Merge branch 'master' into core-updates

.mailmap

@@ -42,17 +42,18 @@ Mathieu Lirzin <mthl@gnu.org> <mthl@openmailbox.org>
 Mathieu Lirzin <mthl@gnu.org> <mathieu.lirzin@openmailbox.org>
 Mathieu Othacehe <m.othacehe@gmail.com>
 Nikita Karetnikov <nikita@karetnikov.org> <nikita.karetnikov@gmail.com>
-ng0 <ng0@n0.is>
+ng0 <ng0@crash.cx>
-ng0 <ng0@n0.is> <ng0@infotropique.org>
+ng0 <ng0@crash.cx> ng0 <ng0@n0.is>
-ng0 <ng0@n0.is> <ng0@no-reply.infotropique.org>
+ng0 <ng0@crash.cx> <ng0@infotropique.org>
-ng0 <ng0@n0.is> <ng0@no-reply.pragmatique.xyz>
+ng0 <ng0@crash.cx> <ng0@no-reply.infotropique.org>
-ng0 <ng0@n0.is> <ng0@pragmatique.xyz>
+ng0 <ng0@crash.cx> <ng0@no-reply.pragmatique.xyz>
-ng0 <ng0@n0.is> <contact.ng0@cryptolab.net>
+ng0 <ng0@crash.cx> <ng0@pragmatique.xyz>
-ng0 <ng0@n0.is> <ng0@we.make.ritual.n0.is>
+ng0 <ng0@crash.cx> <contact.ng0@cryptolab.net>
-ng0 <ng0@n0.is> <ngillmann@runbox.com>
+ng0 <ng0@crash.cx> <ng0@we.make.ritual.n0.is>
-ng0 <ng0@n0.is> <niasterisk@grrlz.net>
+ng0 <ng0@crash.cx> <ngillmann@runbox.com>
-ng0 <ng0@n0.is> <ng@niasterisk.space>
+ng0 <ng0@crash.cx> <niasterisk@grrlz.net>
-ng0 <ng0@n0.is> <ng0@libertad.pw>
+ng0 <ng0@crash.cx> <ng@niasterisk.space>
+ng0 <ng0@crash.cx> <ng0@libertad.pw>
 Pjotr Prins <pjotr.guix@thebird.nl> <pjotr.public01@thebird.nl>
 Pjotr Prins <pjotr.guix@thebird.nl> <pjotr.public12@thebird.nl>
 Pjotr Prins <pjotr.guix@thebird.nl> <pjotr.public12@email>

gnu/local.mk

@@ -903,9 +903,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/mhash-keygen-test-segfault.patch		\
   %D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch		\
   %D%/packages/patches/mpc123-initialize-ao.patch		\
-  %D%/packages/patches/mpv-CVE-2018-6360-1.patch		\
-  %D%/packages/patches/mpv-CVE-2018-6360-2.patch		\
-  %D%/packages/patches/mpv-CVE-2018-6360-3.patch		\
   %D%/packages/patches/module-init-tools-moduledir.patch	\
   %D%/packages/patches/mongodb-support-unknown-linux-distributions.patch	\
   %D%/packages/patches/mozjs17-aarch64-support.patch		\

