Merge branch 'master' into core-updates

31 files changed, 1021 insertions, 725 deletions

diff --git a/gnu/build/install.scm b/gnu/build/install.scm
index 98c547f2e4..c9ebe124fe 100644
--- a/gnu/build/install.scm
+++ b/gnu/build/install.scm
@@ -18,7 +18,6 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu build install)
-  #:use-module (guix store database)
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
   #:use-module (srfi srfi-26)
@@ -27,6 +26,7 @@
             evaluate-populate-directive
             populate-root-file-system
             register-closure
+            install-database-and-gc-roots
             populate-single-profile-directory))
 
 ;;; Commentary:
@@ -141,34 +141,45 @@ includes /etc, /var, /run, /bin/sh, etc., and all the symlinks to SYSTEM."
                 (try))
               (apply throw args)))))))
 
-(define* (register-closure prefix closure
-                           #:key
-                           (deduplicate? #t) (reset-timestamps? #t)
-                           (schema (sql-schema)))
-  "Register CLOSURE in PREFIX, where PREFIX is the directory name of the
-target store and CLOSURE is the name of a file containing a reference graph as
-produced by #:references-graphs..  As a side effect, if RESET-TIMESTAMPS? is
-true, reset timestamps on store files and, if DEDUPLICATE? is true,
-deduplicates files common to CLOSURE and the rest of PREFIX."
-  (let ((items (call-with-input-file closure read-reference-graph)))
-    (register-items items
-                    #:prefix prefix
-                    #:deduplicate? deduplicate?
-                    #:reset-timestamps? reset-timestamps?
-                    #:registration-time %epoch
-                    #:schema schema)))
+(define %root-profile
+  "/var/guix/profiles/per-user/root")
+
+(define* (install-database-and-gc-roots root database profile
+                                        #:key (profile-name "guix-profile"))
+  "Install DATABASE, the store database, under directory ROOT.  Create
+PROFILE-NAME and have it link to PROFILE, a store item."
+  (define (scope file)
+    (string-append root "/" file))
+
+  (define (mkdir-p* dir)
+    (mkdir-p (scope dir)))
+
+  (define (symlink* old new)
+    (symlink old (scope new)))
+
+  (install-file database (scope "/var/guix/db/"))
+  (chmod (scope "/var/guix/db/db.sqlite") #o644)
+  (mkdir-p* "/var/guix/profiles")
+  (mkdir-p* "/var/guix/gcroots")
+  (symlink* "/var/guix/profiles" "/var/guix/gcroots/profiles")
+
+  ;; Make root's profile, which makes it a GC root.
+  (mkdir-p* %root-profile)
+  (symlink* profile
+            (string-append %root-profile "/" profile-name "-1-link"))
+  (symlink* (string-append profile-name "-1-link")
+            (string-append %root-profile "/" profile-name)))
 
 (define* (populate-single-profile-directory directory
                                             #:key profile closure
                                             (profile-name "guix-profile")
-                                            deduplicate?
-                                            register? schema)
+                                            database)
   "Populate DIRECTORY with a store containing PROFILE, whose closure is given
 in the file called CLOSURE (as generated by #:references-graphs.)  DIRECTORY
 is initialized to contain a single profile under /root pointing to PROFILE.
-When REGISTER? is true, initialize DIRECTORY/var/guix/db to reflect the
-contents of the store; DEDUPLICATE? determines whether to deduplicate files in
-the store.
+
+When DATABASE is true, copy it to DIRECTORY/var/guix/db and create
+DIRECTORY/var/guix/gcroots and friends.
 
 PROFILE-NAME is the name of the profile being created under
 /var/guix/profiles, typically either \"guix-profile\" or \"current-guix\".
@@ -177,9 +188,6 @@ This is used to create the self-contained tarballs with 'guix pack'."
   (define (scope file)
     (string-append directory "/" file))
 
-  (define %root-profile
-    "/var/guix/profiles/per-user/root")
-
   (define (mkdir-p* dir)
     (mkdir-p (scope dir)))
 
@@ -189,22 +197,9 @@ This is used to create the self-contained tarballs with 'guix pack'."
   ;; Populate the store.
   (populate-store (list closure) directory)
 
-  (when register?
-    (register-closure (canonicalize-path directory) closure
-                      #:deduplicate? deduplicate?
-                      #:schema schema)
-
-    (mkdir-p* "/var/guix/profiles")
-    (mkdir-p* "/var/guix/gcroots")
-    (symlink* "/var/guix/profiles"
-              "/var/guix/gcroots/profiles"))
-
-  ;; Make root's profile, which makes it a GC root.
-  (mkdir-p* %root-profile)
-  (symlink* profile
-            (string-append %root-profile "/" profile-name "-1-link"))
-  (symlink* (string-append profile-name "-1-link")
-            (string-append %root-profile "/" profile-name))
+  (when database
+    (install-database-and-gc-roots directory database profile
+                                   #:profile-name profile-name))
 
   (match profile-name
     ("guix-profile"
diff --git a/gnu/build/linux-initrd.scm b/gnu/build/linux-initrd.scm
index c65b5aacfa..fb8a1f5b2b 100644
--- a/gnu/build/linux-initrd.scm
+++ b/gnu/build/linux-initrd.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -139,6 +139,12 @@ REFERENCES-GRAPHS."
 
     (write-cpio-archive output "." #:gzip gzip))
 
+  ;; Make sure directories are writable so we can delete files.
+  (for-each make-file-writable
+            (find-files "contents"
+                        (lambda (file stat)
+                          (eq? 'directory (stat:type stat)))
+                        #:directories? #t))
   (delete-file-recursively "contents"))
 
 ;;; linux-initrd.scm ends here
diff --git a/gnu/build/vm.scm b/gnu/build/vm.scm
index 5579886264..746808515f 100644
--- a/gnu/build/vm.scm
+++ b/gnu/build/vm.scm
@@ -25,7 +25,7 @@
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
   #:use-module (guix build syscalls)
-  #:use-module ((guix store database) #:select (reset-timestamps))
+  #:use-module (guix store database)
   #:use-module (gnu build linux-boot)
   #:use-module (gnu build install)
   #:use-module (gnu system uuid)
@@ -191,6 +191,23 @@ the #:references-graphs parameter of 'derivation'."
           (mkdir output)
           (copy-recursively "xchg" output)))))
 
+(define* (register-closure prefix closure
+                           #:key
+                           (deduplicate? #t) (reset-timestamps? #t)
+                           (schema (sql-schema)))
+  "Register CLOSURE in PREFIX, where PREFIX is the directory name of the
+target store and CLOSURE is the name of a file containing a reference graph as
+produced by #:references-graphs..  As a side effect, if RESET-TIMESTAMPS? is
+true, reset timestamps on store files and, if DEDUPLICATE? is true,
+deduplicates files common to CLOSURE and the rest of PREFIX."
+  (let ((items (call-with-input-file closure read-reference-graph)))
+    (register-items items
+                    #:prefix prefix
+                    #:deduplicate? deduplicate?
+                    #:reset-timestamps? reset-timestamps?
+                    #:registration-time %epoch
+                    #:schema schema)))
+
 
 ;;;
 ;;; Partitions.
diff --git a/gnu/local.mk b/gnu/local.mk
index 86f081f7cf..90dbe94025 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -726,7 +726,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/gd-fix-tests-on-i686.patch		\
   %D%/packages/patches/gd-freetype-test-failure.patch		\
   %D%/packages/patches/gdm-CVE-2018-14424.patch			\
-  %D%/packages/patches/gemma-intel-compat.patch			\
   %D%/packages/patches/geoclue-config.patch			\
   %D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch \
   %D%/packages/patches/ghc-dont-pass-linker-flags-via-response-files.patch	\
@@ -838,7 +837,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/java-xerces-xjavac_taskdef.patch	\
   %D%/packages/patches/jbig2dec-ignore-testtest.patch		\
   %D%/packages/patches/json-glib-fix-tests-32bit.patch		\
-  %D%/packages/patches/jq-CVE-2015-8863.patch			\
   %D%/packages/patches/kdbusaddons-kinit-file-name.patch	\
   %D%/packages/patches/khmer-use-libraries.patch                \
   %D%/packages/patches/libziparchive-add-includes.patch		\
@@ -882,6 +880,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libexif-CVE-2017-7544.patch		\
   %D%/packages/patches/libgcrypt-make-yat2m-reproducible.patch	\
   %D%/packages/patches/libgit2-mtime-0.patch			\
+  %D%/packages/patches/libgit2-oom-test.patch			\
   %D%/packages/patches/libgdata-fix-tests.patch			\
   %D%/packages/patches/libgdata-glib-duplicate-tests.patch	\
   %D%/packages/patches/libgnome-encoding.patch			\
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index be3662798b..9d792021bd 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -35,14 +35,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.7")
+    (version "3.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://brick.kernel.dk/snaps/"
-                                  "fio-" version ".tar.gz"))
+                                  "fio-" version ".tar.bz2"))
               (sha256
                (base32
-                "0rw9jf2ikm19lq4jizavdvvp3vfvlm3annq7jsxl2y5nf1pi2qr7"))))
+                "0s8m0wcz5j6sa1hblj80wk3syy5b4shg7y3gabvm9xa3wj0lzasa"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6ce5c0dc96..bab6b2b64d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -201,14 +201,14 @@ genomes and gene ID formats, largely based on the UCSC table browser.")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.22.2")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
+         "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/hpar/")
     (synopsis "Human Protein Atlas in R")
@@ -219,23 +219,24 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
+         "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-memoise" ,r-memoise)
-       ("r-genomicranges" ,r-genomicranges)
+     `(("r-biostrings" ,r-biostrings)
        ("r-bsgenome" ,r-bsgenome)
-       ("r-rtracklayer" ,r-rtracklayer)
        ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
+       ("r-memoise" ,r-memoise)
+       ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)))
     (home-page "https://bioconductor.org/packages/regioneR/")
     (synopsis "Association analysis of genomic regions")
@@ -247,14 +248,14 @@ region sets and other genomic features.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
+         "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (inputs
@@ -292,14 +293,14 @@ occupancy (overlap) analysis and plotting functions.")
 (define-public r-ripseeker
   (package
     (name "r-ripseeker")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RIPSeeker" version))
        (sha256
         (base32
-         "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
+         "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
     (properties `((upstream-name . "RIPSeeker")))
     (build-system r-build-system)
     (propagated-inputs
@@ -325,14 +326,14 @@ processing to visualization and annotation.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.36.0")
+    (version "2.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
+         "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-survival" ,r-survival)
@@ -363,13 +364,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.58.2")
+    (version "1.60.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "07smbb3c30pr5r425g181xsg0rs5jx6x2q6xpwb5dqgicxrz30ga"))))
+                "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
@@ -410,18 +411,19 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.14.2")
+    (version "3.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "13rksc65lxxzyw11galh6xzvgzp5ii0gwiwpvrm395v2r17rhwsc"))))
+         "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-biostrings" ,r-biostrings)
        ("r-delayedarray" ,r-delayedarray)
        ("r-go-db" ,r-go-db)
@@ -437,7 +439,6 @@ determining dependencies between variables, code improvement suggestions.")
        ("r-multtest" ,r-multtest)
        ("r-rbgl" ,r-rbgl)
        ("r-graph" ,r-graph)
-       ("r-biocinstaller" ,r-biocinstaller)
        ("r-regioner" ,r-regioner)
        ("r-dbi" ,r-dbi)
        ("r-ensembldb" ,r-ensembldb)
@@ -465,12 +466,12 @@ enrichedGO (addGeneIDs).")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.58.0")
+    (version "1.60.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
+               (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))
@@ -484,12 +485,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.40.0")
+   (version "1.42.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
+             (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -504,12 +505,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.42.0")
+   (version "2.44.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
+             (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -527,12 +528,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
+               (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -559,14 +560,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.14.0")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
+         "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -585,14 +586,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
+         "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -619,14 +620,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
+         "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -658,14 +659,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
+         "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -686,14 +687,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
+         "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
@@ -718,14 +719,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
+         "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -757,14 +758,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9"))))
+         "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-amap" ,r-amap)))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -777,14 +778,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l"))))
+         "1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -803,14 +804,14 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "1.8.2")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s"))))
+         "0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
@@ -830,14 +831,14 @@ information.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3"))))
+         "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -854,14 +855,14 @@ in omics data.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p"))))
+         "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -890,14 +891,14 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x"))))
+         "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -917,14 +918,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj"))))
+         "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -939,3 +940,32 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
 samples.")
     (license license:artistic2.0)))
+
+(define-public r-biocneighbors
+  (package
+    (name "r-biocneighbors")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BiocNeighbors" version))
+       (sha256
+        (base32
+         "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
+    (properties `((upstream-name . "BiocNeighbors")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppannoy" ,r-rcppannoy)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/BiocNeighbors")
+    (synopsis "Nearest Neighbor Detection for Bioconductor packages")
+    (description
+     "This package implements exact and approximate methods for nearest
+neighbor detection, in a framework that allows them to be easily switched
+within Bioconductor packages or workflows.  The exact algorithm is implemented
+using pre-clustering with the k-means algorithm.  Functions are also provided
+to search for all neighbors within a given distance.  Parallelization is
+achieved for all methods using the BiocParallel framework.")
+    (license license:gpl3)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1cf1de1ae5..1fac960eff 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -262,14 +262,14 @@ instance, it implements several methods to assess contig-wise read coverage.")
     (name "bamtools")
     (version "2.5.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/pezmaster31/bamtools/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pezmaster31/bamtools.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa"))))
+                "0nfb2ypcx9959xnbz6wxh6py3xfizgmg8nrknxl95c507m9hmq8b"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
@@ -438,11 +438,11 @@ BED, GFF/GTF, VCF.")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+                                  "releases/download/v" version
+                                  "/bedtools-" version ".tar.gz"))
               (sha256
                (base32
-                "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))
+                "11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz"))))
     (arguments
      '(#:test-target "test"
        #:phases
@@ -520,13 +520,14 @@ provides the Ribotaper pipeline.")
     (version "0.2.2")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/ratschlab/RiboDiff/"
-                           "archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ratschlab/RiboDiff.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
+         "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2
@@ -563,12 +564,14 @@ independently with transcriptional regulation.")
     (name "bioawk")
     (version "1.0")
     (source (origin
-      (method url-fetch)
-      (uri (string-append "https://github.com/lh3/bioawk/archive/v"
-                          version ".tar.gz"))
-      (file-name (string-append name "-" version ".tar.gz"))
-      (sha256
-       (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/lh3/bioawk.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm"))))
     (build-system gnu-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -582,13 +585,13 @@ independently with transcriptional regulation.")
        (modify-phases %standard-phases
          (delete 'configure) ; There is no configure phase.
          (replace 'install
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let* ((out (assoc-ref outputs "out"))
-                   (bin  (string-append out "/bin"))
-                   (man (string-append out "/share/man/man1")))
-              (mkdir-p man)
-              (copy-file "awk.1" (string-append man "/bioawk.1"))
-              (install-file "bioawk" bin)))))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin  (string-append out "/bin"))
+                    (man (string-append out "/share/man/man1")))
+               (mkdir-p man)
+               (copy-file "awk.1" (string-append man "/bioawk.1"))
+               (install-file "bioawk" bin)))))))
     (home-page "https://github.com/lh3/bioawk")
     (synopsis "AWK with bioinformatics extensions")
     (description "Bioawk is an extension to Brian Kernighan's awk, adding the
@@ -688,38 +691,62 @@ Python.")
 
