ,pkg-config)))
     (home-page "https://github.com/nhayden/Rhtslib")
     (synopsis "High-throughput sequencing library as an R package")
     (description

From 72f11ff9c5ba881e00cca043337928ff12464f67 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:59:23 +0200
Subject: [PATCH 064/117] gnu: r-bamsignals: Update to 1.12.0.

* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7755b28243..abcbb35643 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8477,14 +8477,14 @@ (define-public r-rhtslib
 (define-public r-bamsignals
   (package
     (name "r-bamsignals")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bamsignals" version))
        (sha256
         (base32
-         "15id6mkj95skb4kfafvfs2j7ylydal60c3pspcl7llhwpq6vcqvl"))))
+         "09l4v414ijkjpkvcv2580v13v18ky196f0lv27ldblpa8bddvmns"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)

From b6c2c8f781cb48d3f233651d438e5584384d3bb5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:59:37 +0200
Subject: [PATCH 065/117] gnu: r-mutationalpatterns: Update to 1.6.1.

* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.6.1.
---
 gnu/packages/bioinformatics.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index abcbb35643..12a4260bec 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8599,18 +8599,19 @@ (define-public rcas-web
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "1.4.3")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "0ml4gsp5dfv23xqrknxh25q8q65hly1xb1215lcwyc8hj9z8f941"))))
+         "1yq7351j42mjxn8fd3c5bdxzb2l5s4lvqhjdvv4rwj4f600n6wj9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biostrings" ,r-biostrings)
+       ;; These two packages are suggested packages
        ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
        ("r-genomicranges" ,r-genomicranges)

From c76e8baf9e57a45c19ccc0134499b493b55ea8a9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 11:59:53 +0200
Subject: [PATCH 066/117] gnu: r-tximport: Update to 1.8.0.

* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.8.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 12a4260bec..9138671d2f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8775,13 +8775,13 @@ (define-public r-gkmsvm
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.6.0")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "1gyqcm91hxg1kgjqcz2qw1n56yp9pymjzs50rwcpb2893dr8sp2h"))))
+                "1qjc7ah9dzccpvcjrp9k4qnaz13x6kvy1c1xpdj503km6k528lip"))))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/tximport")
     (synopsis "Import and summarize transcript-level estimates for gene-level analysis")

From d73c5728f345174e9493a25646cd3d1a716fb8b5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:00:10 +0200
Subject: [PATCH 067/117] gnu: r-rhdf5: Update to 2.24.0.

* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.24.0.
[arguments]: Remove.
[propagated-inputs]: Remove r-zlibbioc; add r-rhdf5lib.
[inputs]: Remove perl.
---
 gnu/packages/bioinformatics.scm | 29 ++++-------------------------
 1 file changed, 4 insertions(+), 25 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9138671d2f..ce4ff64af6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8797,39 +8797,18 @@ (define-public r-tximport
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.22.0")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1"))))
+                "15cmmchhk8bnp94gxg0zk9qyzdjx5kv16dzpbnb62mkq7ydmifx6"))))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'unpack-smallhdf5
-           (lambda* (#:key outputs #:allow-other-keys)
-             (system* "tar" "-xzvf"
-                      "src/hdf5source/hdf5small.tgz" "-C" "src/" )
-             (substitute* "src/hdf5/configure"
-               (("/bin/mv") "mv"))
-             ;; Remove timestamp and host system information to make
-             ;; the build reproducible.
-             (substitute* "src/hdf5/src/libhdf5.settings.in"
-               (("Configured on: @CONFIG_DATE@")
-                "Configured on: Guix")
-               (("Uname information:.*")
-                "Uname information: Linux\n")
-               ;; Remove unnecessary store reference.
-               (("C Compiler:.*")
-                "C Compiler: GCC\n"))
-             #t)))))
     (propagated-inputs
-     `(("r-zlibbioc" ,r-zlibbioc)))
+     `(("r-rhdf5lib" ,r-rhdf5lib)))
     (inputs
-     `(("perl" ,perl)
-       ("zlib" ,zlib)))
+     `(("zlib" ,zlib)))
     (home-page "https://bioconductor.org/packages/rhdf5")
     (synopsis "HDF5 interface to R")
     (description

From 62509bbc816440dd59ae6070717c6469af551a24 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:00:50 +0200
Subject: [PATCH 068/117] gnu: r-annotationfilter: Update to 1.4.0.

* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.4.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ce4ff64af6..fb2ce3c29d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8824,13 +8824,13 @@ (define-public r-rhdf5
 (define-public r-annotationfilter
   (package
     (name "r-annotationfilter")
-    (version "1.2.0")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationFilter" version))
               (sha256
                (base32
-                "04zf864c1fvdlaay2r5cn30fc1n5i3czh31fs62qlrvs61wjiscs"))))
+                "1w8ypfdz4g7vnwfrvnhjcpm8waciqyq2cn883ajdwg4vv7a5mj9a"))))
     (properties
      `((upstream-name . "AnnotationFilter")))
     (build-system r-build-system)

From 8f94487da738aadc1e632012f1e0a03bf4defbe9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:01:03 +0200
Subject: [PATCH 069/117] gnu: r-chipseq: Update to 1.30.0.

* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.30.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fb2ce3c29d..ab2ff98073 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9127,14 +9127,14 @@ (define-public multiqc
 (define-public r-chipseq
   (package
     (name "r-chipseq")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chipseq" version))
        (sha256
         (base32
-         "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq"))))
+         "09f8dgl5ni75qkf7nvvppwr3irpplv4xb3ks59ld7l8i2mplcrx7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)

From aae4f716dafe5535978a30cc8ac9c048e33f53f6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:01:15 +0200
Subject: [PATCH 070/117] gnu: r-copywriter: Update to 2.12.0.

* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.12.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ab2ff98073..5d3f16b74b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9179,14 +9179,14 @@ (define-public r-copyhelper
 (define-public r-copywriter
   (package
     (name "r-copywriter")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CopywriteR" version))
        (sha256
         (base32
-         "17fy2lc5yf3nh6v077kv87h53n263hqz2540lzrl0vjiqrl2plca"))))
+         "0b7xwq1va2zclb54f07c5ipmmq4iv2hrlph3j93jz5hmyayv50z3"))))
     (properties `((upstream-name . "CopywriteR")))
     (build-system r-build-system)
     (propagated-inputs

From 19ad568e79a59b2226bffd8bc1d0a1185ffe3009 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:01:43 +0200
Subject: [PATCH 071/117] gnu: r-methylkit: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5d3f16b74b..ff6b45e8e0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9219,13 +9219,13 @@ (define-public r-copywriter
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.4.1")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai"))))
+                "01qmndm5z21p78w7xfp8ynan6jpfg54rnkpj8b86rc081qh0sgjj"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs

From 9547dd86138b9ff40e5d2eb39503cf0f65136bb7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:01:57 +0200
Subject: [PATCH 072/117] gnu: r-sva: Update to 3.28.0.

* gnu/packages/bioinformatics.scm (r-sva): Update to 3.28.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ff6b45e8e0..a010fc188d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9265,14 +9265,14 @@ (define-public r-methylkit
 (define-public r-sva
   (package
     (name "r-sva")
-    (version "3.26.0")
+    (version "3.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sva" version))
        (sha256
         (base32
-         "0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw"))))
+         "0a3jqbz0jp1jxrnjkqfpmca840yqcdwxprdl608bzzx2zb4jl52s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-genefilter" ,r-genefilter)

From a02b82088fe0cf949cea15de011c157d9e916022 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:02:10 +0200
Subject: [PATCH 073/117] gnu: r-protgenerics: Update to 1.12.0.

* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.12.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a010fc188d..955decdead 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9375,14 +9375,14 @@ (define-public r-maldiquant
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ProtGenerics" version))
        (sha256
         (base32
-         "16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni"))))
+         "05jbadw2aiwy8vi2ia0jxg06cmwhly2cq4dy1ag7kdxf1c5i9ccn"))))
     (properties `((upstream-name . "ProtGenerics")))
     (build-system r-build-system)
     (home-page "https://github.com/lgatto/ProtGenerics")

From 39cc4917907c5f0376c30989970b857de49b8e77 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:04:03 +0200
Subject: [PATCH 074/117] gnu: r-mzr: Update to 2.14.0.

* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.14.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
---
 gnu/packages/bioinformatics.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 955decdead..1ac5b7caa1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9395,14 +9395,14 @@ (define-public r-protgenerics
 (define-public r-mzr
   (package
     (name "r-mzr")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c"))
+         "190m2bq5bqxhljaj4f7vz9wj5h5laaxd8zp5jampnql6xc4zmarg"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -9424,12 +9424,14 @@ (define-public r-mzr
              #t)))))
     (inputs
      `(("boost" ,boost) ; use this instead of the bundled boost sources
-       ("netcdf" ,netcdf)))
+       ("netcdf" ,netcdf)
+       ("zlib" ,zlib)))
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-protgenerics" ,r-protgenerics)
        ("r-rcpp" ,r-rcpp)
+       ("r-rhdf5lib" ,r-rhdf5lib)
        ("r-zlibbioc" ,r-zlibbioc)))
     (home-page "https://github.com/sneumann/mzR/")
     (synopsis "Parser for mass spectrometry data files")

From 82589f743003e57a4bf305b4a52185c5fdad6e43 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:04:28 +0200
Subject: [PATCH 075/117] gnu: r-affyio: Update to 1.50.0.

* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.50.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1ac5b7caa1..da4afc7747 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9447,14 +9447,14 @@ (define-public r-mzr
 (define-public r-affyio
   (package
     (name "r-affyio")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyio" version))
        (sha256
         (base32
-         "1pzzp3d3dbmyf34gvivfiprkpscn36rgvhrq853a1d3avcwr5ak9"))))
+         "0sh5wnnchyfpq5n6rchbqmb27byn7kdzn5rgran6i39c81i5z22n"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-zlibbioc" ,r-zlibbioc)))

From 5837f1835be41fab16f033eef66adf7d80557d27 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:04:46 +0200
Subject: [PATCH 076/117] gnu: r-affy: Update to 1.58.0.

* gnu/packages/bioinformatics.scm (r-affy): Update to 1.58.0.
[inputs]: Add zlib.
---
 gnu/packages/bioinformatics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index da4afc7747..b650e1245e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9471,14 +9471,14 @@ (define-public r-affyio
 (define-public r-affy
   (package
     (name "r-affy")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affy" version))
        (sha256
         (base32
-         "0jmbkimma5ffsdkk3xp03g4lpz84gd95nkqakif2nqq6wmx0syrj"))))
+         "0sxq875sigm21sf3qncrfrwfdz9nqw1vldxn3d3hj6aq64jg1ki6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affyio" ,r-affyio)
@@ -9487,6 +9487,8 @@ (define-public r-affy
        ("r-biocinstaller" ,r-biocinstaller)
        ("r-preprocesscore" ,r-preprocesscore)
        ("r-zlibbioc" ,r-zlibbioc)))
+    (inputs
+     `(("zlib" ,zlib)))
     (home-page "https://bioconductor.org/packages/affy")
     (synopsis "Methods for affymetrix oligonucleotide arrays")
     (description

From af8710624d2a58e2aea2142b43533800b817ba98 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:05:08 +0200
Subject: [PATCH 077/117] gnu: r-vsn: Update to 3.48.1.

* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.48.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b650e1245e..16ca1fea1f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9499,14 +9499,14 @@ (define-public r-affy
 (define-public r-vsn
   (package
     (name "r-vsn")
-    (version "3.46.0")
+    (version "3.48.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "vsn" version))
        (sha256
         (base32
-         "18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j"))))
+         "0k6mah3g3zqbfap31xmvig4fn452a18xwwa5y0mfj5mj8588p57h"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)

From 7bd25829711fd3b46f1dde494390aa7a6223052a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:05:28 +0200
Subject: [PATCH 078/117] gnu: r-mzid: Update to 1.18.0.

* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.18.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 16ca1fea1f..e3daa4b7f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9533,14 +9533,14 @@ (define-public r-vsn
 (define-public r-mzid
   (package
     (name "r-mzid")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzID" version))
        (sha256
         (base32
-         "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9"))))
+         "060k0xlhg8q802c6zsb4b8ps0ccd9ybyaz0gnsvqkxb786i2vk40"))))
     (properties `((upstream-name . "mzID")))
     (build-system r-build-system)
     (propagated-inputs

From 0f773b90db18e4e395e04276f902f279f236911d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:05:43 +0200
Subject: [PATCH 079/117] gnu: r-pcamethods: Update to 1.72.0.

* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.72.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e3daa4b7f3..25fa2fd514 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9563,14 +9563,14 @@ (define-public r-mzid
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaMethods" version))
        (sha256
         (base32
-         "0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8"))))
+         "0v99yf8m7ryh6z0r3z0ggpqfnflcq5bn1q1i1cl9b7q4p6b4sa07"))))
     (properties `((upstream-name . "pcaMethods")))
     (build-system r-build-system)
     (propagated-inputs

From 250d78eac95c22c227aa38377627aa6e01f6b1bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:06:13 +0200
Subject: [PATCH 080/117] gnu: r-msnbase: Update to 2.6.1.

* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.1.
[propagated-inputs]: Add r-mass and r-scales.
---
 gnu/packages/bioinformatics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 25fa2fd514..5a1443f83a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9593,14 +9593,14 @@ (define-public r-pcamethods
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.4.2")
+    (version "2.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif"))))
+         "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9614,6 +9614,7 @@ (define-public r-msnbase
        ("r-iranges" ,r-iranges)
        ("r-lattice" ,r-lattice)
        ("r-maldiquant" ,r-maldiquant)
+       ("r-mass" ,r-mass)
        ("r-mzid" ,r-mzid)
        ("r-mzr" ,r-mzr)
        ("r-pcamethods" ,r-pcamethods)
@@ -9622,6 +9623,7 @@ (define-public r-msnbase
        ("r-protgenerics" ,r-protgenerics)
        ("r-rcpp" ,r-rcpp)
        ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
        ("r-vsn" ,r-vsn)
        ("r-xml" ,r-xml)))
     (home-page "https://github.com/lgatto/MSnbase")

From bdc8b40af2553dcd27d8bb581a8865c7e9e08d87 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:06:43 +0200
Subject: [PATCH 081/117] gnu: r-msnid: Update to 1.14.0.

* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.14.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5a1443f83a..cee999ad81 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9636,14 +9636,14 @@ (define-public r-msnbase
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx"))))
+         "172q5chi44104iz4y0g42wrimfp7hlhrfa8vzybx6m0ccrkkhl17"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (propagated-inputs

From 0ebd7a4c9f8df90637bca8566156aa6e6531ed35 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:07:01 +0200
Subject: [PATCH 082/117] gnu: r-aroma-light: Update to 3.10.0.

* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.10.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cee999ad81..7c84c3bdc0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9768,14 +9768,14 @@ (define-public r-seurat
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-    (version "3.8.0")
+    (version "3.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "aroma.light" version))
        (sha256
         (base32
-         "0crnk6851jwypqr5l5jcbbay0vi5vvdjyisaf6z2d69c39wmr6sc"))))
+         "1dxsiwsrwcq9mj573f9vpdzrhagdqzal328ma8076px4gg6khxkn"))))
     (properties `((upstream-name . "aroma.light")))
     (build-system r-build-system)
     (propagated-inputs

From 749b71267791368cb20af2682ae0bcc6503a0a7c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:07:22 +0200
Subject: [PATCH 083/117] gnu: r-deseq: Update to 1.32.0.

* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.32.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7c84c3bdc0..0ba21e366b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9795,14 +9795,14 @@ (define-public r-aroma-light
 (define-public r-deseq
   (package
     (name "r-deseq")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq" version))
        (sha256
         (base32
-         "0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9"))))
+         "0ykxw8ksif026xy25wx50j2sdsrp156aqkmhcgfjkpgcw699glnm"))))
     (properties `((upstream-name . "DESeq")))
     (build-system r-build-system)
     (propagated-inputs

From a67dd4c5e936fc6cc635498f42e34df438ecc1af Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:07:38 +0200
Subject: [PATCH 084/117] gnu: r-edaseq: Update to 2.14.0.

* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0ba21e366b..addd9439f2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9826,14 +9826,14 @@ (define-public r-deseq
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "07zm89zcivyn2261aq9grqmly8ji482kr9h9dyfknfdfrpv7jpwv"))))
+         "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs

From 420415b057511779f2357ca255bbee2547e397ed Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:07:49 +0200
Subject: [PATCH 085/117] gnu: r-interactivedisplaybase: Update to 1.18.0.

* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.18.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index addd9439f2..69070af82b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9864,14 +9864,14 @@ (define-public r-edaseq
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "interactiveDisplayBase" version))
        (sha256
         (base32
-         "01yb945jqqimwjgriza6yy4dnp303cdirxrhl4hjyprfdlmnz5p5"))))
+         "05w58z3i9vkma4jd6rhjaxls4yiq4kwrppgcdq9xrr1pxp99k575"))))
     (properties
      `((upstream-name . "interactiveDisplayBase")))
     (build-system r-build-system)

From 646439c7e383c03208ff9114ffa893fadd6d374d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:08:09 +0200
Subject: [PATCH 086/117] gnu: r-annotationhub: Update to 2.12.0.

* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 69070af82b..2d420af211 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9888,14 +9888,14 @@ (define-public r-interactivedisplaybase
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "2.10.1")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4"))))
+         "11gh7qkgazs90czdqgv74gh2hz26xrmdp6wsz9x5pygbxls8xdw3"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs

From 15cc1a686752c681f2f15ef18d69e7b251cb41b6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:08:27 +0200
Subject: [PATCH 087/117] gnu: r-fastseg: Update to 1.26.0.

* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.26.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2d420af211..f704703346 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9923,14 +9923,14 @@ (define-public r-annotationhub
 (define-public r-fastseg
   (package
     (name "r-fastseg")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fastseg" version))
        (sha256
         (base32
-         "0dd7nr3klwz9ailwshnbynhd62lwb8zbbpj6jf3igpb94yi6x2jp"))))
+         "1yw6hai6hb8qy7akdm4frfp6h4zy93zb68kdj094sanm7kgqmgik"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)

From 419e438d52f2b669ec48d19b3a7f20e6c83f463a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:08:50 +0200
Subject: [PATCH 088/117] gnu: r-keggrest: Update to 1.20.0.

* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f704703346..dd6a6da1d6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9953,14 +9953,14 @@ (define-public r-fastseg
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c"))))
+         "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs

From 1ba126e0e4873f6012114067b9aeb468929cf380 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:09:08 +0200
Subject: [PATCH 089/117] gnu: r-gage: Update to 2.30.0.

* gnu/packages/bioinformatics.scm (r-gage): Update to 2.30.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dd6a6da1d6..9aee14a090 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9977,14 +9977,14 @@ (define-public r-keggrest
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.28.2")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii"))))
+         "0j3cqxy97lpf146wkmdfaq9680gicmzxvhp6w5pxq3j7ipiy7262"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)

From d1463f1b0c0d35f02ed24e03d6e7ede77a6dbe40 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:09:23 +0200
Subject: [PATCH 090/117] gnu: r-genomicfiles: Update to 1.16.0.

* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.16.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9aee14a090..8d6df8ee88 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10006,14 +10006,14 @@ (define-public r-gage
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicFiles" version))
        (sha256
         (base32
-         "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n"))))
+         "0bhsq5czigrjyl9gkb2kpkpl367b3ac5g8s280adkcxggn9g7sxq"))))
     (properties `((upstream-name . "GenomicFiles")))
     (build-system r-build-system)
     (propagated-inputs

From d3fb2ad834ceb85c479471dcff1d931624286ab0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:09:42 +0200
Subject: [PATCH 091/117] gnu: r-complexheatmap: Update to 1.18.0.

* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8d6df8ee88..341b14476a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10039,14 +10039,14 @@ (define-public r-genomicfiles
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
-    (version "1.17.1")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ComplexHeatmap" version))
        (sha256
         (base32
-         "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy"))))
+         "0z57mrginzd40niy51dvnyqgbrij05ji0dbwqs3x2as80sq28i3q"))))
     (properties
      `((upstream-name . "ComplexHeatmap")))
     (build-system r-build-system)

From 19adb8985433bb2e707b7cb3f43dda6f75e321bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:10:00 +0200
Subject: [PATCH 092/117] gnu: r-dirichletmultinomial: Update to 1.22.0.

* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.22.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 341b14476a..ce54e1eb68 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10069,14 +10069,14 @@ (define-public r-complexheatmap
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DirichletMultinomial" version))
        (sha256
         (base32
-         "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1"))))
+         "0vcyp81b90in4ls5nbadc66cw2g9aydr94aqifq5j4b7diq74yfs"))))
     (properties
      `((upstream-name . "DirichletMultinomial")))
     (build-system r-build-system)

From bbcd19fb4d856a068ebce05c56c4d4506c04484d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:10:18 +0200
Subject: [PATCH 093/117] gnu: r-ensembldb: Update to 2.4.1.

* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.4.1.
[propagated-inputs]: Remove r-annotationhub.
---
 gnu/packages/bioinformatics.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ce54e1eb68..b5873cc492 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10098,19 +10098,18 @@ (define-public r-dirichletmultinomial
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.2.2")
+    (version "2.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k"))))
+         "1l2b4cxiycv05mz4z4f3dhx57r9ksha02psc114h30ldm5rxz8w6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-annotationfilter" ,r-annotationfilter)
-       ("r-annotationhub" ,r-annotationhub)
        ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-biostrings" ,r-biostrings)

From 94ae875c0a3999abe06cf273a2f934629fefeebe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:10:47 +0200
Subject: [PATCH 094/117] gnu: r-organismdbi: Update to 1.22.0.

* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.22.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b5873cc492..10c669d3df 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10141,14 +10141,14 @@ (define-public r-ensembldb
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OrganismDbi" version))
        (sha256
         (base32
-         "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8"))))
+         "0hb9ni41bjfy5s5ryw2qmqs2sx3i7j47w1g0l8g1pvn7ppnxb6cv"))))
     (properties `((upstream-name . "OrganismDbi")))
     (build-system r-build-system)
     (propagated-inputs

From 34cc18d4dece2ca225bd0ab9175204e02327e214 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:11:02 +0200
Subject: [PATCH 095/117] gnu: r-biovizbase: Update to 1.28.0.

* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 10c669d3df..17e656d814 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10173,14 +10173,14 @@ (define-public r-organismdbi
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f"))))
+         "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs

From e214a6e6ff67f8e2186cd36bb849d805de58499d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:11:18 +0200
Subject: [PATCH 096/117] gnu: r-ggbio: Update to 1.28.0.

* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 17e656d814..10736eb386 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10214,14 +10214,14 @@ (define-public r-biovizbase
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.26.1")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp"))))
+         "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)

From dcd1f0236cf3450bbbf957d94cd29e78e5d64731 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:11:33 +0200
Subject: [PATCH 097/117] gnu: r-gqtlbase: Update to 1.12.0.

* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.12.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 10736eb386..262eed3f5f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10290,14 +10290,14 @@ (define-public r-gprofiler
 (define-public r-gqtlbase
   (package
     (name "r-gqtlbase")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gQTLBase" version))
        (sha256
         (base32
-         "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035"))))
+         "1m3ajpqjhw1nwwsn372r44xfxq0a9a0pzsnrprzdjp6mh52p9b5m"))))
     (properties `((upstream-name . "gQTLBase")))
     (build-system r-build-system)
     (propagated-inputs

From d26f95d0799d47f08914e4659404f82015b9a750 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:11:55 +0200
Subject: [PATCH 098/117] gnu: r-snpstats: Update to 1.30.0.

* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.30.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 262eed3f5f..fc284e06df 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10325,14 +10325,14 @@ (define-public r-gqtlbase
 (define-public r-snpstats
   (package
     (name "r-snpstats")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "snpStats" version))
        (sha256
         (base32
-         "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir"))))
+         "0iydgfnm053iw860qa1bbh4f6nwzlsf3vhgq92gvl2v4xsz1jbbs"))))
     (properties `((upstream-name . "snpStats")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))

From 9b0b108ed911f625bffd4243c8184e6f1402d30b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:12:10 +0200
Subject: [PATCH 099/117] gnu: r-erma: Update to 0.12.0.