gnu/packages/bioinformatics.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
+;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
@@ -5849,14 +5849,14 @@ information as possible.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.4-5")
+    (version "2.4-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "0cyyvn3xsjn24w590jn6z4xajafv7yzvj6c51vqi9q6m8v5831ya"))))
+         "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -6673,19 +6673,21 @@ also known as views, in a controlled vocabulary.")
 (define-public r-bookdown
   (package
   (name "r-bookdown")
-  (version "0.5")
+  (version "0.6")
   (source (origin
             (method url-fetch)
             (uri (cran-uri "bookdown" version))
             (sha256
              (base32
-              "0zm63kr4f4kja4qpwkzl119zzyciqj7ihajfqgfjpgb4dzaiycxp"))))
+              "1pxxln42kvzl38fjprg6hcnyh1kij75fpj70vwp5hp5il813aszc"))))
   (build-system r-build-system)
   (propagated-inputs
    `(("r-htmltools" ,r-htmltools)
      ("r-knitr" ,r-knitr)
      ("r-rmarkdown" ,r-rmarkdown)
-     ("r-yaml" ,r-yaml)))
+     ("r-yaml" ,r-yaml)
+     ("r-xfun" ,r-xfun)
+     ("ghc-pandoc" ,ghc-pandoc)))
   (home-page "https://github.com/rstudio/bookdown")
   (synopsis "Authoring books and technical documents with R markdown")
   (description "This package provides output formats and utilities for
@@ -6965,13 +6967,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.20.2")
+    (version "3.20.8")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0j5s3i33qmld9l7gs1rzpv601zxyqz711x8mq35hml088c8s99w9"))))
+                "0g7bj6w61blw3m22hw9rc01n554k9qkjizh7njr3j4shmhads58d"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6993,13 +6995,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.24.2")
+    (version "1.24.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "19wgb2kcqy97pm3xgqc781id9fbmzp1hdwzkkhdzpvyf29w4n29j"))))
+                "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -7031,13 +7033,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.34.4")
+    (version "3.34.8")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1vcxf9jg8xngxg5kb9bp8rw5sghpnkpj320iq309m2fp41ahsk3f"))))
+                "0bmxsgz2yll83sd3wbxsrsfd35468igb0d8lldym0d0lqfz906bw"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7086,13 +7088,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.30.0")
+    (version "1.30.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "10ra2sjn17h6gilm9iz0cygp9ijpgbirljlc4drwrnivnw9cmi2a"))))
+                "1wnvvhj8yjsx242y6kfr5vs8kzisa96rxl1rgnnychrrvnvnh3i1"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -7164,13 +7166,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.34.1")
+    (version "2.34.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0jzv8b86vpvavwnzi5xf7y18xmn72zkabkn2kclg1mgl847cq13k"))))
+                "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7322,13 +7324,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.8.0")
+    (version "1.8.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "1011r8l0k8420j31bmh4xdcp6ka5bzf4bqhip84v5b6alpkcbvmf"))))
+                "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -7386,13 +7388,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.38.2")
+    (version "1.38.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "1sjn3976f1sqvrq6jq2hgc60ffxgfr3jlklaxfrk3xad5cv2kr2d"))))
+                "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7431,13 +7433,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.30.0")
+    (version "1.30.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "1khjvq1ffhqavkwf8n7bilknci60lxbg52icrcf2vnb9k8rlpghs"))))
+                "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -7657,13 +7659,13 @@ reference point and sorted by a user defined feature.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.10.0")
+    (version "1.11.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "1ddd8c9w1f1i1ga9rpbwiic8rsaws1chdxx4j38bpyaiy4zhz1ca"))))
+                "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
@@ -8362,14 +8364,14 @@ in SNV base substitution data.")
 (define-public r-wgcna
   (package
     (name "r-wgcna")
-    (version "1.61")
+    (version "1.62")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "WGCNA" version))
        (sha256
         (base32
-         "1vrc2k33a196hrrl7k0z534fp96vv0shmigcr65ny1q0v6lq0h6i"))))
+         "0c52rp09gqphz6g5x9jzkdcsyvfrknq0dkq9saslgy8q8ap974vx"))))
     (properties `((upstream-name . "WGCNA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8467,14 +8469,14 @@ factors bound at the specific regions.")
 (define-public r-gkmsvm
   (package
     (name "r-gkmsvm")
-    (version "0.71.0")
+    (version "0.79.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gkmSVM" version))
        (sha256
         (base32
-         "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0"))))
+         "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
     (properties `((upstream-name . "gkmSVM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8941,13 +8943,13 @@ number detection tools.")
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.4.0")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "0h53w2mrjrg2n0ndi12k9j6cwclgwcgpy25nz7nyj971aisw02xn"))))
+                "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9311,14 +9313,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.4.0")
+    (version "2.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0dqfimljhrx3gac8d1k72gppx27lz8yckyb12v4604nbviw7xd3r"))))
+         "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9391,13 +9393,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.1.0")
+    (version "2.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x"))
+                "1yarzhbylkfk4vwp7f8710zpdglkfww2db3hmq69hjllgg80ykmw"))
               ;; Delete pre-built jar.
               (snippet
                '(begin (delete-file "inst/java/ModularityOptimizer.jar")
@@ -9434,8 +9436,8 @@ Main-Class: ModularityOptimizer\n")))
        ("r-fnn" ,r-fnn)
        ("r-fpc" ,r-fpc)
        ("r-gdata" ,r-gdata)
-       ("r-ggjoy" ,r-ggjoy)
        ("r-ggplot2" ,r-ggplot2)
+       ("r-ggridges" ,r-ggridges)
        ("r-gplots" ,r-gplots)
        ("r-gridextra" ,r-gridextra)
        ("r-hmisc" ,r-hmisc)
@@ -9452,6 +9454,7 @@ Main-Class: ModularityOptimizer\n")))
        ("r-ranger" ,r-ranger)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
        ("r-rcppprogress" ,r-rcppprogress)
        ("r-reshape2" ,r-reshape2)
        ("r-rocr" ,r-rocr)
@@ -9661,14 +9664,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "1i3i88lj57wvpgjf75a23msgfsjv8pr2b4j1faga276p4fsblkhj"))))
+         "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9685,14 +9688,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.28.0")
+    (version "2.28.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "1r14p88q3y736pkqm4pdimf1izy1xy3xgivmj3cr4dv65kjny1zk"))))
+         "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -9806,14 +9809,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.2.0")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1"))))
+         "1vk6j0r5cczxmwbfzzkgayna66rxkfa3q2jikz649qvdiybhls40"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -9975,14 +9978,14 @@ interval to data view, mismatch pileup, and several splicing summaries.")
 (define-public r-gprofiler
   (package
     (name "r-gprofiler")
-    (version "0.6.1")
+    (version "0.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gProfileR" version))
        (sha256
         (base32
-         "1qix15d0wa9nspdclcawml94mng4qmr2jciv7d24py315wfsvv8p"))))
+         "08dsnja3g8qvqlgwhx9c9f8p8psn3qr5ddn84dhizkgglj30v2wj"))))
     (properties `((upstream-name . "gProfileR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10401,6 +10404,228 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
     ;; Any version of the LGPL.
     (license license:lgpl3+)))
 