 (define-public python-biom-format
   (package
-   (name "python-biom-format")
-   (version "2.1.6")
-   (source
-    (origin
-     (method url-fetch)
-     ;; Use GitHub as source because PyPI distribution does not contain
-     ;; test data: https://github.com/biocore/biom-format/issues/693
-     (uri (string-append "https://github.com/biocore/biom-format/archive/"
-                         version ".tar.gz"))
-     (file-name (string-append name "-" version ".tar.gz"))
-     (sha256
-      (base32
-       "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj"))))
-   (build-system python-build-system)
-   (propagated-inputs
-    `(("python-numpy" ,python-numpy)
-      ("python-scipy" ,python-scipy)
-      ("python-future" ,python-future)
-      ("python-click" ,python-click)
-      ("python-h5py" ,python-h5py)
-      ("python-pandas" ,python-pandas)))
-   (native-inputs
-    `(("python-nose" ,python-nose)))
-   (home-page "http://www.biom-format.org")
-   (synopsis "Biological Observation Matrix (BIOM) format utilities")
-   (description
-    "The BIOM file format is designed to be a general-use format for
+    (name "python-biom-format")
+    (version "2.1.7")
+    (source
+     (origin
+       (method git-fetch)
+       ;; Use GitHub as source because PyPI distribution does not contain
+       ;; test data: https://github.com/biocore/biom-format/issues/693
+       (uri (git-reference
+             (url "https://github.com/biocore/biom-format.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-cython
+           (lambda _ (setenv "USE_CYTHON" "1") #t))
+         (add-after 'unpack 'disable-broken-test
+           (lambda _
+             (substitute* "biom/tests/test_cli/test_validate_table.py"
+               (("^(.+)def test_invalid_hdf5" m indent)
+                (string-append indent
+                               "@npt.dec.skipif(True, msg='Guix')\n"
+                               m)))
+             #t))
+         (add-before 'reset-gzip-timestamps 'make-files-writable
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (for-each (lambda (file) (chmod file #o644))
+                         (find-files out "\\.gz"))
+               #t))))))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)
+       ("python-flake8" ,python-flake8)
+       ("python-future" ,python-future)
+       ("python-click" ,python-click)
+       ("python-h5py" ,python-h5py)
+       ("python-pandas" ,python-pandas)))
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-nose" ,python-nose)))
+    (home-page "http://www.biom-format.org")
+    (synopsis "Biological Observation Matrix (BIOM) format utilities")
+    (description
+     "The BIOM file format is designed to be a general-use format for
 representing counts of observations e.g. operational taxonomic units, KEGG
 orthology groups or lipid types, in one or more biological samples
 e.g. microbiome samples, genomes, metagenomes.")
-   (license license:bsd-3)
-   (properties `((python2-variant . ,(delay python2-biom-format))))))
+    (license license:bsd-3)
+    (properties `((python2-variant . ,(delay python2-biom-format))))))
 
 (define-public python2-biom-format
   (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
@@ -2741,16 +2768,14 @@ genes in incomplete assemblies or complete genomes.")
       (version "2.3")
       (source
        (origin
-         (method url-fetch)
-         (uri (string-append
-               "https://github.com/ctSkennerton/fxtract/archive/"
-               version ".tar.gz"))
-         (file-name (string-append "ctstennerton-util-"
-                                   (string-take util-commit 7)
-                                   "-checkout"))
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/ctSkennerton/fxtract.git")
+               (commit version)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
-           "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
+           "0hab3gpwf4w9s87qlbswq6ws1qqybh4dcqk79q1ahyldzai5fgp5"))))
       (build-system gnu-build-system)
       (arguments
        `(#:make-flags (list
@@ -2804,19 +2829,22 @@ comment or quality sections.")
 (define-public gemma
   (package
     (name "gemma")
-    (version "0.96")
+    (version "0.98")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/xiangzhou/GEMMA.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
-              (patches (search-patches "gemma-intel-compat.patch"))))
+                "1s3ncnbn45r2hh1cvrqky1kbqq6546biypr4f5mkw1kqlrgyh0yg"))))
     (inputs
-     `(("gsl" ,gsl)
+     `(("eigen" ,eigen)
+       ("gfortran" ,gfortran "lib")
+       ("gsl" ,gsl)
        ("lapack" ,lapack)
+       ("openblas" ,openblas)
        ("zlib" ,zlib)))
     (build-system gnu-build-system)
     (arguments
@@ -2831,6 +2859,15 @@ comment or quality sections.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
+         (add-after 'unpack 'find-eigen
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Ensure that Eigen headers can be found
+             (setenv "CPLUS_INCLUDE_PATH"
+                     (string-append (getenv "CPLUS_INCLUDE_PATH")
+                                    ":"
+                                    (assoc-ref inputs "eigen")
+                                    "/include/eigen3"))
+             #t))
          (add-before 'build 'bin-mkdir
           (lambda _
             (mkdir-p "bin")
@@ -2854,16 +2891,16 @@ association studies (GWAS).")
 (define-public grit
   (package
     (name "grit")
-    (version "2.0.2")
+    (version "2.0.5")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/nboley/grit/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/nboley/grit.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
+                "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2
@@ -2875,13 +2912,7 @@ association studies (GWAS).")
              (delete-file "grit/sparsify_support_fns.c")
              (delete-file "grit/call_peaks_support_fns.c")
              (substitute* "setup.py"
-               (("Cython.Setup") "Cython.Build")
-               ;; Add numpy include path to fix compilation
-               (("pyx\", \\]")
-                (string-append "pyx\", ], include_dirs = ['"
-                               (assoc-ref inputs "python-numpy")
-                               "/lib/python2.7/site-packages/numpy/core/include/"
-                               "']")))
+               (("Cython.Setup") "Cython.Build"))
              #t)))))
     (inputs
      `(("python-scipy" ,python2-scipy)
@@ -2975,16 +3006,11 @@ particular, reads spanning multiple exons.")
     (source
      (origin
        (method url-fetch)
-       ;; FIXME: a better source URL is
-       ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
-       ;;                "/downloads/hisat2-" version "-source.zip")
-       ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"
-       ;; but it is currently unavailable.
-       (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz")
-       (file-name (string-append name "-" version ".tar.gz"))
+       (uri (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
+                           "/downloads/hisat2-" version "-source.zip"))
        (sha256
         (base32
-         "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50"))))
+         "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no check target
@@ -3091,14 +3117,14 @@ from high-throughput sequencing assays.")
     (name "java-htsjdk")
     (version "2.3.0") ; last version without build dependency on gradle
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/samtools/htsjdk/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/samtools/htsjdk.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq"))
+                "1b178ixcabanm834ydjl3jiakpyxdmki32hqfv2abrzn3rcwa28i"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete pre-built binaries
@@ -3655,14 +3681,14 @@ data.  It also provides the @command{bgzip}, @command{htsfile}, and
     (name "idr")
     (version "2.0.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/nboley/idr/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/nboley/idr.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3"))
+                "04j876h6z444v2q79drxx283d3k5snd72kj895wbalnl42206x9g"))
               ;; Delete generated C code.
               (snippet
                '(begin (delete-file "idr/inv_cdf.c") #t))))
@@ -3800,16 +3826,16 @@ data.")
 (define-public kaiju
   (package
     (name "kaiju")
-    (version "1.6.2")
+    (version "1.6.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/bioinformatics-centre/kaiju/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/bioinformatics-centre/kaiju")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1kdn4rxs0kr9ibmrgrfcci71aa6j6gr71dbc8pff7731rpab6kj7"))))
+                "119pzi0ddzv9mjg4wwa6han0cwr3k3ssn7kirvsjfcq05mi5ka0x"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.
@@ -3823,8 +3849,7 @@ data.")
              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
                (mkdir-p bin)
                (chdir "..")
-               (copy-recursively "bin" bin)
-               (copy-recursively "util" bin))
+               (copy-recursively "bin" bin))
              #t)))))
     (inputs
      `(("perl" ,perl)
@@ -4679,14 +4704,14 @@ different command-line tools:
     (name "prodigal")
     (version "2.6.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/hyattpd/Prodigal/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/hyattpd/Prodigal.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"))))
+                "1fs1hqk83qjbjhrvhw6ni75zakx5ki1ayy3v6wwkn3xvahc9hi5s"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no check target
@@ -6322,14 +6347,14 @@ data types as well.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf"))))
+         "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -6349,13 +6374,13 @@ microarrays.")
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms"))))
+                "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)
@@ -6372,14 +6397,14 @@ penalized least squares regression method.")
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g"))))
+         "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -6397,14 +6422,14 @@ penalized least squares regression method.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi"))))
+         "0p64s1n1627yafnp25wjr4b22p34lqw574fx2qg4s1m0lffh1z6i"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -6424,14 +6449,14 @@ high-throughput sequencing experiments.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.20.0")
+    (version "1.22.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "1wjnfpb41a9mmf9a22bz4zh7r1d4id50vpdc1mn5vfzrz7li9qik"))))
+         "1b2bmvcsfzvks47d7w46zplcwz0kgcdhx5xmx3x9lp2gvx2p84r5"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6461,14 +6486,14 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "1mqb3mdxcsi3largsl7k27bvqrgps9ixv806xvmf29pw0xn05sg1"))))
+         "0jh1640cnzpk8x3155cqc8dvrs1rciw3d6nv2k70baw96bhrynp8"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6504,14 +6529,14 @@ exploration of the results.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.22.2")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "17kmy7nvpyyj6w5jyrjciw87rydmmmc8q6cnwqjv1j7li9bp09gr"))))
+         "13yvhf3yskmvhs8szs6rkw93h81h5xqa3h19h91pp6nprhc8s3ll"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -6534,14 +6559,14 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "0hj972mmqpyi5fx1rq33kysavdyz4nspi6gcffzi3rv339m0anhf"))))
+         "0jy95m38c4qp0a12097hhm2gg63k96k6ydhb11dy379h3ziapcar"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs `(("r-graph" ,r-graph)))
@@ -6555,14 +6580,14 @@ the graph algorithms contained in the Boost library.")
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "11bv92svik399q677jv96b71i4bq68xxyxn1yijpdik2lq4hgl7a"))))
+         "110al7x0ig8plzrprvhwc7xshi1jzpj2n8llhhg2fh6v6k0k6awr"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6582,14 +6607,14 @@ Enrichment Analysis} (GSEA).")
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.46.0")
+    (version "2.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "03wfqa8d1dgwsm327zl2mpkq7dq3mzhq12598qz3ylfhrwplbgx0"))))
+         "1jdm83bwdfhpfm1y6hwgvxzj6l83h1bdkqv23799kzywnwm016kv"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6613,14 +6638,14 @@ analysis.")
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.46.0")
+    (version "2.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "1i5mydz5d95w2k28qr9j01hmbnl2id55jq94jvcpcyp1pvinkdq0"))))
+         "0wlqqgfynwqnqhckhsfjwg9zkj6hkmzwd5y76dhqz720vy21rcln"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6644,14 +6669,14 @@ testing and other simple calculations.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "038z3z7qaw5bpgjzy91sjkybsny6jwjjsrnnq4gdqdw9ss1qy1fb"))))
+         "0iks123i1adkb9i2q4wvfqdmmj9dy867jvngj9757y8gj6xbcpy1"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -6686,14 +6711,14 @@ ungapped alignment formats.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "1550pd63mmky0vgkmpni7zf14kqz1741wv63nfaw29kcmhh3m5lm"))))
+         "0l26q8zjdmzg84g7f25gv9z60sykybahlpg5bg9bmpbg5lzcsx04"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6732,14 +6757,14 @@ annotation infrastructure.")
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "1kjb14apyly44qdlx2ld6gr69wlazd4mbhs58l35hir12aphgrzp"))))
+         "1ph92fv44b90v7mk4b1mjvv0dlrhl8ba01klxbnd0vs4qn9zxplh"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7051,13 +7076,13 @@ barplots or heatmaps.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.26.0")
+    (version "0.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "19qxhy2cd3pykkhzbb5q3crgaxf65cpzf2mkfsz16gqhi8flj72p"))))
+                "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -7071,13 +7096,13 @@ packages.")
 (define-public r-biocinstaller
   (package
     (name "r-biocinstaller")
-    (version "1.30.0")
+    (version "1.32.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocInstaller" version))
               (sha256
                (base32
-                "1xg1gi1hf5vflp71ji21gnmr4kcjpx8a6c47cllpc7yqnjv5nfg0"))))
+                "1s1f9qhyf3mc73ir25x2zlgi9hf45a37lg4z8fbva4i21hqisgsl"))))
     (properties
      `((upstream-name . "BiocInstaller")))
     (build-system r-build-system)
@@ -7090,13 +7115,13 @@ Bioconductor, CRAN, and Github.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.48.3")
+    (version "1.50.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1rxvwikqivsgxjjcazlszy8xgz346lfh5rw4llxw6fz38fjgb0k5"))))
+                "0hjm3r58i0r9qhyar9pk250cx7sfijg0lnvi12a9s6brmmbip1a3"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -7140,19 +7165,20 @@ authoring books and technical documents with R Markdown.")
 