* gnu/packages/bioinformatics.scm (r-erma): Update to 0.12.0.
[propagated-inputs]: Remove r-foreach; add r-biocparallel, r-genomeinfodb, and
r-iranges.
---
 gnu/packages/bioinformatics.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fc284e06df..57a70cf332 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10384,24 +10384,26 @@ (define-public r-homo-sapiens
 (define-public r-erma
   (package
     (name "r-erma")
-    (version "0.10.1")
+    (version "0.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "erma" version))
        (sha256
         (base32
-         "1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav"))))
+         "1ka68n18yizlyvb8bpwwcl4hqbsasg8hw8jb3vgy3cd4szji87hh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-foreach" ,r-foreach)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicfiles" ,r-genomicfiles)
        ("r-genomicranges" ,r-genomicranges)
        ("r-ggplot2" ,r-ggplot2)
        ("r-homo-sapiens" ,r-homo-sapiens)
+       ("r-iranges" ,r-iranges)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
        ("r-shiny" ,r-shiny)

From 45c29a6e5cdbe675c33193d19b0a4dcddc31f183 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:12:54 +0200
Subject: [PATCH 100/117] gnu: r-ldblock: Update to 1.10.0.

* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.10.0.
[propagated-inputs]: Add r-biocgenerics.
---
 gnu/packages/bioinformatics.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 57a70cf332..d51b9e9984 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10422,17 +10422,18 @@ (define-public r-erma
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0"))))
+         "0c24zvnwsp39d3q0bps13sc441jj9ms2zi34xsb8c392lqmbypvd"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-erma" ,r-erma)
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-erma" ,r-erma)
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicfiles" ,r-genomicfiles)
        ("r-go-db" ,r-go-db)

From 6929b97583418fca05875339eac3ac3683780766 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:13:23 +0200
Subject: [PATCH 101/117] gnu: r-gqtlstats: Update to 1.12.0.

* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.12.0.
[propagated-inputs]: Add r-homo-sapiens; remove r-ldblock.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d51b9e9984..d8151d57ac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10454,14 +10454,14 @@ (define-public r-ldblock
 (define-public r-gqtlstats
   (package
     (name "r-gqtlstats")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gQTLstats" version))
        (sha256
         (base32
-         "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq"))))
+         "19g8qhfgngdc14cw9k4i44cxhs3qva87x56gjzmn25k1yj8qgsp1"))))
     (properties `((upstream-name . "gQTLstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10484,8 +10484,8 @@ (define-public r-gqtlstats
        ("r-ggplot2" ,r-ggplot2)
        ("r-gqtlbase" ,r-gqtlbase)
        ("r-hardyweinberg" ,r-hardyweinberg)
+       ("r-homo-sapiens" ,r-homo-sapiens)
        ("r-iranges" ,r-iranges)
-       ("r-ldblock" ,r-ldblock)
        ("r-limma" ,r-limma)
        ("r-mgcv" ,r-mgcv)
        ("r-plotly" ,r-plotly)

From fecbbac286c94933a707513b1be35891e9a82984 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:13:51 +0200
Subject: [PATCH 102/117] gnu: r-gviz: Update to 1.24.0.

* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.24.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d8151d57ac..d13f1426f8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10508,14 +10508,14 @@ (define-public r-gqtlstats
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.22.3")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "1grjzrjpzkw572pbvpsvdnfkfgwybl0cnjd7nnk2xdr26wnbsi9a"))))
+         "1fhli7ahkl5r43j0hc89ib41mfadj6qyrg36i03ncz8zs6iqwpx4"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs

From 2d3c172b728362d3d815bbac33908923c0e8ee23 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:14:06 +0200
Subject: [PATCH 103/117] gnu: r-gwascat: Update to 2.12.0.

* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.12.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d13f1426f8..1662fef311 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10554,14 +10554,14 @@ (define-public r-gviz
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi"))))
+         "08ba9il4vbjjwlbwmqg4ai6ya1p09js9agn95sw0dhc9gqln42hx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)

From 8db6256f4b16150c5b9684f6cdcf8723fbe82af6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:14:23 +0200
Subject: [PATCH 104/117] gnu: r-sushi: Update to 1.18.0.

* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.18.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1662fef311..06959d3595 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10594,13 +10594,13 @@ (define-public r-gwascat
 (define-public r-sushi
   (package
     (name "r-sushi")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Sushi" version))
               (sha256
                (base32
-                "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g"))))
+                "1m15hmg4k0qhshyn65xfj5hx7xbaf0kxqw70lxisak6pj1w00l41"))))
     (properties `((upstream-name . "Sushi")))
     (build-system r-build-system)
     (propagated-inputs

From 4dedecbe7078b8bc688ca4f610097ed8f078ff5d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:14:52 +0200
Subject: [PATCH 105/117] gnu: r-fithic: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.6.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 06959d3595..d761e1f569 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10616,13 +10616,13 @@ (define-public r-sushi
 (define-public r-fithic
   (package
     (name "r-fithic")
-    (version "1.4.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "FitHiC" version))
               (sha256
                (base32
-                "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n"))))
+                "06w4q836bi1mvkbl1saghv4r5p4hxpjg8cp7kgad13ls450kqmyd"))))
     (properties `((upstream-name . "FitHiC")))
     (build-system r-build-system)
     (propagated-inputs

From c6c619c1790bf8e4b1348ba9601b7736dc58ed51 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:15:07 +0200
Subject: [PATCH 106/117] gnu: r-hitc: Update to 1.24.0.

* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.24.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d761e1f569..f74f2d69d4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10640,13 +10640,13 @@ (define-public r-fithic
 (define-public r-hitc
   (package
     (name "r-hitc")
-    (version "1.22.1")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "HiTC" version))
               (sha256
                (base32
-                "0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl"))))
+                "0qkk5139f51lwwy1yh7nbkflh5d69prirmhniwam34nlg9rzjm2z"))))
     (properties `((upstream-name . "HiTC")))
     (build-system r-build-system)
     (propagated-inputs

From 5cd725d002a83d13cf58a2778866b61a1b980878 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:15:23 +0200
Subject: [PATCH 107/117] gnu: r-qvalue: Update to 2.12.0.

* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f74f2d69d4..d4b9e31cf2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10669,14 +10669,14 @@ (define-public r-hitc
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i"))))
+         "1ndwkj0hh7v4lwylq1v0fkxqs7mfmbcj8kxbdpj1wkvf131z2ns8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)

From 0840352835737e07a1f133acd69fff132db8ae4e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:15:39 +0200
Subject: [PATCH 108/117] gnu: r-hdf5array: Update to 1.8.0.

* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d4b9e31cf2..f51c247b40 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10698,14 +10698,14 @@ (define-public r-qvalue
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh"))))
+         "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (propagated-inputs

From e9c417361e2612a71344fccaaa58862c8aa02592 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:16:03 +0200
Subject: [PATCH 109/117] gnu: r-rhdf5lib: Update to 1.2.1.

* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.2.1.
[arguments]: Adjust substitutions.
---
 gnu/packages/bioinformatics.scm | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f51c247b40..f4eb281cb7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10724,14 +10724,14 @@ (define-public r-hdf5array
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.0.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w"))))
+         "1y59acac6v8hrhv84gghn9ifsni9xxxacaj177rrl4frmkrz4x3c"))))
     (properties `((upstream-name . "Rhdf5lib")))
     (build-system r-build-system)
     (arguments
@@ -10742,10 +10742,10 @@ (define-public r-rhdf5lib
              (for-each delete-file '("configure" "configure.ac"))
              ;; Do not make other packages link with the proprietary libsz.
              (substitute* "R/zzz.R"
-               (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'")
-                "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'")
-               (("'%s/libhdf5.a %s/libsz.a'")
-                "'%s/libhdf5.a %s/libhdf5.a'"))
+               (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'")
+                "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'")
+               (("'%s/libhdf5.a %s/libsz.a -lz'")
+                "'%s/libhdf5.a %s/libhdf5.a -lz'"))
              (with-directory-excursion "src"
                (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
                (rename-file (string-append "hdf5-" ,(package-version hdf5))
@@ -10772,8 +10772,7 @@ (define-public r-rhdf5lib
                  (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
                  ;; szip is non-free software
                  (("cp \\$\\{SZIP_LIB\\}.*") "")
-                 (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}")
-                  "PKG_LIBS = ${HDF5_LIB}\n")))
+                 (("\\$\\{USER_LIB_DIR\\}libsz.a") "")))
              #t)))))
     (inputs
      `(("zlib" ,zlib)))

From fd613234b746ce45d60f300191f303982f1ac54d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:16:42 +0200
Subject: [PATCH 110/117] gnu: r-beachmat: Update to 1.2.1.

* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1.
[inputs]: Add zlib.
---
 gnu/packages/bioinformatics.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f4eb281cb7..df2d9aa56c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10789,17 +10789,18 @@ (define-public r-rhdf5lib
 (define-public r-beachmat
   (package
     (name "r-beachmat")
-    (version "1.0.2")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beachmat" version))
        (sha256
         (base32
-         "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz"))))
+         "1w90v0jx1zgrfxzx99gdkk0dz2vi25hr51jml1bvq33i64rj7996"))))
     (build-system r-build-system)
     (inputs
-     `(("hdf5" ,hdf5)))
+     `(("hdf5" ,hdf5)
+       ("zlib" ,zlib)))
     (propagated-inputs
      `(("r-delayedarray" ,r-delayedarray)
        ("r-hdf5array" ,r-hdf5array)

From d99e0938fa30954216bbe2dd3de9a4bd17cdf893 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 12:16:59 +0200
Subject: [PATCH 111/117] gnu: r-singlecellexperiment: Update to 1.2.0.

* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index df2d9aa56c..82177e754c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10817,14 +10817,14 @@ (define-public r-beachmat
 (define-public r-singlecellexperiment
   (package
     (name "r-singlecellexperiment")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleCellExperiment" version))
        (sha256
         (base32
-         "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars"))))
+         "0mz3chia250v8v6q8r5cqv5fc4bpcw1hhrfr3p7l5i4xi85scpka"))))
     (properties
      `((upstream-name . "SingleCellExperiment")))
     (build-system r-build-system)

From 8ec56b2956697bedf9d85aa1cb03205639ada323 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 13:34:59 +0200
Subject: [PATCH 112/117] gnu: r-delayedmatrixstats: Update to 1.2.0.

* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 82177e754c..fb4a8c85c8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10930,14 +10930,14 @@ (define-public r-scran
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.0.3")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "1cxjbjdq9hg9cm95rci0al7a4pk2h73ym276ahw9q4977zbg6381"))))
+         "1dasghfy8x27zzmd0igag4mc1gxxxbchsl4hpc1050dj3wnw9w3y"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)

From d7e3299987b2b08f06b545b3032f52f0a3421bc1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 13:35:20 +0200
Subject: [PATCH 113/117] gnu: r-scran: Update to 1.8.2.

* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.2.
[propagated-inputs]: Remove r-zoo; add r-delayedmatrixstats and r-delayedarray.
---
 gnu/packages/bioinformatics.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fb4a8c85c8..e9477501b3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10888,19 +10888,21 @@ (define-public r-scater
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.6.9")
+    (version "1.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm"))))
+         "0nbn5x75gf9d0p18w7vpkbv30cpdqvp5bz8xvila0h7jla7xdyih"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-biocparallel" ,r-biocparallel)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
        ("r-dt" ,r-dt)
        ("r-dynamictreecut" ,r-dynamictreecut)
        ("r-edger" ,r-edger)
@@ -10917,8 +10919,7 @@ (define-public r-scran
        ("r-singlecellexperiment" ,r-singlecellexperiment)
        ("r-statmod" ,r-statmod)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-viridis" ,r-viridis)
-       ("r-zoo" ,r-zoo)))
+       ("r-viridis" ,r-viridis)))
     (home-page "https://bioconductor.org/packages/scran")
     (synopsis "Methods for single-cell RNA-Seq data analysis")
     (description "This package implements a variety of low-level analyses of

From 7799a01ef1b36c2a0f20ee07981bb5cd7fd64313 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 13:35:58 +0200
Subject: [PATCH 114/117] gnu: r-rgraphviz: Update to 2.24.0.

* gnu/packages/graph.scm (r-rgraphviz): Update to 2.24.0.
---
 gnu/packages/graph.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index a9ee949855..b393919e66 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -155,14 +155,14 @@ (define-public r-diffusionmap
 (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

From 83402242eaacbea480a0aa746b024bf44ad23b7d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 13:36:09 +0200
Subject: [PATCH 115/117] gnu: r-mvtnorm: Update to 1.0-8.

* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.0-8.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7a6b674a1d..9b27736f7a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3533,13 +3533,13 @@ (define-public r-r-rsp
 (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)))

From 41f17554d88795bf35fbfc3e05301a6d2f64cca0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 13:36:26 +0200
Subject: [PATCH 116/117] import: cran: Update to Bioconductor 3.7.

* guix/import/cran.scm (%bioconductor-version): Update to 3.7.
---
 guix/import/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index ec2b7e6029..49e5d2d358 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -128,9 +128,9 @@ (define* (maybe-inputs package-inputs #:optional (type 'inputs))
 (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/"

From 92963798a6b81989c52bc199ef224605d9b90063 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 2 Jun 2018 13:42:05 +0200
Subject: [PATCH 117/117] gnu: r-scater: Update to 1.8.0.

* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.0.
[propagated-inputs]: Add r-delayedarray ad r-delayedmatrixstats; remove
r-matrixstats and r-biomart.
---
 gnu/packages/bioinformatics.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e9477501b3..2445991746 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10844,27 +10844,27 @@ (define-public r-singlecellexperiment
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.6.3")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn"))))
+                "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
        ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biomart" ,r-biomart)
        ("r-data-table" ,r-data-table)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
        ("r-dplyr" ,r-dplyr)
        ("r-edger" ,r-edger)
        ("r-ggbeeswarm" ,r-ggbeeswarm)
        ("r-ggplot2" ,r-ggplot2)
        ("r-limma" ,r-limma)
        ("r-matrix" ,r-matrix)
-       ("r-matrixstats" ,r-matrixstats)
        ("r-plyr" ,r-plyr)
        ("r-rcpp" ,r-rcpp)
        ("r-reshape2" ,r-reshape2)