+(define-public r-hdf5array
+  (package
+    (name "r-hdf5array")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HDF5Array" version))
+       (sha256
+        (base32
+         "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh"))))
+    (properties `((upstream-name . "HDF5Array")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-iranges" ,r-iranges)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/HDF5Array")
+    (synopsis "HDF5 back end for DelayedArray objects")
+    (description "This package provides an array-like container for convenient
+access and manipulation of HDF5 datasets.  It supports delayed operations and
+block processing.")
+    (license license:artistic2.0)))
+
+(define-public r-rhdf5lib
+  (package
+    (name "r-rhdf5lib")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rhdf5lib" version))
+       (sha256
+        (base32
+         "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w"))))
+    (properties `((upstream-name . "Rhdf5lib")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-hdf5
+           (lambda* (#:key inputs #:allow-other-keys)
+             (for-each delete-file '("configure" "configure.ac"))
+             ;; Do not make other packages link with the proprietary libsz.
+             (substitute* "R/zzz.R"
+               (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'")
+                "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'")
+               (("'%s/libhdf5.a %s/libsz.a'")
+                "'%s/libhdf5.a %s/libhdf5.a'"))
+             (with-directory-excursion "src"
+               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+               (rename-file (string-append "hdf5-" ,(package-version hdf5))
+                            "hdf5")
+               (rename-file "Makevars.in" "Makevars")
+               (substitute* "Makevars"
+                 (("HDF5_CXX_LIB=.*")
+                  (string-append "HDF5_CXX_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
+                 (("HDF5_LIB=.*")
+                  (string-append "HDF5_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
+                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+                 ;; szip is non-free software
+                 (("cp \\$\\{SZIP_LIB\\}.*") "")
+                 (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}")
+                  "PKG_LIBS = ${HDF5_LIB}\n")))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("hdf5" ,hdf5)))
+    (native-inputs
+     `(("hdf5-source" ,(package-source hdf5))))
+    (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
+packages.")
+    (license license:artistic2.0)))
+
+(define-public r-beachmat
+  (package
+    (name "r-beachmat")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "beachmat" version))
+       (sha256
+        (base32
+         "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz"))))
+    (build-system r-build-system)
+    (inputs
+     `(("hdf5" ,hdf5)))
+    (propagated-inputs
+     `(("r-delayedarray" ,r-delayedarray)
+       ("r-hdf5array" ,r-hdf5array)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-rhdf5lib" ,r-rhdf5lib)))
+    (home-page "https://bioconductor.org/packages/beachmat")
+    (synopsis "Compiling Bioconductor to handle each matrix type")
+    (description "This package provides a consistent C++ class interface for a
+variety of commonly used matrix types, including sparse and HDF5-backed
+matrices.")
+    (license license:gpl3)))
+
+(define-public r-singlecellexperiment
+  (package
+    (name "r-singlecellexperiment")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "SingleCellExperiment" version))
+       (sha256
+        (base32
+         "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars"))))
+    (properties
+     `((upstream-name . "SingleCellExperiment")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/SingleCellExperiment")
+    (synopsis "S4 classes for single cell data")
+    (description "This package defines an S4 class for storing data from
+single-cell experiments.  This includes specialized methods to store and
+retrieve spike-in information, dimensionality reduction coordinates and size
+factors for each cell, along with the usual metadata for genes and
+libraries.")
+    (license license:gpl3)))
+
+(define-public r-scater
+  (package
+    (name "r-scater")
+    (version "1.6.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scater" version))
+              (sha256
+               (base32
+                "0fp68n0xnbf90wrprqawsbilg9x7v2scp0dxb3936g20025csrdd"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biomart" ,r-biomart)
+       ("r-data-table" ,r-data-table)
+       ("r-dplyr" ,r-dplyr)
+       ("r-edger" ,r-edger)
+       ("r-ggbeeswarm" ,r-ggbeeswarm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-limma" ,r-limma)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("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")
+    (description "This package provides a collection of tools for doing
+various analyses of single-cell RNA-seq gene expression data, with a focus on
+quality control.")
+    (license license:gpl2+)))
+
+(define-public r-scran
+  (package
+    (name "r-scran")
+    (version "1.6.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scran" version))
+       (sha256
+        (base32
+         "0zfm5i8xrnzb3894xygqd6zkbwaa2x3z74wbxw39fcjhyhxv2hmb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("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)
+       ("r-rcpp" ,r-rcpp)
+       ("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-zoo" ,r-zoo)))
+    (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
+single-cell RNA-seq data.  Methods are provided for normalization of
+cell-specific biases, assignment of cell cycle phase, and detection of highly
+variable and significantly correlated genes.")
+    (license license:gpl3)))
+
 (define htslib-for-sambamba
   (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
     (package