 (define-public r-biocstyle
   (package
-   (name "r-biocstyle")
-   (version "2.8.2")
+    (name "r-biocstyle")
+    (version "2.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "17m901ylz00w1a3nq5f910v55zixm1nr6rb3qrsbhqd94qzr0l2p"))))
+                "01lm8xljilj666fcl3wnw82dxkcxnlr294lddr553rm8xr5nwg31"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bookdown" ,r-bookdown)
+     `(("r-biocmanager" ,r-biocmanager)
+       ("r-bookdown" ,r-bookdown)
        ("r-knitr" ,r-knitr)
        ("r-rmarkdown" ,r-rmarkdown)
        ("r-yaml" ,r-yaml)))
@@ -7166,13 +7192,13 @@ functionality.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "1srp1g809f1nn0fyqknr7r6dq89bw1xpjvmygr7cw6ffknbc671s"))))
+                "0zamvs5jar38293ff27imvwy0ra25y64ls9z8w3q1y4jcp8p8pg7"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
@@ -7199,8 +7225,9 @@ functionality.")
      `(("r-codetools" ,r-codetools)
        ("r-graph" ,r-graph)
        ("r-httr" ,r-httr)
+       ("r-knitr" ,r-knitr)
        ("r-optparse" ,r-optparse)
-       ("r-biocinstaller" ,r-biocinstaller)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-biocviews" ,r-biocviews)
        ("r-stringdist" ,r-stringdist)))
     (home-page "https://bioconductor.org/packages/BiocCheck")
@@ -7235,13 +7262,13 @@ that accept short and long options.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.54.0")
+    (version "1.56.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DNAcopy" version))
               (sha256
                (base32
-                "03hfhmmc5y60r2gcgm367w2fr7qj115l74m9bp3h9qpn5yci0d8n"))))
+                "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
     (properties
      `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
@@ -7257,13 +7284,13 @@ abnormal copy number.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.18.3")
+    (version "0.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "02bps2rpjqx2npwxq3x62ncwi9ggr165cwi56h6hld28bw2gddy8"))))
+                "0qgiykjhnsvvpcp3zwmrnpx3bv3msvj0szchyvb1yb0fxw716xc5"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -7309,13 +7336,13 @@ utilities for sequence data management under the ACNUC system.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.14.12")
+    (version "2.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "1ar8sqqgjdy00dbgrxnacqy6gwir5xax76yf0vjxi2vj2skqb0kn"))))
+                "0ljppsk611xi72gc8mbdx1311b63b1ijd401jz5xmxk5frla1nc1"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -7361,13 +7388,13 @@ ID and species.  It is used by functions in the GenomeInfoDb package.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "0yhnqhaydmmq7ihmhj3rbal4afq5p993l2qqrd0n5wmbyg7glg2d"))))
+                "1xqpgngd8by0yn627v9kz26a03v5a1lhcfwlnx2i0ivplk9bd40s"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -7389,13 +7416,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.22.5")
+    (version "3.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0pkcdkh8mwdaca6xa8a7vwdfh46r03rkxwkrf17pwwd4557j7lj7"))))
+                "0ihihgzrgb4q3xc8xkzp1v76ndgihrj4gas00fa25vggfs1v6hvg"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7417,13 +7444,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.26.1")
+    (version "1.28.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "1r55ki951dj81qvy73knfcy69ik5vzkd56wnk3f6vvf9vngqb8jr"))))
+                "0gvah258mkaafhbna81zwknx8qr3lidbcx5qvwk39q3yswr9mi49"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -7455,13 +7482,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.36.5")
+    (version "3.38.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "0d13w95si7l6fqfsdf6k50v4l573hhfva6mvd94v26iba24p2f6x"))))
+                "1wkh362rmn24q7bkinb6nx62a31wl3r3myg5l326gx65wpwdnx97"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7474,13 +7501,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.20.0")
+    (version "0.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "1zjlhh9lsyhg0js1858csyw2389kbrzdqnqnha833wazkwxilp3f"))))
+                "01fph1ydd6g0rl5mcw54spx22glq2kqv7wyw8bqw0plmabzcwwdm"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -7510,13 +7537,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.32.7")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "1lh54asabrmk982636avpp1kcfzakwxi31cbj3jc8mkhar1mkyrx"))))
+                "0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -7539,13 +7566,13 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.40.0")
+    (version "2.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "1iwds2a5ir29k19dbpynlc7nn836cw2gamchhgpi2jf2xar9m9jz"))))
+                "10nr6nrkj5vlq8hsgbhbhv669z0dbpz4m3vz9k32rx1czbrrqwin"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
@@ -7561,13 +7588,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.42.1")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "0afkbzli08vq02r2pr9phrz3rxd6ilp1w7yw8y99nbjiz14f8b1c"))))
+                "1954vimkx5yb9irppq8vssq0f3yjkg36w38b9r0rqmijx1ps7x5d"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -7588,13 +7615,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.36.1")
+    (version "2.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0b70s350ffc74v3xz5c3jpazr9zxdb7gjmjfj7aghlsrizrspill"))))
+                "1lshkknp7dmr3p6dd2zbv86cc71h53ggh9ji83jcjym8sgbbspl2"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7621,13 +7648,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.14.2")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "1llb5a62hn4yxpdgqdh2l7i5zd06mjkk8hagsna69cq65wv6iifm"))))
+                "0g16cy0vjapqkb188z63r1b6y96m9g8vx0a3v2qavzxc177k0cja"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -7646,13 +7673,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.48.0")
+    (version "2.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "118b490jk87ydigm6ln25ms4kskzkw0akmh77clzznhzpqnxsi6j"))))
+                "0zw0dj67fnpbz4iqnam5fxs92c1c8w8d7mzl0rkq4ksx0xl8vgg7"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -7672,13 +7699,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "1.32.3")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "1hpjr22h33pf4fgv0sj83rqzv6l5l7s6fpmmqvchh45ikks1mnhq"))))
+                "01v4bjhj2i126pwyk0v9lvmfp2ih495xsq903k3xa2z24bjxphbi"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -7716,13 +7743,13 @@ files.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.6.6")
+    (version "0.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0rkp0mfsq3wfnib389dh3i44ab0wiz8skkjcv4596dwgq50jqpf2"))))
+                "0cl5anqkjwvqx19snjhz0zj8cp8ibckiifl28h821h50g62nvb2f"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -7747,13 +7774,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.10.1")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "0v3zxl9cqsv79ag5cnvzlhvgaz5cr8f4rn7flmwnwpqd508cznl1"))))
+                "07805572xhpj5mfwq6kw1ha21wgalqvhh4ydvafyl1bnf3r20vps"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -7778,13 +7805,13 @@ samples.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "00pi2cnkkbj2023fg2x2cmglkdalwzy1vr3glsikwz7ix9yylcaw"))))
+                "0a3zhwripfw2508fvgx3wzqa8nq8vnslg97a911znpwvxh53jl24"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
@@ -7811,13 +7838,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.40.6")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "1wxxxlyps19dw3i0pw4mlm3kinnswsc35rgvlnbwvpnpjbca6w4l"))))
+                "0a4mhd926w9slkfil5xgngjsfdj024a4w57w2bm3d4r0pj8y5da7"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7858,13 +7885,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.32.3")
+    (version "1.34.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "06prj5iih3ywsgq00lgfl29p3f8j23a0kqqhzhqcgjrrwsp94588"))))
+                "0slq6hv5bmc3bgrl824jzmr6db3fvaj6b7ihwmdn76pgqqbq2fq6"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -7923,13 +7950,13 @@ information about the latest version of the Gene Ontologies.")
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.32.0")
+    (version "2.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "05yxnkid8bgw9lkm90if9fg63djhgvbailfa3qsfqa5c0zjmixw1"))))
+                "1j1jcd16j564kr6qz28140fzmnh9xasi84v1c1fi98sqv30zq9bh"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
@@ -7956,13 +7983,13 @@ dependencies between GO terms can be implemented and applied.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.48.0")
+    (version "1.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1rk2piqq5dppkd51ln3r872d7ng3rvq98071mnd0xdv2xwnyn5g8"))))
+                "07z4zxx0khrc86qqvc7vxww8df9fh6pyks9ajxkc9gdqr5nn79j7"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
@@ -8017,13 +8044,13 @@ genome data packages and support for efficient SNP representation.")
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.54.0")
+    (version "1.56.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "1d3cpfaqlq2gnb3hsc2yhxwkrnbd7m6ifif32yp0ya0jr5brl4hr"))))
+                "08z0pj1dz5iq967nwj67qyka7ir7m5an2ggv7bsrlz3apzfsla33"))))
     (inputs
      `(("gfortran" ,gfortran)))
     (build-system r-build-system)
@@ -8037,13 +8064,13 @@ microarray data, using nearest neighbor averaging.")
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "seqPattern" version))
               (sha256
                (base32
-                "0dw0yldfcf0ibvpqxlpx1ijnjf9lma47w9w22siszzhw09i0wp3w"))))
+                "0di83qi83mrlw7i12khsq55d03hlazcywaa9m9pki1sfhafpq733"))))
     (properties
      `((upstream-name . "seqPattern")))
     (build-system r-build-system)
@@ -8064,13 +8091,13 @@ reference point and sorted by a user defined feature.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "1vdmdyrq0n7pf8cvy2950v7hrcrcbd9zl4fg7dcmyly3iiwdyirp"))))
+                "0g0v4alfpqlinqinjnyzl3mrjnpbdx9ri34mcaiqbvbvg8ic8wvg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
@@ -8242,14 +8269,14 @@ annotations for the genome of the model mouse Mus musculus.")
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqLogo" version))
        (sha256
         (base32
-         "16xvqcdknix9vjm8mrixi6nyfsr45jm844jh1x90m8044lwrsic1"))))
+         "022vr9ydwcivs7rw7kwj73gfk5gc7ckwa1q66vhd4kw9ylh70v68"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/seqLogo")
@@ -8488,14 +8515,14 @@ Biostrings objects.")
 (define-public r-motifrg
   (package
     (name "r-motifrg")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifRG" version))
        (sha256
         (base32
-         "0mxhyidkyd2zqahdbg69y20r550z78lvr1r3pbjymnwfg4hcfq1p"))))
+         "1wxww6i0jgyapqclcwy0zzf9kqjvrvylr89z7yhg1izi7jnw2fka"))))
     (properties `((upstream-name . "motifRG")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8540,13 +8567,13 @@ two-dimensional genome scans.")
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "zlibbioc" version))
               (sha256
                (base32
-                "1rwr0mci8a712q0isavi4jmhm94gwivc4nr8j7r4kw05flp4g7gz"))))
+                "0bjvzy24kab7ank02cc1qk2ikcz4dllgf66wpsdl0d3zp4gn3l2h"))))
     (properties
      `((upstream-name . "zlibbioc")))
     (build-system r-build-system)
@@ -8582,14 +8609,14 @@ secondary structure and comparative analysis in R.")
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "16ywnb8cmr2xabd1i21b92rfziw7xfbv25yv16ipw617p41wa39z"))))
+         "1h4q54f8za3aaxgy186zf2165sar5c3cgxkk44lq5hzx5pxkl5wn"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8609,14 +8636,14 @@ of other R packages who wish to make use of HTSlib.")
 (define-public r-bamsignals
   (package
     (name "r-bamsignals")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bamsignals" version))
        (sha256
         (base32
-         "141q3p4lzwiqk1mfxi8q1q84axjl0gyiqg59xd3sp4viny4jqmgv"))))
+         "19irfx1y1izf903vq59wxsdbf88g143zy9l89gxqawh7jfxds8w8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -8639,41 +8666,33 @@ paired-end data.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.6.0")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "0vmn7a0rm2ban0kaxrf5danhss2r4hfhnwh5889fjcgqy300fdd5"))))
+                "0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad"))))
     (build-system r-build-system)
-    (native-inputs
-     `(("r-testthat" ,r-testthat)
-       ;; During vignette building knitr checks that "pandoc-citeproc"
-       ;; is in the PATH.
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
        ("r-biomart" ,r-biomart)
        ("r-biostrings" ,r-biostrings)
        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
-       ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
-       ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
        ("r-cowplot" ,r-cowplot)
        ("r-data-table" ,r-data-table)
        ("r-dbi" ,r-dbi)
        ("r-dt" ,r-dt)
        ("r-genomation" ,r-genomation)
+       ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggseqlogo" ,r-ggseqlogo)
        ("r-knitr" ,r-knitr)
        ("r-motifrg" ,r-motifrg)
        ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-org-ce-eg-db" ,r-org-ce-eg-db)
-       ("r-org-dm-eg-db" ,r-org-dm-eg-db)
-       ("r-org-mm-eg-db" ,r-org-mm-eg-db)
        ("r-pbapply" ,r-pbapply)
        ("r-pheatmap" ,r-pheatmap)
        ("r-plotly" ,r-plotly)
@@ -8739,14 +8758,14 @@ library implementing most of the pipeline's features.")
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "1.6.1")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "1yq7351j42mjxn8fd3c5bdxzb2l5s4lvqhjdvv4rwj4f600n6wj9"))))
+         "0w9lg1zs106h6rqvy8mhikq6q6q9syw6c1prcxr38ssh85rcih12"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -8915,13 +8934,13 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "1qjc7ah9dzccpvcjrp9k4qnaz13x6kvy1c1xpdj503km6k528lip"))))
+                "0za2js8hqjgz8ria09cglynffj4w9vrzg85nmn1xgpvmc1xk813h"))))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/tximport")
     (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
@@ -8937,13 +8956,13 @@ of gene-level counts.")
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.24.0")
+    (version "2.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "15cmmchhk8bnp94gxg0zk9qyzdjx5kv16dzpbnb62mkq7ydmifx6"))))
+                "0xmpkfdsmgl79ffffj7cf9fx3zxki2rk0xn25k778kr3s0sbmhis"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rhdf5lib" ,r-rhdf5lib)))
@@ -8964,13 +8983,13 @@ the available RAM.")
 (define-public r-annotationfilter
   (package
     (name "r-annotationfilter")
-    (version "1.4.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationFilter" version))
               (sha256
                (base32
-                "1w8ypfdz4g7vnwfrvnhjcpm8waciqyq2cn883ajdwg4vv7a5mj9a"))))
+                "0wrr10cxjzmxx46vjzq2nsf6xlqz1sqwx4xm0sk3d77ff8wmph4x"))))
     (properties
      `((upstream-name . "AnnotationFilter")))
     (build-system r-build-system)
@@ -9267,14 +9286,14 @@ common bioinformatics tools.")
 (define-public r-chipseq
   (package
     (name "r-chipseq")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chipseq" version))
        (sha256
         (base32
-         "09f8dgl5ni75qkf7nvvppwr3irpplv4xb3ks59ld7l8i2mplcrx7"))))
+         "1pp1rm5fs3hlar5x4dl3a3b4gara7qwf81dbvka6r1n78hrf9x1b"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -9319,14 +9338,14 @@ GenomicRanges Bioconductor package.")
 (define-public r-copywriter
   (package
     (name "r-copywriter")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CopywriteR" version))
        (sha256
         (base32
-         "0b7xwq1va2zclb54f07c5ipmmq4iv2hrlph3j93jz5hmyayv50z3"))))
+         "0aamxafdk98n7s92jyqs65d6ljpnc2463vanvsw80p44qn6l6awn"))))
     (properties `((upstream-name . "CopywriteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9359,13 +9378,13 @@ number detection tools.")
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.6.3")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "1nla74d2sjs51yyvvxf038a03mhw9appvjzj60vr2vd3p5lhqn9k"))))
+                "0mz6lil1wax931incnw5byx0v9i8ryhwq9mv0nv8s48ai33ch3x6"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9405,14 +9424,14 @@ TAB-Seq.")
 (define-public r-sva
   (package
     (name "r-sva")
-    (version "3.28.0")
+    (version "3.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sva" version))
        (sha256
         (base32
-         "0a3jqbz0jp1jxrnjkqfpmca840yqcdwxprdl608bzzx2zb4jl52s"))))
+         "1xf0hlrqjxl0y3x13mrkxghiv39fd9v2g8gq3qzbf1wj7il6bph3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-genefilter" ,r-genefilter)
@@ -9515,14 +9534,14 @@ as allowing spectra with different resolutions.")
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ProtGenerics" version))
        (sha256
         (base32
-         "05jbadw2aiwy8vi2ia0jxg06cmwhly2cq4dy1ag7kdxf1c5i9ccn"))))
+         "053mmxhzncqgigl2iqjlq56qzimlw2zzw31wpzw19rf7rld1vi3b"))))
     (properties `((upstream-name . "ProtGenerics")))
     (build-system r-build-system)
     (home-page "https://github.com/lgatto/ProtGenerics")
@@ -9535,14 +9554,14 @@ proteomics packages.")
 (define-public r-mzr
   (package
     (name "r-mzr")
-    (version "2.14.0")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "190m2bq5bqxhljaj4f7vz9wj5h5laaxd8zp5jampnql6xc4zmarg"))
+         "0li1y6p95ljiva4lvfmql9sipn4dq42sknbh60b36ycjppnf8lj5"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -9564,11 +9583,11 @@ proteomics packages.")
              #t)))))
     (inputs
      `(("boost" ,boost) ; use this instead of the bundled boost sources
-       ("netcdf" ,netcdf)
        ("zlib" ,zlib)))
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
+       ("r-ncdf4" ,r-ncdf4)
        ("r-protgenerics" ,r-protgenerics)
        ("r-rcpp" ,r-rcpp)
        ("r-rhdf5lib" ,r-rhdf5lib)
@@ -9587,14 +9606,14 @@ previously been used in XCMS.")
 (define-public r-affyio
   (package
     (name "r-affyio")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyio" version))
        (sha256
         (base32
-         "0sh5wnnchyfpq5n6rchbqmb27byn7kdzn5rgran6i39c81i5z22n"))))
+         "1s4zp1211vf0krxzch9v3q3r6vs8hihqppq18i2fpvwlknfja7c1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-zlibbioc" ,r-zlibbioc)))
@@ -9611,20 +9630,20 @@ CDF file formats.")
 (define-public r-affy
   (package
     (name "r-affy")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affy" version))
        (sha256
         (base32
-         "0sxq875sigm21sf3qncrfrwfdz9nqw1vldxn3d3hj6aq64jg1ki6"))))
+         "0x8h4fk2igv7vykqfvf6v9whmx3344v5rf3gyfajd431xkjldz6k"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affyio" ,r-affyio)
        ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocinstaller" ,r-biocinstaller)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-preprocesscore" ,r-preprocesscore)
        ("r-zlibbioc" ,r-zlibbioc)))
     (inputs
@@ -9639,14 +9658,14 @@ analysis.")
 (define-public r-vsn
   (package
     (name "r-vsn")
-    (version "3.48.1")
+    (version "3.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "vsn" version))
        (sha256
         (base32
-         "0k6mah3g3zqbfap31xmvig4fn452a18xwwa5y0mfj5mj8588p57h"))))
+         "1g6qkpykw99jm2wv2i61dg2ffwk0n8fm4s5pm2q4c024vw5c9b69"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -9673,14 +9692,14 @@ and specific in detecting differential transcription.")