gnu/packages/ccache.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2016, 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
@@ -30,7 +30,7 @@
 (define-public ccache
   (package
     (name "ccache")
-    (version "3.3.5")
+    (version "3.4")
     (source
      (origin
       (method url-fetch)
@@ -38,7 +38,7 @@
                           version ".tar.xz"))
       (sha256
        (base32
-        "1iih5d171rq29366c1z90dri2h8173yyc8rm2740wxiqx6k7c18r"))))
+        "0sfisvjs2iham29flxgmnfg7kzqz66bhk6q0qcwbdv1n569say5j"))))
     (build-system gnu-build-system)
     (native-inputs `(("perl" ,perl)     ;for test.sh
                      ("which" ,(@ (gnu packages base) which))))
@@ -47,14 +47,14 @@
      '(#:phases (modify-phases %standard-phases
                  (add-before 'check 'setup-tests
                    (lambda _
-                     (substitute* '("test/test_hashutil.c" "test.sh")
+                     (substitute* '("unittest/test_hashutil.c" "test/suites/base.bash")
                        (("#!/bin/sh") (string-append "#!" (which "sh"))))
                      #t))
                  (add-before 'check 'munge-failing-test
                    (lambda _
                      ;; XXX The new ‘Multiple -fdebug-prefix-map’ test added in
                      ;; 3.3.5 fails (why?).  Force it to report success instead.
-                     (substitute* "test.sh"
+                     (substitute* "test/suites/debug_prefix_map.bash"
                        (("grep \"name\"") "true"))
                      #t)))))
     (home-page "https://ccache.samba.org/")

gnu/packages/check.scm

@@ -144,6 +144,23 @@ unit testing.  Test output is in XML for automatic testing and GUI based for
 supervised tests.")
     (license license:lgpl2.1))) ; no copyright notices. LGPL2.1 is in the tarball
 
+;; Some packages require this newer version of cppunit.  However, it needs
+;; C++11 support, which is not enabled by default in our current GCC, and
+;; updating in-place would require adding CXXFLAGS to many dependent packages.
+;; Thus, keep as a separate variable for now.
+;; TODO: Remove this when our default GCC is updated to 6 or higher.
+(define-public cppunit-1.14
+  (package
+    (inherit cppunit)
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://dev-www.libreoffice.org/src/"
+                                  "cppunit-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1027cyfx5gsjkdkaf6c2wnjh68882grw8n672018cj3vs9lrhmix"))))))
+
 (define-public catch-framework
   (package
     (name "catch")

gnu/packages/compression.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
@@ -1728,6 +1728,7 @@ Compression ratios of 2:1 to 3:1 are common for text files.")
 (define-public unzip
   (package (inherit zip)
     (name "unzip")
+    (replacement unzip/fixed)
     (version "6.0")
     (source
      (origin
@@ -1778,6 +1779,20 @@ recreates the stored directory structure by default.")
     (license (license:non-copyleft "file://LICENSE"
                                    "See LICENSE in the distribution."))))
 
+(define unzip/fixed
+  (package/inherit unzip
+    (arguments
+      (substitute-keyword-arguments (package-arguments unzip)
+        ((#:phases phases)
+          `(modify-phases ,phases
+             (add-after 'unpack 'fortify
+               (lambda _
+                 ;; Mitigate CVE-2018-1000035, an exploitable buffer overflow.
+                 ;; This environment variable is recommended in 'unix/Makefile'
+                 ;; for passing flags to the C compiler.
+                 (setenv "LOCAL_UNZIP" "-D_FORTIFY_SOURCE=1")
+                 #t))))))))
+
 (define-public zziplib
   (package
     (name "zziplib")

gnu/packages/cran.scm

@@ -95,13 +95,13 @@ error stream.")
 (define-public r-rcpp
   (package
     (name "r-rcpp")
-    (version "0.12.14")
+    (version "0.12.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rcpp" version))
        (sha256
-        (base32 "0qvyxggddyg87lza45hjl0a2prabdyshkqzkz418vi777zygqa6s"))))
+        (base32 "1pnv6sl4vdn69ygmgrb1b3gsigfdcfb56wnzikic93l8gkvdsvxv"))))
     (build-system r-build-system)
     (home-page "http://www.rcpp.org")
     (synopsis "Seamless R and C++ integration")
@@ -206,14 +206,14 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.")
 (define-public r-shape
   (package
     (name "r-shape")
-    (version "1.4.3")
+    (version "1.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shape" version))
        (sha256
         (base32
-         "1v9xp60p813rnx41vchkh32qmcb4z2zp9l7r1a8a6f8aqylnq3vj"))))
+         "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/shape")
     (synopsis "Functions for plotting graphical shapes")
@@ -321,14 +321,14 @@ rows, dropping names) to see if the modified versions are identical.")
 (define-public r-dendextend
   (package
     (name "r-dendextend")
-    (version "1.6.0")
+    (version "1.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dendextend" version))
        (sha256
         (base32
-         "0pichh08zi12lpxzc061dmv4smj6lizygd1xymln8wfz18sf7923"))))
+         "1krvqadnnh53xx5ql7bwzxaif6a317jzbs1m00gnc6jnj03rfl5d"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-fpc" ,r-fpc)
@@ -542,14 +542,14 @@ plot networks.")
 (define-public r-proxy
   (package
     (name "r-proxy")
-    (version "0.4-20")
+    (version "0.4-21")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "proxy" version))
        (sha256
         (base32
-         "15g6dacdmlbkcnimblscghl23aj732cn6qwbs583r4im9v5nvbla"))))
+         "1vih8gsfzv97h5c8ixd1qjnn02i7fzla2p9fdj2wpisqhx0p0xv0"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/proxy")
     (synopsis "Distance and similarity measures")
@@ -562,14 +562,14 @@ most popular ones.")
 (define-public r-sp
   (package
     (name "r-sp")
-    (version "1.2-5")
+    (version "1.2-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sp" version))
        (sha256
         (base32
-         "09yydnacp33yx0kn537k96fjlbf75fjafqfknpa5gvci4l888bqd"))))
+         "0q04yfgyjannsrzl0ppwcv0simrxrrbx2iz5mzaafc5x38zf0q3d"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -989,20 +989,44 @@ testing framework of Wald are generic and can therefore also be used in other
 contexts.")
     (license license:gpl2+)))
 
+(define-public r-squarem
+  (package
+    (name "r-squarem")
+    (version "2017.10-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "SQUAREM" version))
+       (sha256
+        (base32
+         "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
+    (properties `((upstream-name . "SQUAREM")))
+    (build-system r-build-system)
+    (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
+    (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
+    (description
+     "This package provides algorithms for accelerating the convergence of
+slow, monotone sequences from smooth, contraction mapping such as the EM
+algorithm.  It can be used to accelerate any smooth, linearly convergent
+acceleration scheme.  A tutorial style introduction to this package is
+available in a vignette.")
+    (license license:gpl2+)))
+
 (define-public r-lava
   (package
     (name "r-lava")
-    (version "1.5.1")
+    (version "1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lava" version))
        (sha256
         (base32
-         "1vcm04h9i39gmf2prl5d4j4il4gs6skzr6y2fvl1vn4hklna87f4"))))
+         "02xf5d968raz9gnq5ywy04wz29xpdyca1hm79vbbg1mcxvzdl1dz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-numderiv" ,r-numderiv)
+       ("r-squarem" ,r-squarem)
        ("r-survival" ,r-survival)))
     (home-page "https://github.com/kkholst/lava")
     (synopsis "Latent variable models")
@@ -1014,14 +1038,14 @@ variable models.")
 (define-public r-drr
   (package
     (name "r-drr")
-    (version "0.0.2")
+    (version "0.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DRR" version))
        (sha256
         (base32
-         "1scfwp6ry6apxzqjclsmn2frxp9qfw6zxsxn5w0j0q3sz42hz1h2"))))
+         "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
     (properties `((upstream-name . "DRR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1106,14 +1130,14 @@ calendar objects.")
 (define-public r-ddalpha
   (package
     (name "r-ddalpha")
-    (version "1.3.1")
+    (version "1.3.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ddalpha" version))
        (sha256
         (base32
-         "0pczw9543y7f92m7gyk7rxcjn8vsjaldc5vl0r56ywip9i374zbh"))))
+         "13w8ir5rd80rka4mq343zd4wn93vfw870lzfqrd3cxgwb1bwcw7y"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
@@ -1279,14 +1303,14 @@ provides a one-row summary of model-level statistics.")
 (define-public r-recipes
   (package
     (name "r-recipes")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "recipes" version))
        (sha256
         (base32
-         "0id46c7iaf49miw4kxpidsbg3hdywav43n1lh2zd1vg5946bzg04"))))
+         "1car3a3mqn87pz049cbgkaayz86970mvkapk6al2k7jjw76306l9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
@@ -2072,3 +2096,86 @@ around the relevant area.  This work is based on the @code{ggplot2} and
 dendrogram panes, and the placing of factor variables in the sides of the
 heatmap.")
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-xfun
+  (package
+    (name "r-xfun")
+    (version "0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "xfun" version))
+       (sha256
+        (base32
+         "1sm51gmwgw876d6d1q8smxmfgfh6zsnykfx8qp8z6jmh0fvd89pj"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/yihui/xfun")
+    (synopsis "Miscellaneous functions")
+    (description
+     "This package provides miscellaneous functions commonly used in other
+packages maintained by Yihui Xie.")
+    (license license:expat)))
+
+(define-public r-utf8
+  (package
+    (name "r-utf8")
+    (version "1.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "utf8" version))
+       (sha256
+        (base32
+         "03s4j6059q0nly68vpk6wy3p3f5ypakw93fj35kzd82b4z1r9cs3"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/patperry/r-utf8")
+    (synopsis "Unicode text processing")
+    (description
+     "This package provides tools to process and print UTF-8 encoded
+international text (Unicode).  Input, validate, normalize, encode, format, and
+display.")
+    (license license:asl2.0)))
+
+(define-public r-pillar
+  (package
+    (name "r-pillar")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pillar" version))
+       (sha256
+        (base32
+         "1gh3j2pbbf5y4d5nyqnlr0x27jjyvjjspcccmw61airs1n6rx8jq"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cli" ,r-cli)
+       ("r-crayon" ,r-crayon)
+       ("r-rlang" ,r-rlang)
+       ("r-utf8" ,r-utf8)))
+    (home-page "https://github.com/r-lib/pillar")
+    (synopsis "Coloured formatting for columns")
+    (description
+     "This package provides a @code{pillar} generic designed for formatting
+columns of data using the full range of colours provided by modern
+terminals.")
+    (license license:gpl3)))
+
+(define-public r-uuid
+  (package
+    (name "r-uuid")
+    (version "0.1-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "uuid" version))
+       (sha256
+        (base32
+         "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
+    (build-system r-build-system)
+    (home-page "http://www.rforge.net/uuid")
+    (synopsis "Tools for generating and handling of UUIDs")
+    (description
+     "This package provides tools for generating and handling of
+@dfn{Universally Unique Identifiers} (UUIDs).")
+    (license license:expat)))