 (define-public r-mzid
   (package
     (name "r-mzid")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzID" version))
        (sha256
         (base32
-         "060k0xlhg8q802c6zsb4b8ps0ccd9ybyaz0gnsvqkxb786i2vk40"))))
+         "08jbq223viwknsmsi30hyxyxslvmb0l4wx3vmqlkl6qk4vfmxzjz"))))
     (properties `((upstream-name . "mzID")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9703,14 +9722,14 @@ specific parser.")
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaMethods" version))
        (sha256
         (base32
-         "0v99yf8m7ryh6z0r3z0ggpqfnflcq5bn1q1i1cl9b7q4p6b4sa07"))))
+         "0ik82s9bsdj4a1mmv0a3k6yisa92mxx7maf3dvip1r8gqlm3dyng"))))
     (properties `((upstream-name . "pcaMethods")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9733,14 +9752,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.6.4")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "1civd8b1rd5n6ys52dazw5m1yy2wq7049dbbyhzv7pjpa1m2x1rm"))))
+         "0nnlydpklmv9kwlk3gkjgabx7l6y4gav3imq98w8wskb1fhm50c0"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9776,14 +9795,14 @@ of mass spectrometry based proteomics data.")
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "172q5chi44104iz4y0g42wrimfp7hlhrfa8vzybx6m0ccrkkhl17"))))
+         "0hgq4argllhh5hvxqi8vkf1blc3nibsslhx4zsv2mcv4yj75bv4n"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9878,14 +9897,14 @@ discovery of differentially expressed genes and markers.")
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-    (version "3.10.0")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "aroma.light" version))
        (sha256
         (base32
-         "1dxsiwsrwcq9mj573f9vpdzrhagdqzal328ma8076px4gg6khxkn"))))
+         "0vfifgpqxjjncbiv6gvlk9jmj14j90r9f30bqk3ks9v1csjnjhrb"))))
     (properties `((upstream-name . "aroma.light")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9905,14 +9924,14 @@ classes.")
 (define-public r-deseq
   (package
     (name "r-deseq")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq" version))
        (sha256
         (base32
-         "0ykxw8ksif026xy25wx50j2sdsrp156aqkmhcgfjkpgcw699glnm"))))
+         "1klv1xrh3173srywr6dnq6i7m9djn4gc9aflr1p3a6yjlqcq6fya"))))
     (properties `((upstream-name . "DESeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9936,14 +9955,14 @@ distribution.")
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.14.1")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "0970w9d5ddqw1qxqqafdidkxh6hmcv9j5djwgnpz3fgl05kmysg8"))))
+         "1gjqzn1kg9qwyz2gwjyy9xzzr1lnc7xd5zwdyvzkadz97gckzxwf"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9974,14 +9993,14 @@ global-scaling and full-quantile normalization.")
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "interactiveDisplayBase" version))
        (sha256
         (base32
-         "05w58z3i9vkma4jd6rhjaxls4yiq4kwrppgcdq9xrr1pxp99k575"))))
+         "04xz3dkwan2s5ic1mwkdfnggm0l41mgqfagx160bcsrpkw6z7ark"))))
     (properties
      `((upstream-name . "interactiveDisplayBase")))
     (build-system r-build-system)
@@ -9998,20 +10017,20 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "2.12.1")
+    (version "2.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "02ls279k1qlch147vw8kwvlhcqyzvi495bgv110m0xnnbpgbln6g"))))
+         "00288x3na0izpmbcvsqac1br1qwry86vwc2slj1l47crdfb7za6c"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocinstaller" ,r-biocinstaller)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-curl" ,r-curl)
        ("r-httr" ,r-httr)
        ("r-interactivedisplaybase" ,r-interactivedisplaybase)
@@ -10033,14 +10052,14 @@ by the user, helping with quick and reproducible access.")
 (define-public r-fastseg
   (package
     (name "r-fastseg")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fastseg" version))
        (sha256
         (base32
-         "1yw6hai6hb8qy7akdm4frfp6h4zy93zb68kdj094sanm7kgqmgik"))))
+         "1l8mdjpfpgwqdss2ywjkb8b4h55wf8v6kmyxdlvy04ds2hj16sb1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -10063,14 +10082,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.20.2")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "0whmmbkq8bmc3ll20l4cv6hhxjgzbkrs97japljzg07ncn1fffsa"))))
+         "0blpd5a7whd2sswfhqd17h58hg06ymaf80gapdr9ja43hnnlj309"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10087,14 +10106,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.30.0")
+    (version "2.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "0j3cqxy97lpf146wkmdfaq9680gicmzxvhp6w5pxq3j7ipiy7262"))))
+         "07b098wvryxf0zd423nk6h52s3gyngwjcx2vplqybpbpgl8h2931"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10116,14 +10135,14 @@ analysis using other methods.")
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicFiles" version))
        (sha256
         (base32
-         "0bhsq5czigrjyl9gkb2kpkpl367b3ac5g8s280adkcxggn9g7sxq"))))
+         "0qf2yj4lfnnk64fk125n8sqms01shfqiik04nasx2z3k129ykpxp"))))
     (properties `((upstream-name . "GenomicFiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10149,14 +10168,14 @@ provide added flexibility for data combination and manipulation.")
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ComplexHeatmap" version))
        (sha256
         (base32
-         "0qjwz1hzpjnc90jiinjkikfnr0shi72q3zfdjjz7pxydy0mglq8n"))))
+         "0s01dzcfj1lmpqfpsbqw7r4858krfzy499lz4cwx4fq3mbyvy2aj"))))
     (properties
      `((upstream-name . "ComplexHeatmap")))
     (build-system r-build-system)
@@ -10179,14 +10198,14 @@ self-defined annotation graphics.")
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DirichletMultinomial" version))
        (sha256
         (base32
-         "0vcyp81b90in4ls5nbadc66cw2g9aydr94aqifq5j4b7diq74yfs"))))
+         "19bzn0a5jal1xv0ad6wikxc7wrk582hczqamlln0vb2ffwkj1z3f"))))
     (properties
      `((upstream-name . "DirichletMultinomial")))
     (build-system r-build-system)
@@ -10208,14 +10227,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.4.1")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1l2b4cxiycv05mz4z4f3dhx57r9ksha02psc114h30ldm5rxz8w6"))))
+         "12jqz9h6w4mxyfr43w5qbwmacn512aw0mnl0zvhsg5i7p4qj45ks"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10251,21 +10270,21 @@ chromosome region or transcript models of lincRNA genes.")
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OrganismDbi" version))
        (sha256
         (base32
-         "0hb9ni41bjfy5s5ryw2qmqs2sx3i7j47w1g0l8g1pvn7ppnxb6cv"))))
+         "11pyv56cy4iy095h40k6k0mpjdlh6gsb4ld3s57nfa9nd4ypx3yi"))))
     (properties `((upstream-name . "OrganismDbi")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocinstaller" ,r-biocinstaller)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-dbi" ,r-dbi)
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicranges" ,r-genomicranges)
@@ -10283,14 +10302,14 @@ the fact that each of these packages implements a select methods.")
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.28.2")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "0wc45j3hfn01i44bkkxjj3n8b8xzbkkcdv35mrkzb1f9yprkf8gq"))))
+         "0v54mcn3rnnfx8dmcrms5z3rgq19n3hp4r23azlgzwq6hjw7cccx"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10325,14 +10344,14 @@ effort and encourages consistency.")
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.28.5")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "19s2v40fycwf44fl3lm791y635xzw67b30sq2g0qq4a6phjik42d"))))
+         "0wq49qqzkcn8s19xgaxf2s1j1a563d7pbhhvris6fhxfdjsz4934"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10402,14 +10421,14 @@ organisms via the @code{g:Profiler} toolkit.")
 (define-public r-gqtlbase
   (package
     (name "r-gqtlbase")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gQTLBase" version))
        (sha256
         (base32
-         "1m3ajpqjhw1nwwsn372r44xfxq0a9a0pzsnrprzdjp6mh52p9b5m"))))
+         "1lbk1m1mkvbk30flk5pf3pcrnm2s0sj5r48kbjgad39dsvd8zgqx"))))
     (properties `((upstream-name . "gQTLBase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10437,14 +10456,14 @@ and more.")
 (define-public r-snpstats
   (package
     (name "r-snpstats")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "snpStats" version))
        (sha256
         (base32
-         "0iydgfnm053iw860qa1bbh4f6nwzlsf3vhgq92gvl2v4xsz1jbbs"))))
+         "1pplx4pf9bqi7v5v1l74yknc1s61carvbqkf327ky7vbvp0bck33"))))
     (properties `((upstream-name . "snpStats")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -10496,14 +10515,14 @@ several related annotation packages.")
 (define-public r-erma
   (package
     (name "r-erma")
-    (version "0.12.0")
+    (version "0.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "erma" version))
        (sha256
         (base32
-         "1ka68n18yizlyvb8bpwwcl4hqbsasg8hw8jb3vgy3cd4szji87hh"))))
+         "0hj9iz904rr1y66442lkxjywkw1ydyxxlhmjirawbf09ic5ad4g9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10534,14 +10553,14 @@ by Ernst and Kellis.")
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "0c24zvnwsp39d3q0bps13sc441jj9ms2zi34xsb8c392lqmbypvd"))))
+         "0xbf4pmhrk5fnd1iz5wzjvdr75v114bwpznhcig4wiqmxc27sips"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -10566,14 +10585,14 @@ defining LD blocks.")
 (define-public r-gqtlstats
   (package
     (name "r-gqtlstats")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gQTLstats" version))
        (sha256
         (base32
-         "19g8qhfgngdc14cw9k4i44cxhs3qva87x56gjzmn25k1yj8qgsp1"))))
+         "1sg9kw59dlayj7qxql9pd93d4hmml504sa3kkfpzfh3xri7m5pxf"))))
     (properties `((upstream-name . "gQTLstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10620,14 +10639,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "1fhli7ahkl5r43j0hc89ib41mfadj6qyrg36i03ncz8zs6iqwpx4"))))
+         "05zk9hf30afg6rjg97lzn5v8xij90v8zm09y9vcz0asmc3c8xs0a"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10666,14 +10685,14 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "08ba9il4vbjjwlbwmqg4ai6ya1p09js9agn95sw0dhc9gqln42hx"))))
+         "1fnyjydhicq4ayrv0lqjv48h9bd72h40s6l82g1h2ng0icwz38g0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10706,13 +10725,13 @@ EMBL-EBI GWAS catalog.")
 (define-public r-sushi
   (package
     (name "r-sushi")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Sushi" version))
               (sha256
                (base32
-                "1m15hmg4k0qhshyn65xfj5hx7xbaf0kxqw70lxisak6pj1w00l41"))))
+                "0dv5di0hgbvk9cxnqhyf18mdjl50k6bk00a89r6zgp83rbxwr1r8"))))
     (properties `((upstream-name . "Sushi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10728,13 +10747,13 @@ visualizations for publication-quality multi-panel figures.")
 (define-public r-fithic
   (package
     (name "r-fithic")
-    (version "1.6.0")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "FitHiC" version))
               (sha256
                (base32
-                "06w4q836bi1mvkbl1saghv4r5p4hxpjg8cp7kgad13ls450kqmyd"))))
+                "15xd8mz7660q4zr9p74mq1pqps4iz7pxp8f9ifn21gwg94aq1avn"))))
     (properties `((upstream-name . "FitHiC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10752,13 +10771,13 @@ assays such as Hi-C.")
 (define-public r-hitc
   (package
     (name "r-hitc")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "HiTC" version))
               (sha256
                (base32
-                "0qkk5139f51lwwy1yh7nbkflh5d69prirmhniwam34nlg9rzjm2z"))))
+                "11f96k1707g6milpjgnrjf3b5r42hsrxhb5d8znkcr3y3mrskdbj"))))
     (properties `((upstream-name . "HiTC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10781,14 +10800,14 @@ provided.")
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "1ndwkj0hh7v4lwylq1v0fkxqs7mfmbcj8kxbdpj1wkvf131z2ns8"))))
+         "03qxshqwwq1rj23p6pjrz08jm3ziikvy9badi4mz2rcwy2nz783a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -10810,14 +10829,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1s44zgm9jg82bk4b8k3dh7xw7mxychlfm3grs8516mxnw91zpvy5"))))
+         "1w7ad8cfsbh5xx82m3l4lc0vbmj9lcsqxxpiy3ana2ycgn1bqv3g"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10836,14 +10855,20 @@ block processing.")
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.2.1")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "1y59acac6v8hrhv84gghn9ifsni9xxxacaj177rrl4frmkrz4x3c"))))
+         "01gpz780g850ql20b2ql6pvr678ydk4nq4sn5iiih94a4crb9lz1"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Delete bundled binaries
+           (delete-file-recursively "src/winlib/")
+           #t))))
     (properties `((upstream-name . "Rhdf5lib")))
     (build-system r-build-system)
     (arguments
@@ -10860,7 +10885,7 @@ block processing.")
                 "'%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))
+               (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
                             "hdf5")
                ;; Remove timestamp and host system information to make
                ;; the build reproducible.
@@ -10889,9 +10914,9 @@ block processing.")
     (inputs
      `(("zlib" ,zlib)))
     (propagated-inputs
-     `(("hdf5" ,hdf5)))
+     `(("hdf5" ,hdf5-1.10)))
     (native-inputs
-     `(("hdf5-source" ,(package-source hdf5))))
+     `(("hdf5-source" ,(package-source hdf5-1.10))))
     (home-page "https://bioconductor.org/packages/Rhdf5lib")
     (synopsis "HDF5 library as an R package")
     (description "This package provides C and C++ HDF5 libraries for use in R
@@ -10901,20 +10926,21 @@ packages.")
 (define-public r-beachmat
   (package
     (name "r-beachmat")
-    (version "1.2.1")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beachmat" version))
        (sha256
         (base32
-         "1w90v0jx1zgrfxzx99gdkk0dz2vi25hr51jml1bvq33i64rj7996"))))
+         "07zgmms0qg8gw7x0js46965bbhpfj2aa1h5ixdz9r332bxv9cdmr"))))
     (build-system r-build-system)
     (inputs
      `(("hdf5" ,hdf5)
        ("zlib" ,zlib)))
     (propagated-inputs
-     `(("r-delayedarray" ,r-delayedarray)
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedarray" ,r-delayedarray)
        ("r-hdf5array" ,r-hdf5array)
        ("r-rcpp" ,r-rcpp)
        ("r-rhdf5" ,r-rhdf5)
@@ -10929,14 +10955,14 @@ matrices.")
 (define-public r-singlecellexperiment
   (package
     (name "r-singlecellexperiment")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleCellExperiment" version))
        (sha256
         (base32
-         "0mz3chia250v8v6q8r5cqv5fc4bpcw1hhrfr3p7l5i4xi85scpka"))))
+         "19r4r7djrn46qlijkj1g926vcklxzcrxjlxv6cg43m9j9jgfs3dj"))))
     (properties
      `((upstream-name . "SingleCellExperiment")))
     (build-system r-build-system)
@@ -10956,39 +10982,31 @@ libraries.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.8.4")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "173lfpas2fqsp4xxsw01wkxd4496c5p8himw9b4r9z4npxkfyv16"))))
+                "1kwa9n70c5j0xcj6nkmlkzjr63cnj78mp8nhg58n07fq1ijm4ns3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
-       ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-data-table" ,r-data-table)
+       ("r-biocparallel" ,r-biocparallel)
        ("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-plyr" ,r-plyr)
        ("r-rcpp" ,r-rcpp)
        ("r-reshape2" ,r-reshape2)
-       ("r-rhdf5" ,r-rhdf5)
        ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-rjson" ,r-rjson)
        ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-shinydashboard" ,r-shinydashboard)
        ("r-singlecellexperiment" ,r-singlecellexperiment)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tximport" ,r-tximport)
        ("r-viridis" ,r-viridis)))
     (home-page "https://github.com/davismcc/scater")
     (synopsis "Single-cell analysis toolkit for gene expression data in R")
@@ -11000,26 +11018,24 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.8.4")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "17vq9vb9ak7n4mcqpwnm9x3z91vmr7xnsgj8f45b8dbj7m0v126j"))))
+         "1viyzrwfm9vccsf54c6g7k1dn7skkfx4ml1jy12q67wa20sx8l03"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
        ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocneighbors" ,r-biocneighbors)
        ("r-biocparallel" ,r-biocparallel)
        ("r-delayedarray" ,r-delayedarray)
        ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-dt" ,r-dt)
        ("r-dynamictreecut" ,r-dynamictreecut)
        ("r-edger" ,r-edger)
-       ("r-fnn" ,r-fnn)
-       ("r-ggplot2" ,r-ggplot2)
        ("r-igraph" ,r-igraph)
        ("r-limma" ,r-limma)
        ("r-matrix" ,r-matrix)
@@ -11027,11 +11043,9 @@ quality control.")
        ("r-rhdf5lib" ,r-rhdf5lib)
        ("r-s4vectors" ,r-s4vectors)
        ("r-scater" ,r-scater)
-       ("r-shiny" ,r-shiny)
        ("r-singlecellexperiment" ,r-singlecellexperiment)
        ("r-statmod" ,r-statmod)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-viridis" ,r-viridis)))
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
     (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
@@ -11043,19 +11057,21 @@ variable and significantly correlated genes.")
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "1dasghfy8x27zzmd0igag4mc1gxxxbchsl4hpc1050dj3wnw9w3y"))))
+         "03fk2avl1vyjv2wslczkc82qr0zmp1ra8iimd47pbmnnm839ly4w"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-delayedarray" ,r-delayedarray)
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-hdf5array" ,r-hdf5array)
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
        ("r-matrixstats" ,r-matrixstats)
@@ -14132,9 +14148,30 @@ absolute GSEA.")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'create-cabal-file
-           (lambda _ (invoke "hpack") #t)))))
+           (lambda _ (invoke "hpack") #t))
+         ;; These tools are expected to be installed alongside ngless.
+         (add-after 'install 'link-tools
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+               (symlink (string-append (assoc-ref inputs "prodigal")
+                                       "/bin/prodigal")
+                        (string-append bin "ngless-" ,version "-prodigal"))
+               (symlink (string-append (assoc-ref inputs "minimap2")
+                                       "/bin/minimap2")
+                        (string-append bin "ngless-" ,version "-minimap2"))
+               (symlink (string-append (assoc-ref inputs "samtools")
+                                       "/bin/samtools")
+                        (string-append bin "ngless-" ,version "-samtools"))
+               (symlink (string-append (assoc-ref inputs "bwa")
+                                       "/bin/bwa")
+                        (string-append bin "ngless-" ,version "-bwa"))
+               #t))))))
     (inputs
-     `(("ghc-aeson" ,ghc-aeson)
+     `(("prodigal" ,prodigal)
+       ("bwa" ,bwa)
+       ("samtools" ,samtools)
+       ("minimap2" ,minimap2)
+       ("ghc-aeson" ,ghc-aeson)
        ("ghc-ansi-terminal" ,ghc-ansi-terminal)
        ("ghc-async" ,ghc-async)
        ("ghc-atomic-write" ,ghc-atomic-write)
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index 1cac8b9fb4..30d86bd09f 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -186,8 +186,8 @@ their dependencies.")
       (license l:gpl3+))))
 