gnu/packages/crypto.scm

@@ -87,16 +87,18 @@ communication, encryption, decryption, signatures, etc.")
 (define-public libmd
   (package
     (name "libmd")
-    (version "0.0.0")
+    (version "1.0.0")
     (source (origin
             (method url-fetch)
-            (uri (string-append
+            (uri
-                  "https://archive.hadrons.org/software/libmd/libmd-"
+             (list
-                  version
+              (string-append "https://archive.hadrons.org/software/libmd/libmd-"
-                  ".tar.xz"))
+                             version ".tar.xz")
+              (string-append "https://libbsd.freedesktop.org/releases/libmd-"
+                             version ".tar.xz")))
             (sha256
              (base32
-              "121s73pgbqsnmy6xblbrkj9y44c5zzzpf2hcmh6zvcvg4dk26gzx"))))
+              "1iv45npzv0gncjgcpx5m081861zdqxw667ysghqb8721yrlyl6pj"))))
     (build-system gnu-build-system)
     (synopsis "Message Digest functions from BSD systems")
     (description

gnu/packages/emacs.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2016, 2017 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2015, 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016 Adriano Peluso <catonano@gmail.com>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2016 Matthew Jordan <matthewjordandevops@yandex.com>
 ;;; Copyright © 2016, 2017 Roel Janssen <roel@gnu.org>
@@ -280,6 +280,7 @@ editor (without an X toolkit)" )
               (uri (git-reference
                     (url "git://git.hcoop.net/git/bpt/emacs.git")
                     (commit "41120e0f595b16387eebfbf731fff70481de1b4b")))
+              (file-name (string-append name "-" version "-checkout"))
               (patches (search-patches "guile-emacs-fix-configure.patch"))
               (sha256
                (base32
@@ -957,7 +958,7 @@ light user interface.")
 (define-public emacs-emms-player-mpv
   (package
     (name "emacs-emms-player-mpv")
-    (version "0.0.10")
+    (version "0.0.13")
     (source
      (origin
        (method url-fetch)
@@ -966,7 +967,7 @@ light user interface.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1q81fpmwr8hpdgq71vbdai2nml4yyqbmk4ffdyl4irlwph8gfjyq"))))
+         "01i0bz7wdqzcnv5r63m9xgl07yf1nmn86dwy00rcfsn5za46y3r3"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emms" ,emms)))
@@ -1621,6 +1622,7 @@ management tasks from Emacs.  To begin with, run @code{M-x guix-about} or
               (uri (string-append
                     "https://github.com/Emacs-D-Mode-Maintainers/Emacs-D-Mode/"
                     "archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0knpgi55jm09282aqf8pv55zillpnpzf9f4sgm6gwsmvxf17xaw0"))))
@@ -2385,6 +2387,7 @@ the speedbar window.")
               (uri (git-reference
                     (commit "880706469338ab59b5bb7dbe8460016f89755364")
                     (url "https://github.com/gregsexton/ob-ipython.git")))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1scf25snbds9ymagpny30ijbsg479r3nm0ih01dy4m9d0g7qryb7"))))

gnu/packages/embedded.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
@@ -525,6 +525,9 @@ with a layered architecture of JTAG interface and TAP support.")
           `(modify-phases ,phases
              (add-after 'unpack 'chdir
                (lambda _ (chdir "gcc") #t))))))
+      (native-inputs
+       `(("gcc-4" ,gcc-4.9)
+         ,@(package-native-inputs propeller-gcc-6)))
       (home-page "https://github.com/parallaxinc/propgcc")
       (supported-systems (delete "aarch64-linux" %supported-systems)))))
 