 (define-public cuirass
-  (let ((commit "fe2b73c2353d106431ed0659345391f14ed64600")
-        (revision "20"))
+  (let ((commit "0b40dca734468e8b12b3ff58e3e779679f17d38e")
+        (revision "21"))
     (package
       (name "cuirass")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -199,7 +199,7 @@ their dependencies.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "00ldbig2p14qpwrl2i2hnhb9idgbbf0kqnlh4n79rmz96blm7463"))))
+                  "1kdxs8dzdyldfs4wsz5hb64hprkbrnq5ljdll631f3bj8pbvvvc1"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index df869794db..ec950ce0ac 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -492,13 +492,13 @@ print, summary, plot, update, etc.
 (define-public r-ps
   (package
     (name "r-ps")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ps" version))
        (sha256
-        (base32 "0ai8igdkysmks1ihbp3h3s552da2hskxqwrvp4cx7vwn91x9f3wd"))))
+        (base32 "1zxylcb0nr4qb5v6j199mc2pfgf2bpf00jrw47jajmv59qb0fwmx"))))
     (build-system r-build-system)
     (home-page "http://ps.r-lib.org")
     (synopsis "List, query, and manipulate system processes")
@@ -539,14 +539,14 @@ is configured appropriately so R can use them.")
 (define-public r-pkgload
   (package
     (name "r-pkgload")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgload" version))
        (sha256
         (base32
-         "0mm0avvan528zbrcrxigl5fkd7za01fb0qhlqrqvm3ar0115cqa8"))))
+         "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-desc" ,r-desc)
@@ -891,14 +891,14 @@ in main memory.")
 (define-public r-ffbase
   (package
     (name "r-ffbase")
-    (version "0.12.5")
+    (version "0.12.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ffbase" version))
        (sha256
         (base32
-         "1h5x6rbb1nrpzf4ywkizn8ij0bz3mlz46byh46ylxhicg1ribi24"))))
+         "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bit" ,r-bit)
@@ -1762,14 +1762,14 @@ provided.")
 (define-public r-ipred
   (package
     (name "r-ipred")
-    (version "0.9-7")
+    (version "0.9-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ipred" version))
        (sha256
         (base32
-         "0q53cqs46501wsd4cmfsmr78l8nv1hkbamk9m0ns5qy02df5r254"))))
+         "01xcg3c121ndfpz9dirqxszknh4yb1p222p7f1wbwwhdrg1i27cw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)
@@ -1789,14 +1789,14 @@ problems as well as resampling based estimators of prediction error.")
 (define-public r-psych
   (package
     (name "r-psych")
-    (version "1.8.4")
+    (version "1.8.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "psych" version))
        (sha256
         (base32
-         "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf"))))
+         "0n3frgzsfmnan6cp3yyq5h6c28v5pd7q5a42pp6byaa7n7d1v478"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreign" ,r-foreign)
@@ -2319,14 +2319,14 @@ training models for classification or ranking.")
 (define-public r-xts
   (package
     (name "r-xts")
-    (version "0.11-1")
+    (version "0.11-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xts" version))
        (sha256
         (base32
-         "17d3g14xkxa1a5z5gd3gk1xjqfkjg1ik3i12q0arina8frql3jhd"))))
+         "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-zoo" ,r-zoo)))
     (home-page "https://github.com/joshuaulrich/xts")
@@ -4814,14 +4814,14 @@ vice versa), or to deal with multiple declared missing values.")
 (define-public r-sjmisc
   (package
     (name "r-sjmisc")
-    (version "2.7.5")
+    (version "2.7.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjmisc" version))
        (sha256
         (base32
-         "05fjqfr2rfk11065zqkzb9mbqd6mgdkw9jdhq3by425a7f8m2dcg"))))
+         "1jhrigikjpkdar3jxvi7qhqsg6lgjkjqhqll9vaay98b88rfc2im"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
@@ -4829,15 +4829,12 @@ vice versa), or to deal with multiple declared missing values.")
        ("r-dplyr" ,r-dplyr)
        ("r-haven" ,r-haven)
        ("r-magrittr" ,r-magrittr)
-       ("r-pillar" ,r-pillar)
        ("r-purrr" ,r-purrr)
        ("r-rlang" ,r-rlang)
        ("r-sjlabelled" ,r-sjlabelled)
        ("r-stringdist" ,r-stringdist)
        ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-tidyselect" ,r-tidyselect)))
+       ("r-tidyr" ,r-tidyr)))
     (home-page "https://github.com/strengejacke/sjmisc")
     (synopsis "Data and variable transformation functions")
     (description
@@ -4899,14 +4896,14 @@ functions.")
 (define-public r-flextable
   (package
     (name "r-flextable")
-    (version "0.4.5")
+    (version "0.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flextable" version))
        (sha256
         (base32
-         "09j2y0z7rkc0w1cl9pp1cpk6fnzzfr6245mxa3ca42z9k2cy2jfl"))))
+         "0fa42dvf0wyl91w4v0rywm3xgw9n03cfyl28ficrv8iabz4k4382"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-gdtools" ,r-gdtools)
@@ -6823,14 +6820,14 @@ Rcpp, RStudio projects, and more.")
 (define-public r-sessioninfo
   (package
     (name "r-sessioninfo")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sessioninfo" version))
        (sha256
         (base32
-         "01c0m8yzadpwd825hky6as0f8ka4xyz7zfy0ih2iy7qqw11w6qn5"))))
+         "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -6846,14 +6843,14 @@ more information about packages, and where they were installed from.")
 (define-public r-remotes
   (package
     (name "r-remotes")
-    (version "2.0.1")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "remotes" version))
        (sha256
         (base32
-         "1xkzlciv68jyf4j8hads0i47nxbgsy1kv7258c6zzyq66z0amhss"))))
+         "0rsjxmhwpr51ilsdjfqn06mj8yr2d7nckcn3arv1ljn23qfkpcxa"))))
     (build-system r-build-system)
     (home-page "https://github.com/r-lib/remotes#readme")
     (synopsis "R package installation from remote repositories")
@@ -6888,14 +6885,14 @@ directories or URLs with their associated programs.")
 (define-public r-rcmdcheck
   (package
     (name "r-rcmdcheck")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rcmdcheck" version))
        (sha256
         (base32
-         "13liz9lmx9xgc0f7pjiz3sp8ygvazx2zslbiwz3p9fimfsx1yfsg"))))
+         "1ga19jqix0zs7xyz2j155zyagwbv22r6dgv55g6wdjigc67qfsix"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -6907,6 +6904,7 @@ directories or URLs with their associated programs.")
        ("r-prettyunits" ,r-prettyunits)
        ("r-r6" ,r-r6)
        ("r-rprojroot" ,r-rprojroot)
+       ("r-sessioninfo" ,r-sessioninfo)
        ("r-withr" ,r-withr)
        ("r-xopen" ,r-xopen)))
     (home-page "https://github.com/r-Lib/rcmdcheck#readme")
@@ -6943,14 +6941,14 @@ quick reporting.")
 (define-public r-pander
   (package
     (name "r-pander")
-    (version "0.6.2")
+    (version "0.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pander" version))
        (sha256
         (base32
-         "0gd7rqkpbraznip8jmri9lqa8ajg1sryyplhd6m633wg91whiipi"))))
+         "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -7225,3 +7223,105 @@ R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
 al. (2016)).")
     (license license:gpl2)))
+
+(define-public r-weights
+  (package
+    (name "r-weights")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "weights" version))
+       (sha256
+        (base32
+         "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gdata" ,r-gdata)
+       ("r-hmisc" ,r-hmisc)
+       ("r-mice" ,r-mice)))
+    (home-page
+     "https://cran.r-project.org/web/packages/weights/")
+    (synopsis "Weighting and weighted statistics")
+    (description "This package Provides a variety of functions for producing
+simple weighted statistics, such as weighted Pearson's correlations, partial
+correlations, Chi-Squared statistics, histograms, and t-tests.  Also now
+includes some software for quickly recoding survey data and plotting point
+estimates from interaction terms in regressions (and multiply imputed
+regressions).  NOTE: Weighted partial correlation calculations pulled to
+address a bug.")
+  (license license:gpl2+)))
+
+(define-public r-rcppannoy
+  (package
+    (name "r-rcppannoy")
+    (version "0.0.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppAnnoy" version))
+       (sha256
+        (base32
+         "1ik50ancfgcvh03n4jsqwjk8lf056rbgd70q4l4didmvh5kcyjd1"))))
+    (properties `((upstream-name . "RcppAnnoy")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
+    (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
+    (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
+    (description
+     "Annoy is a small C++ library for Approximate Nearest Neighbors written
+for efficient memory usage as well an ability to load from and save to disk.
+This package provides an R interface.")
+    ;; Annoy is released under ASL 2.0, but this wrapper is released under
+    ;; GPLv2+.
+    (license (list license:gpl2+ license:asl2.0))))
+
+(define-public r-ncdf4
+  (package
+    (name "r-ncdf4")
+    (version "1.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ncdf4" version))
+       (sha256
+        (base32
+         "0lwjjis0b83c4l3xvqai4ckzrskd6mychck1iwxcxgjvh0d77mgd"))))
+    (build-system r-build-system)
+    (inputs
+     `(("netcdf" ,netcdf)
+       ("zlib" ,zlib)))
+    (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
+    (synopsis "R interface to Unidata netCDF format data files")
+    (description
+     "This package provides a high-level R interface to data files written
+using Unidata's netCDF library (version 4 or earlier), which are binary data
+files that are portable across platforms and include metadata information in
+addition to the data sets.  Using this package, netCDF files can be opened and
+data sets read in easily.  It is also easy to create new netCDF dimensions,
+variables, and files, in either version 3 or 4 format, and manipulate existing
+netCDF files.")
+    (license license:gpl3+)))
+
+(define-public r-biocmanager
+  (package
+    (name "r-biocmanager")
+    (version "1.30.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "BiocManager" version))
+       (sha256
+        (base32
+         "0mfvx1xzsgiag9p42kdyqg8fvajyakrdy3z2smhdlaawzbi0qmax"))))
+    (properties `((upstream-name . "BiocManager")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/BiocManager/")
+    (synopsis "Access the Bioconductor project package repository")
+    (description
+     "This package provides a convenient tool to install and update
+Bioconductor packages.")
+    (license license:artistic2.0)))
diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 3d6727bbde..cec013074f 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -221,14 +221,14 @@ compatible to GNU Pth.")
 (define-public gnupg
   (package
     (name "gnupg")
-    (version "2.2.10")
+    (version "2.2.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnupg/gnupg/gnupg-" version
                                   ".tar.bz2"))
               (sha256
                (base32
-                "05f9804g72pffdxgvxjmjzkfcpjg1x221g9rwcr8fi51hrxd77br"))))
+                "1ncwqjhcxh46fgkp84g2lhf91amcha7abk6wdm1kagzm7q93wv29"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index cb314719b7..67b306de6d 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -156,14 +156,14 @@ model.")
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "1037hzfxxcn46w6y88wm3kk2nixj0s8bk0hkmnshpxih3kmnvqby"))))
+         "0bp6517xsih0wng2rgkh9z4r1afqhwl3h04z6ssm7p4cdj0ahm4y"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     ;; FIXME: Rgraphviz bundles the sources of an older variant of
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index bf2f2a14a4..0c65f0e78d 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2017 David Thompson <davet@gnu.org>
-;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; Copyright © 2017, 2018 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -68,6 +68,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages image)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages slang)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages networking)
@@ -1112,7 +1113,7 @@ Guile's foreign function interface.")
   (package
     (name "guile-sqlite3")
     (version "0.1.0")
-    (home-page "https://notabug.org/civodul/guile-sqlite3.git")
+    (home-page "https://notabug.org/guile-sqlite3/guile-sqlite3.git")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2243,4 +2244,39 @@ using S-expressions.")
 tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
     (license license:gpl3+)))
 
+;; There has not been any release yet.
+(define-public guile-newt
+  (let ((commit "596ad760bee1be419d71271732f0f30eaee55143")
+        (revision "0"))
+    (package
+      (name "guile-newt")
+      (version (string-append "0-" revision "." (string-take commit 9)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://gitlab.com/mothacehe/guile-newt")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "18qqbi0bc7vp2vlrhib3p3wwgn7wrlv5728dn0avirhw4fxxivnf"))))
+      (build-system gnu-build-system)
+      (arguments
+       '(#:make-flags
+         '("GUILE_AUTO_COMPILE=0"))) ;to prevent guild warnings
+      (inputs
+       `(("guile" ,guile-2.2)
+         ("newt" ,newt)))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("pkg-config" ,pkg-config)))
+      (synopsis "Guile bindings to Newt")
+      (description
+       "This package provides bindings for Newt, a programming library for
+color text mode, widget based user interfaces.  The bindings are written in pure
+Scheme by using Guile’s foreign function interface.")
+      (home-page "https://gitlab.com/mothacehe/guile-newt")
+      (license license:gpl3+))))
+
 ;;; guile.scm ends here
diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index 21e7b12d3e..6729f1f322 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -317,8 +317,8 @@ generator library for C++.")
                 (string-append (assoc-ref inputs "tzdata")
                                "/share/zoneinfo")))
 