gnu/packages/golang.scm

@@ -208,7 +208,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
   (package
     (inherit go-1.4)
     (name "go")
-    (version "1.9.3")
+    (version "1.9.4")
     (source
      (origin
        (method url-fetch)
@@ -216,7 +216,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                            name version ".src.tar.gz"))
        (sha256
         (base32
-         "1bj73hrr7jjdg0w6snwkqb5y3yrlks5nrs2lgnkyy0hyx7b0lgaf"))))
+         "01nw8rfvf10naja0wq0kabsm012sbqq76hd4b8c7g28n6ggshwq5"))))
     (arguments
      (substitute-keyword-arguments (package-arguments go-1.4)
        ((#:phases phases)

gnu/packages/haskell-check.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Danny Milosavljevic <dannym@scratchpost.org>
@@ -180,7 +180,7 @@ timer functions of different operating systems via a unified API.")
 (define-public ghc-tasty
   (package
     (name "ghc-tasty")
-    (version "0.11.0.1")
+    (version "0.11.0.4")
     (source
      (origin
        (method url-fetch)
@@ -190,12 +190,13 @@ timer functions of different operating systems via a unified API.")
              ".tar.gz"))
        (sha256
         (base32
-         "1chapivmmwsb1ghwagvdm80bfj3hdk75m94z4p212ng2i4ghpjkx"))))
+         "05pxjzgbgjdn7477xry0ssjrnmnsydqiq6nm6ck8n2da1baliqp0"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-stm" ,ghc-stm)
        ("ghc-mtl" ,ghc-mtl)
        ("ghc-tagged" ,ghc-tagged)
+       ("ghc-regex-tdfa" ,ghc-regex-tdfa)
        ("ghc-regex-tdfa-rc" ,ghc-regex-tdfa-rc)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
        ("ghc-unbounded-delays" ,ghc-unbounded-delays)
@@ -310,10 +311,36 @@ only those tests that failed in the last run, or to only run the tests that have
 been added since previous test run.")
   (license license:bsd-3)))
 
+(define-public ghc-tasty-expected-failure
+  (package
+    (name "ghc-tasty-expected-failure")
+    (version "0.11.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "tasty-expected-failure/tasty-expected-failure-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0r555f18d2gj96pjyc13chn1nxaxl81am4xgip3mvvjhw8s5mva1"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-tagged" ,ghc-tagged)
+       ("ghc-tasty" ,ghc-tasty)))
+    (home-page "http://github.com/nomeata/tasty-expected-failure")
+    (synopsis "Mark tasty tests as failure expected")
+    (description
+     "With the function @code{Test.Tasty.ExpectedFailure.expectFail} in the
+provided module @code{Test.Tasty.ExpectedFailure}, you can mark that you
+expect test cases to fail, and not to pass. This can be used for test-driven
+development.")
+    (license license:expat)))
+
 (define-public ghc-quickcheck-instances
   (package
     (name "ghc-quickcheck-instances")
-    (version "0.3.12")
+    (version "0.3.16.1")
     (source
      (origin
        (method url-fetch)
@@ -323,18 +350,22 @@ been added since previous test run.")
              version ".tar.gz"))
        (sha256
         (base32
-         "1wwvkzpams7i0j7nk5qj8vvhj8x5zcbgbgrpczszgvshva4bkmfx"))))
+         "01v5bs7r9yvhkvb4yc9bqnacy8r6cy2gr9lnmwx40n5apgi0gcbz"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-old-time" ,ghc-old-time)
+     `(("ghc-quickcheck" ,ghc-quickcheck)
-       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-base-compat" ,ghc-base-compat)
+       ("ghc-case-insensitive" ,ghc-case-insensitive)
        ("ghc-hashable" ,ghc-hashable)
-       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-old-time" ,ghc-old-time)
        ("ghc-scientific" ,ghc-scientific)
-       ("ghc-vector" ,ghc-vector)
+       ("ghc-tagged" ,ghc-tagged)
-       ("ghc-text" ,ghc-text)))
+       ("ghc-text" ,ghc-text)
-    (home-page
+       ("ghc-transformers-compat" ,ghc-transformers-compat)
-     "https://github.com/aslatter/qc-instances")
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-uuid-types" ,ghc-uuid-types)
+       ("ghc-vector" ,ghc-vector)))
+    (home-page "https://github.com/aslatter/qc-instances")
     (synopsis "Common quickcheck instances")
     (description "This package provides QuickCheck instances for types
 provided by the Haskell Platform.")
@@ -390,7 +421,7 @@ use HUnit assertions as QuickCheck properties.")
 (define-public ghc-quickcheck
   (package
     (name "ghc-quickcheck")
-    (version "2.8.2")
+    (version "2.10.1")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -401,21 +432,38 @@ use HUnit assertions as QuickCheck properties.")
              ".tar.gz"))
        (sha256
         (base32
-         "1ai6k5v0bibaxq8xffcblc6rwmmk6gf8vjyd9p2h3y6vwbhlvilq"))))
+         "1rfmns3lj3hl93k1jws85ajkkw7z9ll8cw292n9m7zald1w5dfqx"))))
     (build-system haskell-build-system)
     (arguments
      `(#:tests? #f  ; FIXME: currently missing libraries used for tests.
        #:configure-flags '("-f base4")))
     (inputs
-     `(("ghc-tf-random" ,ghc-tf-random)))
+     `(("ghc-random" ,ghc-random)
-    (home-page
+       ("ghc-tf-random" ,ghc-tf-random)))
-     "https://github.com/nick8325/quickcheck")
+    (home-page "https://github.com/nick8325/quickcheck")
-    (synopsis
+    (synopsis "Automatic testing of Haskell programs")
-     "Automatic testing of Haskell programs")
     (description
-     "QuickCheck is a library for random testing of program properties.")
+     "QuickCheck is a library for random testing of program properties.  The
+programmer provides a specification of the program, in the form of properties
+which functions should satisfy, and QuickCheck then tests that the properties
+hold in a large number of randomly generated cases.  Specifications are
+expressed in Haskell, using combinators defined in the QuickCheck library.")
     (license license:bsd-3)))
 