-             ;; Don't phone home to check for updates.¬
-             (substitute* "system/addon-manifest.xml"¬
+             ;; Don't phone home to check for updates.
+             (substitute* "system/addon-manifest.xml"
                (("<addon optional=\\\"true\\\">service.xbmc.versioncheck</addon>")
                 ""))
 
diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index f373383a8a..2e05820f72 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -939,7 +939,7 @@ converting QuarkXPress file format.  It supports versions 3.1 to 4.1.")
 (define-public libreoffice
   (package
     (name "libreoffice")
-    (version "6.1.2.1")
+    (version "6.1.3.2")
     (source
      (origin
        (method url-fetch)
@@ -949,7 +949,7 @@ converting QuarkXPress file format.  It supports versions 3.1 to 4.1.")
          (version-prefix version 3) "/libreoffice-" version ".tar.xz"))
        (sha256
         (base32
-         "149ziasibplihfxlzafzcm4737ns30hg9175967b43c81yv5f335"))
+         "0i4gf3qi16fg7dxq2l4vhkwh4f5lx7xd1ilpzcw26vccqkv3hvyl"))
        (patches (search-patches "libreoffice-icu.patch"
                                 "libreoffice-glm.patch"))))
     (build-system glib-or-gtk-build-system)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index e8fc8fdea9..2f5798c055 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -884,6 +884,25 @@ extremely large and complex data collections.")
     (license (license:x11-style
               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 
+(define-public hdf5-1.10
+  (package (inherit hdf5)
+    (version "1.10.4")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
+                                "hdf5-" (version-major+minor version)
+                                "/hdf5-" version "/src/hdf5-"
+                                version ".tar.bz2")
+                 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
+                                "current"
+                                (apply string-append
+                                       (take (string-split version #\.) 2))
+                                "/src/hdf5-" version ".tar.bz2")))
+      (sha256
+       (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
+      (patches (list (search-patch "hdf5-config-date.patch")))))))
+
 (define-public hdf-java
   (package
    (name "hdf-java")
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index ac2ed81895..fdbfab796c 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -284,7 +284,7 @@ score, keyboard, guitar, drum and controller views.")
          ("pulseaudio" ,pulseaudio)
          ("qtbase" ,qtbase)
          ("qtx11extras" ,qtx11extras)
-         ("sqlite" ,sqlite)
+         ("sqlite" ,sqlite-with-column-metadata)
          ("sparsehash" ,sparsehash)
          ("taglib" ,taglib)))
       (home-page "http://clementine-player.org")
diff --git a/gnu/packages/patches/gemma-intel-compat.patch b/gnu/packages/patches/gemma-intel-compat.patch
deleted file mode 100644
index f12ec56d9b..0000000000
--- a/gnu/packages/patches/gemma-intel-compat.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-From da1ed24209121f7b0f03f360b1029d7125a38e70 Mon Sep 17 00:00:00 2001
-From: Efraim Flashner <efraim@flashner.co.il>
-Date: Tue, 4 Jul 2017 12:44:53 +0300
-Subject: [PATCH] Add NO_INTEL_COMPAT flag to Makefile.
-
-see also: https://github.com/xiangzhou/GEMMA/pull/47
-
----
- Makefile | 12 ++++++++----
- 1 file changed, 8 insertions(+), 4 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 5bb8748..712b1ad 100644
---- a/Makefile
-+++ b/Makefile
-@@ -11,6 +11,7 @@
- SYS = LNX
- # Leave blank after "=" to disable; put "= 1" to enable
- WITH_LAPACK = 1
-+NO_INTEL_COMPAT = 
- FORCE_32BIT = 
- FORCE_DYNAMIC = 
- DIST_NAME = gemma-0.96
-@@ -64,10 +65,13 @@ endif
-   HDR += $(SRC_DIR)/lapack.h
- endif
- 
--ifdef FORCE_32BIT
--  CPPFLAGS += -m32
--else
--  CPPFLAGS += -m64
-+ifdef NO_INTEL_COMPAT
-+  else
-+  ifdef FORCE_32BIT
-+    CPPFLAGS += -m32
-+  else
-+    CPPFLAGS += -m64
-+  endif
- endif
- 
- ifdef FORCE_DYNAMIC
--- 
-2.13.2
-
diff --git a/gnu/packages/patches/jq-CVE-2015-8863.patch b/gnu/packages/patches/jq-CVE-2015-8863.patch
deleted file mode 100644
index 20b3bb3f06..0000000000
--- a/gnu/packages/patches/jq-CVE-2015-8863.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-Fix CVE-2015-8863 (Off-by-one error in the tokenadd function in
-jv_parse.c in jq allows remote attackers to cause a denial of service
-(crash) via a long JSON-encoded number, which triggers a heap-based
-buffer overflow):
-
-<https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2015-8863>
-
-Copied from upstream code repository:
-
-<https://github.com/stedolan/jq/commit/8eb1367ca44e772963e704a700ef72ae2e12babd>
-
-From 8eb1367ca44e772963e704a700ef72ae2e12babd Mon Sep 17 00:00:00 2001
-From: Nicolas Williams <nico@cryptonector.com>
-Date: Sat, 24 Oct 2015 17:24:57 -0500
-Subject: [PATCH] Heap buffer overflow in tokenadd() (fix #105)
-
-This was an off-by one: the NUL terminator byte was not allocated on
-resize.  This was triggered by JSON-encoded numbers longer than 256
-bytes.
----
- jv_parse.c | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/jv_parse.c b/jv_parse.c
-index 3102ed4..84245b8 100644
---- a/jv_parse.c
-+++ b/jv_parse.c
-@@ -383,7 +383,7 @@ static pfunc stream_token(struct jv_parser* p, char ch) {
- 
- static void tokenadd(struct jv_parser* p, char c) {
-   assert(p->tokenpos <= p->tokenlen);
--  if (p->tokenpos == p->tokenlen) {
-+  if (p->tokenpos >= (p->tokenlen - 1)) {
-     p->tokenlen = p->tokenlen*2 + 256;
-     p->tokenbuf = jv_mem_realloc(p->tokenbuf, p->tokenlen);
-   }
-@@ -485,7 +485,7 @@ static pfunc check_literal(struct jv_parser* p) {
-     TRY(value(p, v));
-   } else {
-     // FIXME: better parser
--    p->tokenbuf[p->tokenpos] = 0; // FIXME: invalid
-+    p->tokenbuf[p->tokenpos] = 0;
-     char* end = 0;
-     double d = jvp_strtod(&p->dtoa, p->tokenbuf, &end);
-     if (end == 0 || *end != 0)
diff --git a/gnu/packages/patches/libgit2-oom-test.patch b/gnu/packages/patches/libgit2-oom-test.patch
new file mode 100644
index 0000000000..9667d1c0da
--- /dev/null
+++ b/gnu/packages/patches/libgit2-oom-test.patch
@@ -0,0 +1,62 @@
+Fix a test failure on 32-bit platforms as reported
+at <https://github.com/libgit2/libgit2/issues/4868>.
+
+From 415a8ae9c9b6ac18f0524b6af8e58408b426457d Mon Sep 17 00:00:00 2001
+From: Edward Thomson <ethomson@edwardthomson.com>
+Date: Thu, 13 Sep 2018 13:27:07 +0100
+Subject: [PATCH] tests: don't run buf::oom on 32-bit systems
+
+On a 32-bit Linux systems, the value large enough to make malloc
+guarantee a failure is also large enough that valgrind considers it
+"fishy".  Skip this test on those systems entirely.
+---
+ tests/buf/oom.c | 14 +++++++++-----
+ 1 file changed, 9 insertions(+), 5 deletions(-)
+
+diff --git a/tests/buf/oom.c b/tests/buf/oom.c
+index 2741a8ddf2..ec3bad9979 100644
+--- a/tests/buf/oom.c
++++ b/tests/buf/oom.c
+@@ -11,12 +11,8 @@
+  */
+ #if defined(GIT_ARCH_64) && defined(__linux__)
+ # define TOOBIG 0x0fffffffffffffff
+-#elif defined(__linux__)
+-# define TOOBIG 0x0fffffff
+ #elif defined(GIT_ARCH_64)
+ # define TOOBIG 0xffffffffffffff00
+-#else
+-# define TOOBIG 0xffffff00
+ #endif
+ 
+ /**
+@@ -25,13 +21,18 @@
+  * will fail.  And because the git_buf_grow() wrapper always
+  * sets mark_oom, the code in git_buf_try_grow() will free
+  * the internal buffer and set it to git_buf__oom.
+- * 
++ *
+  * We initialized the internal buffer to (the static variable)
+  * git_buf__initbuf.  The purpose of this test is to make sure
+  * that we don't try to free the static buffer.
++ *
++ * Skip this test entirely on 32-bit platforms; a buffer large enough
++ * to guarantee malloc failures is so large that valgrind considers
++ * it likely to be an error.
+  */
+ void test_buf_oom__grow(void)
+ {
++#ifdef GIT_ARCH_64
+ 	git_buf buf = GIT_BUF_INIT;
+ 
+ 	git_buf_clear(&buf);
+@@ -40,6 +41,9 @@ void test_buf_oom__grow(void)
+ 	cl_assert(git_buf_oom(&buf));
+ 
+ 	git_buf_free(&buf);
++#else
++    cl_skip();
++#endif
+ }
+ 
+ void test_buf_oom__grow_by(void)
diff --git a/gnu/packages/slang.scm b/gnu/packages/slang.scm
index 24eb5fa137..185d441919 100644
--- a/gnu/packages/slang.scm
+++ b/gnu/packages/slang.scm
@@ -50,13 +50,21 @@
                '(begin
                   (substitute* "src/Makefile.in"
                     (("/bin/ln") "ln"))
-                  (substitute* "configure"
-                    (("-ltermcap") ""))
                   #t))))
     (build-system gnu-build-system)
     (arguments
      '(#:parallel-tests? #f
-       #:parallel-build? #f)) ; there's at least one race
+       #:parallel-build? #f  ; there's at least one race
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'substitute-before-config
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((ncurses (assoc-ref inputs "ncurses")))
+               (substitute* "configure"
+                 (("MISC_TERMINFO_DIRS=\"\"")
+                  (string-append "MISC_TERMINFO_DIRS="
+                                 "\"" ncurses "/share/terminfo" "\"")))
+               #t))))))
     (inputs
      `(("readline" ,readline)
        ("zlib" ,zlib)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d9a20cd818..bb942b4fea 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -339,14 +339,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-51")
+    (version "7.3-51.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "0yp5ssfm9mahrp30y1hkqgjg70mzs6w065ba8h7j5ky1z6msdsdy"))))
+         "14907ia8418mp3p1rs1i2f1x5b6kk5z998dk353a29j3xqf3ybyq"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
@@ -467,13 +467,13 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
 (define-public r-lattice
   (package
     (name "r-lattice")
-    (version "0.20-35")
+    (version "0.20-38")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "lattice" version))
               (sha256
                (base32
-                "0pcnmaz3lr62ly0dcy5hnnqxshc4yqd43hrvlz3almgc9l7sna88"))))
+                "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx"))))
     (build-system r-build-system)
     (home-page "http://lattice.r-forge.r-project.org/")
     (synopsis "High-level data visualization system")
@@ -487,14 +487,14 @@ also flexible enough to handle most nonstandard requirements.")
 (define-public r-matrix
   (package
     (name "r-matrix")
-    (version "1.2-14")
+    (version "1.2-15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Matrix" version))
        (sha256
         (base32
-         "15hknim84nj3f54vkchca5ac0c3ip15v1by18k5parmn8wsl19j9"))))
+         "1mshhyia6imh939p8labxi0wv21lal7csmccxi42klpgdh1j89kv"))))
     (properties `((upstream-name . "Matrix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -614,14 +614,14 @@ analysis.")
 (define-public r-survival
   (package
     (name "r-survival")
-    (version "2.42-6")
+    (version "2.43-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "survival" version))
        (sha256
         (base32
-         "1bsxc2fir9pbvdzy9n474fkl7har606h9zhspp0z67wnjpp48g73"))))
+         "0220fjsq4ycx1n5zc5h39wdbj5j6xr8rzqbcixx2p25akzdn7kqk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -2233,13 +2233,13 @@ tables, autolinks and strikethrough text.")
 (define-public r-roxygen2
   (package
     (name "r-roxygen2")
-    (version "6.1.0")
+    (version "6.1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "roxygen2" version))
               (sha256
                (base32
-                "0ji9k4s1bvfbl8wimfqj1lqr33h1claaz30vb5pgksxyg77j5xaa"))))
+                "0wq29ilqas8yn2z8v49fk0hbgchg29nmyyhwczgdipz0cbhbfipd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-brew" ,r-brew)
@@ -3085,13 +3085,13 @@ using the multicore functionality of the parallel package.")
 (define-public r-dt
   (package
     (name "r-dt")
-    (version "0.4")
+    (version "0.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DT" version))
               (sha256
                (base32
-                "06gsqz7p2fv6hc3fm3759gaa50krcfrqrmy7qbxyam6a36w9daix"))))
+                "1s5d3sld4l8zygpkvprvlbqa0pm2cv1bm7h7p999wxlap28vnnqf"))))
     (properties
      `((upstream-name . "DT")))
     (build-system r-build-system)
@@ -3099,7 +3099,8 @@ using the multicore functionality of the parallel package.")
      `(("r-crosstalk" ,r-crosstalk)
        ("r-htmltools" ,r-htmltools)
        ("r-htmlwidgets" ,r-htmlwidgets)
-       ("r-magrittr" ,r-magrittr)))
+       ("r-magrittr" ,r-magrittr)
+       ("r-promises" ,r-promises)))
     (home-page "http://rstudio.github.io/DT")
     (synopsis "R wrapper of the DataTables JavaScript library")
     (description
@@ -3665,14 +3666,14 @@ selection.")
 (define-public r-tidyr
   (package
     (name "r-tidyr")
-    (version "0.8.1")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyr" version))
        (sha256
         (base32
-         "0485f19mkkglc4bv57y6bm6l9rfgd878hsz2xdg1nwgbqchjhgix"))))
+         "03s9dv6c2dj65a769h8fgy9878y46rdq7x65i53kd44kag80i9cr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -4031,14 +4032,14 @@ hierarchical clustering dendrograms.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "1afar1z7959v7mbzsqa77vqfh0yc7y3nv5ayx71485a8scwsfwbk"))))
+         "0ijyjqi8mxxf350dhvgp36swwww5ag7ac9a6r6ymihc5syjr4w4j"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -5016,14 +5017,14 @@ decompositions of such matrices, and solutions of linear systems.")
 (define-public r-modelmetrics
   (package
     (name "r-modelmetrics")
-    (version "1.2.0")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
         (uri (cran-uri "ModelMetrics" version))
         (sha256
          (base32
-          "1sgdyrf6fbsn18gk8slir4a1yhv133kfhyg2crfs759nff4aw89h"))))
+          "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6"))))
     (properties `((upstream-name . "ModelMetrics")))
     (build-system r-build-system)
     (propagated-inputs
diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 48b52d2002..5d681b816e 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -30,7 +30,7 @@
 (define-public syncthing
   (package
     (name "syncthing")
-    (version "0.14.51")
+    (version "0.14.52")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/syncthing/syncthing"
@@ -38,7 +38,7 @@
                                   "/syncthing-source-v" version ".tar.gz"))
               (sha256
                (base32
-                "17phn8l2afhgzh0q9ambi28awj2m905sr1bicq2wc7ghypk5vgqh"))
+                "1hhn72l74vb9l32i1a54ry2l85ji78cq6isd20lxxdk0bjqc4m29"))
               (modules '((guix build utils)))
               ;; Delete bundled ("vendored") free software source code.
               (snippet '(begin
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 5cdc081398..116377c8fa 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -187,96 +187,112 @@ text-based approach to terminal recording.")
     (license license:gpl3)))
 
 (define-public libtsm
-  (package
-    (name "libtsm")
-    (version "3")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://freedesktop.org/software/kmscon/releases/"
-                    "libtsm-" version ".tar.xz"))
-              (sha256
-               (base32
-                "01ygwrsxfii0pngfikgqsb4fxp8n1bbs47l7hck81h9b9bc1ah8i"))))
-    (build-system gnu-build-system)
-    (native-inputs
-     `(("pkg-config" ,pkg-config)))
-    (inputs
-     `(("libxkbcommon" ,libxkbcommon)))
-    (synopsis "Xterm state machine library")
-    (description "TSM is a state machine for DEC VT100-VT520 compatible
+  (let ((commit "f70e37982f382b03c6939dac3d5f814450bda253")
+        (revision "1"))
+    (package
+      (name "libtsm")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                ;; The freedesktop repository is no longer maintained.
+                (uri (git-reference
+                      (url (string-append "https://github.com/Aetf/" name))
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "0mwn91i5h5d518i1s05y7hzv6bc13vzcvxszpfh77473iwg4wprx"))))
+      (build-system cmake-build-system)
+      (arguments
+       `(#:configure-flags '("-DBUILD_TESTING=ON")))
+      (native-inputs
+       `(("pkg-config" ,pkg-config)))
+      (inputs
+       `(("libxkbcommon" ,libxkbcommon)
+         ("check" ,check)))
+      (synopsis "Xterm state machine library")
+      (description "TSM is a state machine for DEC VT100-VT520 compatible
 terminal emulators.  It tries to support all common standards while keeping
 compatibility to existing emulators like xterm, gnome-terminal, konsole, etc.")
-    (home-page "https://www.freedesktop.org/wiki/Software/libtsm")
-    ;; Hash table implementation is lgpl2.1+ licensed.
-    ;; The wcwidth implementation in external/wcwidth.{h,c} uses a license
-    ;; derived from ISC.
-    ;; UCS-4 to UTF-8 encoding is copied from "terminology" which is released
-    ;; under the bsd 2 license.
-    (license (list license:expat license:lgpl2.1+ license:isc license:bsd-2))))
+      (home-page "https://www.freedesktop.org/wiki/Software/libtsm")
+      ;; Hash table implementation is lgpl2.1+ licensed.
+      ;; The wcwidth implementation in external/wcwidth.{h,c} uses a license
+      ;; derived from ISC.
+      ;; UCS-4 to UTF-8 encoding is copied from "terminology" which is released
+      ;; under the bsd 2 license.
+      (license (list license:expat license:lgpl2.1+ license:isc license:bsd-2)))))
 
 (define-public kmscon
-  (package
-    (name "kmscon")
-    (version "8")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://freedesktop.org/software/kmscon/releases/"
-                    "kmscon-" version ".tar.xz"))
-              (sha256
-               (base32
-                "0axfwrp3c8f4gb67ap2sqnkn75idpiw09s35wwn6kgagvhf1rc0a"))
-              (modules '((guix build utils)))
-              (snippet
-               ;; Use elogind instead of systemd.
-               '(begin
-                  (substitute* "configure"
-                    (("libsystemd-daemon libsystemd-login")
-                     "libelogind"))
-                  (substitute* "src/uterm_systemd.c"
-                    (("#include <systemd/sd-login.h>")
-                     "#include <elogind/sd-login.h>")
-                    ;; We don't have this header.
-                    (("#include <systemd/sd-daemon\\.h>")
-                     "")
-                    ;; Replace the call to 'sd_booted' by the truth value.
-                    (("sd_booted\\(\\)")
-                     "1"))
-                  #t))))
-    (build-system gnu-build-system)
-    (native-inputs
-     `(("pkg-config" ,pkg-config)
-       ("libxslt" ,libxslt)                       ;to build the man page
-       ("libxml2" ,libxml2)                       ;for XML_CATALOG_FILES
-       ("docbook-xsl" ,docbook-xsl)))
-    (inputs
-     `(("libdrm" ,libdrm)
-       ("libtsm" ,libtsm)
-       ("libxkbcommon" ,libxkbcommon)
-       ("logind" ,elogind)
-       ("mesa" ,mesa)
-       ("pango" ,pango)
-       ("udev" ,eudev)))
-    (synopsis "Linux KMS-based terminal emulator")
-    (description "Kmscon is a terminal emulator based on Linux's @dfn{kernel
+  (let ((commit "01dd0a231e2125a40ceba5f59fd945ff29bf2cdc")
+        (revision "1"))
+    (package
+      (name "kmscon")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                ;; The freedesktop repository is no longer maintained.
+                (uri (git-reference
+                      (url (string-append "https://github.com/Aetf/" name))
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "0q62kjsvy2iwy8adfiygx2bfwlh83rphgxbis95ycspqidg9py87"))
+                (modules '((guix build utils)))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:phases (modify-phases %standard-phases
+                    (add-after 'unpack 'autogen.sh
+                      (lambda _
+                        (zero? (system* "sh" "autogen.sh"))))
+                    ;; Use elogind instead of systemd.
+                    (add-before 'configure 'remove-systemd
+                      (lambda _
+                        (substitute* "configure"
+                          (("libsystemd-daemon libsystemd-login")
+                           "libelogind"))
+                        (substitute* "src/uterm_systemd.c"
+                          (("#include <systemd/sd-login.h>")
+                           "#include <elogind/sd-login.h>")
+                          ;; We don't have this header.
+                          (("#include <systemd/sd-daemon\\.h>")
+                           "")
+                          ;; Replace the call to 'sd_booted' by the truth value.
+                          (("sd_booted\\(\\)")
+                           "1")))))))
+      (native-inputs
+       `(("pkg-config" ,pkg-config)
+         ("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("libtool" ,libtool)
+         ("libxslt" ,libxslt)                       ;to build the man page
+         ("libxml2" ,libxml2)                       ;for XML_CATALOG_FILES
+         ("docbook-xsl" ,docbook-xsl)))
+      (inputs
+       `(("libdrm" ,libdrm)
+         ("libtsm" ,libtsm)
+         ("libxkbcommon" ,libxkbcommon)
+         ("logind" ,elogind)
+         ("mesa" ,mesa)
+         ("pango" ,pango)
+         ("udev" ,eudev)))
+      (synopsis "Linux KMS-based terminal emulator")
+      (description "Kmscon is a terminal emulator based on Linux's @dfn{kernel
 mode setting} (KMS).  It can replace the in-kernel virtual terminal (VT)
 implementation with a user-space console.  Compared to the Linux console,
 kmscon provides enhanced features including XKB-compatible internationalized
 keyboard support, UTF-8 input/font support, hardware-accelerated rendering,
 multi-seat support, a replacement for @command{mingetty}, and more.")
-    (home-page "https://www.freedesktop.org/wiki/Software/kmscon")
-    ;; Hash table implementation is lgpl2.1+ licensed.
-    ;; The wcwidth implementation in external/wcwidth.{h,c} uses a license
-    ;; derived from ISC.
-    ;; UCS-4 to UTF-8 encoding is copied from "terminology" which is released
-    ;; under the bsd 2 license.
-    ;; Unifont-Font is from http://unifoundry.com/unifont.html and licensed
-    ;; under the terms of the GNU GPL.
-    (license (list license:expat license:lgpl2.1+ license:bsd-2
-                   license:gpl2+))
-    (supported-systems (filter (cut string-suffix? "-linux" <>)
-                               %supported-systems))))
+      (home-page "https://www.freedesktop.org/wiki/Software/kmscon")
+      ;; Hash table implementation is lgpl2.1+ licensed.
+      ;; The wcwidth implementation in external/wcwidth.{h,c} uses a license
+      ;; derived from ISC.
+      ;; UCS-4 to UTF-8 encoding is copied from "terminology" which is released
+      ;; under the bsd 2 license.
+      ;; Unifont-Font is from http://unifoundry.com/unifont.html and licensed
+      ;; under the terms of the GNU GPL.
+      (license (list license:expat license:lgpl2.1+ license:bsd-2
+                     license:gpl2+))
+      (supported-systems (filter (cut string-suffix? "-linux" <>)
+                                 %supported-systems)))))
 
 (define-public libtermkey
   (package
diff --git a/gnu/packages/terraform.scm b/gnu/packages/terraform.scm
index 71b214ed0a..f14b152fdb 100644
--- a/gnu/packages/terraform.scm
+++ b/gnu/packages/terraform.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,13 +22,12 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
-  #:use-module (guix build-system go)
-  #:use-module (gnu packages golang))
+  #:use-module (guix build-system go))
 
 (define-public terraform-docs
   (package
     (name "terraform-docs")
-    (version "0.3.0")
+    (version "0.5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -36,11 +36,8 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xchpik32ab8m89s6jv671vswg8xhprfvh6s5md0zd36482d2nmm"))))
+                "12w2yr669hk5kxdb9rrzsn8hwvx8rzrc1rmn8hs9l8z1bkfhr4gg"))))
     (build-system go-build-system)
-    (native-inputs
-     `(("go-github-com-hashicorp-hcl" ,go-github-com-hashicorp-hcl)
-       ("go-github-com-tj-docopt" ,go-github-com-tj-docopt)))
     (arguments
      '(#:import-path "github.com/segmentio/terraform-docs"))
     (synopsis "Generate documentation from Terraform modules")
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index b9a2ff2ea0..04d28044dd 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -469,7 +469,8 @@ everything from small to very large projects with speed and efficiency.")
               (sha256
                (base32
                 "15kp4sq72kh762bm7dgspyrk0a6siarvll3k7nrhs0xy77idf80g"))
-              (patches (search-patches "libgit2-mtime-0.patch"))
+              (patches (search-patches "libgit2-mtime-0.patch"
+                                       "libgit2-oom-test.patch"))
 
               ;; Remove bundled software.
               (snippet '(begin
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index fee2cb7762..a482ef2515 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -614,14 +614,14 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).")
 (define-public ffmpeg
   (package
     (name "ffmpeg")
-    (version "4.0.3")
+    (version "4.1")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1vg229mxcrm415cq6q1nfm891hm4x56mb5p4cqjnlqnky7ikfg15"))))
+               "150rrm549fy1x71c9whmyi5knyd9sliwvmcsm438bdgg4v8c93m3"))))
     (build-system gnu-build-system)
     (inputs
      `(("fontconfig" ,fontconfig)
@@ -1269,7 +1269,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.10.05")
+    (version "2018.11.03")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1277,7 +1277,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1iq02kwxdgh07bf0w0fvbsjbdshs4kja35gy8m70ji9cj10l1mbw"))))
+                "11phhwhr1g050h4625d5jsgcsjnnv7jc6xcrbn7zdzd32f6gy2lj"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 89e850bedc..3732f26eba 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -195,14 +195,14 @@ Interface} specification.")
     (name "nginx")
     ;; Consider updating the nginx-documentation package if the nginx package is
     ;; updated.
-    (version "1.14.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nginx.org/download/nginx-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1d9c0avfpbwvzyg53b59ks8shpnrxnbnshcd7ziizflsyv5vw5ax"))))
+                "19542jxcjf4dvrqvgb5vr36mhbzcjrxc3v0xh451rm60610rf2dz"))))
     (build-system gnu-build-system)
     (inputs `(("openssl" ,openssl)
               ("pcre" ,pcre)
@@ -4166,19 +4166,15 @@ It uses the uwsgi protocol for all the networking/interprocess communications.")
 (define-public jq
   (package
     (name "jq")
-    (version "1.5")
+    (version "1.6")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/stedolan/" name
-                                  "/releases/download/" name "-" version
-                                  "/" name "-" version ".tar.gz"))
+              (uri (string-append "https://github.com/stedolan/jq"
+                                  "/releases/download/jq-" version
+                                  "/jq-" version ".tar.gz"))
               (sha256
                (base32
-                "0g29kyz4ykasdcrb0zmbrp2jqs9kv1wz9swx849i2d1ncknbzln4"))
-              ;; This patch has been pushed and the vulnerability will be
-              ;; fixed in the next release after 1.5.
-              ;; https://github.com/stedolan/jq/issues/995
-              (patches (search-patches "jq-CVE-2015-8863.patch"))))
+                "1a76f46a652i2g333kfvrl6mp2w7whf6h1yly519izg4y967h9cn"))))
     (inputs
      `(("oniguruma" ,oniguruma)))
     (native-inputs
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index d7dbc5c768..d3e68c4c07 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -5453,6 +5453,58 @@ The XCB util module provides the following libraries:
       "file://COPYING"
       "See COPYING in the distribution."))))
 
+(define-public xcb-util-errors
+  (let ((commit "5d660ebe872cadcdc85de9d6f9afe05de629c030")
+        (revision "1"))
+    (package
+      (name "xcb-util-errors")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://anongit.freedesktop.org/git/xcb/util-errors.git")
+                      (commit commit)
+                      (recursive? #t)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "12bah0iz5k6b9hwlc5zffyfg2gnrajll3gn5s8zmazgynvw72ahg"))))
+     (build-system gnu-build-system)
+     (outputs '("out"))
+     (inputs
+      `(("util-macros" ,util-macros)
+        ("xcb-proto" ,xcb-proto)))
+     (propagated-inputs
+      `(("libxcb" ,libxcb)))
+     (native-inputs
+      `(("autoconf" ,autoconf)
+        ("automake" ,automake)
+        ("libtool" ,libtool)
+        ("python-2" ,python-2)
+        ("pkg-config" ,pkg-config)))
+     (arguments
+      `(#:phases
+        (modify-phases %standard-phases
+          (replace 'bootstrap
+            (lambda _
+              ;; The default 'bootstrap' phase would run 'autogen.sh', which
+              ;; would try to run ./configure and fail due to unpatched
+              ;; shebangs.
+              (invoke "autoreconf" "-v" "--install"))))))
+     (home-page "https://cgit.freedesktop.org/xcb/util-errors/")
+     (synopsis "XCB helper library for printing information about X11 errors")
+     (description
+      "The XCB util module provides a number of libraries which sit on
+top of libxcb, the core X protocol library, and some of the extension
+libraries.  These experimental libraries provide convenience functions
+and interfaces which make the raw X protocol more usable.  Some of the
+libraries also provide client-side code which is not strictly part of
+the X protocol but which has traditionally been provided by Xlib.
+
+The XCB util-errors module provides a utility library that gives human
+readable names to error codes, event codes, and also to major and minor
+numbers.")
+     (license license:x11))))
 
 (define-public xcb-util-image
   (package
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 47c7d8bb27..3409bd352c 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2040,6 +2041,8 @@ This service is not part of @var{%base-services}."
                            (default (file-append shadow "/bin/login")))
   (login-arguments         kmscon-configuration-login-arguments
                            (default '("-p")))
+  (auto-login              kmscon-configuration-auto-login
+                           (default #f))
   (hardware-acceleration?  kmscon-configuration-hardware-acceleration?
                            (default #f))) ; #t causes failure
 
@@ -2051,14 +2054,20 @@ This service is not part of @var{%base-services}."
            (virtual-terminal (kmscon-configuration-virtual-terminal config))
            (login-program (kmscon-configuration-login-program config))
            (login-arguments (kmscon-configuration-login-arguments config))
+           (auto-login (kmscon-configuration-auto-login config))
            (hardware-acceleration? (kmscon-configuration-hardware-acceleration? config)))
 
        (define kmscon-command
          #~(list
             #$(file-append kmscon "/bin/kmscon") "--login"
             "--vt" #$virtual-terminal
+            "--no-switchvt" ;Prevent a switch to the virtual terminal.
             #$@(if hardware-acceleration? '("--hwaccel") '())
-            "--" #$login-program #$@login-arguments))
+            "--login" "--"
+            #$login-program #$@login-arguments
+            #$@(if auto-login
+                   #~(#$auto-login)
+                   #~())))
 
        (shepherd-service
         (documentation "kmscon virtual terminal")
diff --git a/gnu/services/cuirass.scm b/gnu/services/cuirass.scm
index 496b2d06c8..36e90fc825 100644
--- a/gnu/services/cuirass.scm
+++ b/gnu/services/cuirass.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
-;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
@@ -54,6 +54,8 @@
                     (default "/var/log/cuirass.log"))
   (cache-directory  cuirass-configuration-cache-directory ;string (dir-name)
                     (default "/var/cache/cuirass"))
+  (ttl              cuirass-configuration-ttl     ;integer
+                    (default (* 30 24 3600)))
   (user             cuirass-configuration-user ;string
                     (default "cuirass"))
   (group            cuirass-configuration-group ;string
@@ -86,6 +88,7 @@
          (group            (cuirass-configuration-group config))
          (interval         (cuirass-configuration-interval config))
          (database         (cuirass-configuration-database config))
+         (ttl              (cuirass-configuration-ttl config))
          (port             (cuirass-configuration-port config))
          (host             (cuirass-configuration-host config))
          (specs            (cuirass-configuration-specifications config))
@@ -102,6 +105,7 @@
                             "--specifications"
                             #$(scheme-file "cuirass-specs.scm" specs)
                             "--database" #$database
+                            "--ttl" #$(string-append (number->string ttl) "s")
                             "--port" #$(number->string port)
                             "--listen" #$host
                             "--interval" #$(number->string interval)
diff --git a/gnu/services/dns.scm b/gnu/services/dns.scm
index 16bd039f59..24ef886682 100644
--- a/gnu/services/dns.scm
+++ b/gnu/services/dns.scm
@@ -763,9 +763,9 @@ manually.")
         (use-modules (guix build utils)
                      (ice-9 rdelim))
         (let ((ddclient-user
-               #$(passwd:uid (getpw (ddclient-configuration-user config))))
+               (passwd:uid (getpw #$(ddclient-configuration-user config))))
               (ddclient-group
-               #$(passwd:gid (getpw (ddclient-configuration-group config))))
+               (passwd:gid (getpw #$(ddclient-configuration-group config))))
               (ddclient-secret-file
                #$(ddclient-configuration-secret-file config)))
           ;; 'ddclient' complains about ddclient.conf file permissions, which