+(define-public ghc-quickcheck-latest
+  (package (inherit ghc-quickcheck)
+    (version "2.11.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/QuickCheck/QuickCheck-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0xhqk35fkzlbjcqbabg6962jkv8d688nzmz7ng4bm84x2d95d328"))))))
+
 (define-public ghc-test-framework
   (package
     (name "ghc-test-framework")
@@ -429,6 +477,8 @@ use HUnit assertions as QuickCheck properties.")
         (base32
          "0wxjgdvb1c4ykazw774zlx86550848wbsvgjgcrdzcgbb9m650vq"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:configure-flags (list "--allow-newer=time")))
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)
        ("ghc-quickcheck" ,ghc-quickcheck)))
@@ -478,7 +528,7 @@ reporting and test statistics output.")
 (define-public ghc-test-framework-quickcheck2
   (package
     (name "ghc-test-framework-quickcheck2")
-    (version "0.3.0.3")
+    (version "0.3.0.4")
     (source
      (origin
        (method url-fetch)
@@ -487,14 +537,7 @@ reporting and test statistics output.")
                            "test-framework-quickcheck2-" version ".tar.gz"))
        (sha256
         (base32
-         "12p1zwrsz35r3j5gzbvixz9z1h5643rhihf5gqznmc991krwd5nc"))
+         "0vj834337r6jzr3258cv68ly2sv5999mklpsrfngyk51kywsyqyp"))))
-       (modules '((guix build utils)))
-       (snippet
-        ;; The Hackage page and the cabal file linked there for this package
-        ;; both list 2.9 as the upper version limit, but the source tarball
-        ;; specifies 2.8.  Assume the Hackage page is correct.
-        '(substitute* "test-framework-quickcheck2.cabal"
-           (("QuickCheck >= 2.4 && < 2.8") "QuickCheck >= 2.4 && < 2.9")))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
@@ -545,7 +588,7 @@ using Template Haskell")
 (define-public ghc-hunit
   (package
     (name "ghc-hunit")
-    (version "1.2.5.2")
+    (version "1.3.1.2")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -556,7 +599,7 @@ using Template Haskell")
              ".tar.gz"))
        (sha256
         (base32
-         "0hcs6qh8bqhip1kkjjnw7ccgcsmawdz5yvffjj5y8zd2vcsavx8a"))))
+         "10akdh4fl615rrshxi3m5gf414il1q42z4zqyb6q4jasmscvzpms"))))
     (build-system haskell-build-system)
     (home-page "http://hunit.sourceforge.net/")
     (synopsis "Unit testing framework for Haskell")
@@ -568,7 +611,7 @@ JUnit tool for Java.")
 (define-public hspec-discover
   (package
     (name "hspec-discover")
-    (version "2.2.0")
+    (version "2.2.4")
     (source
      (origin
        (method url-fetch)
@@ -578,7 +621,7 @@ JUnit tool for Java.")
              ".tar.gz"))
        (sha256
         (base32
-         "0w3awzbljf4hqhxrjrxqa1lfcclg92bhmq641gz2q80vycspapzx"))))
+         "1bz7wb8v0bx1amiz4bpj34xq97d1ia29n3f654wcrh6lacydp3dv"))))
     (build-system haskell-build-system)
     (arguments `(#:haddock? #f)) ; Haddock phase fails because there are no
                                  ; documentation files.
@@ -592,7 +635,7 @@ runs Hspec tests.")
 (define-public ghc-hspec-core
   (package
     (name "ghc-hspec-core")
-    (version "2.2.0")
+    (version "2.2.4")
     (source
      (origin
        (method url-fetch)
@@ -602,7 +645,7 @@ runs Hspec tests.")
              ".tar.gz"))
        (sha256
         (base32
-         "1wgd55k652jaf81nkvciyqi67ycj7zamr4nd9z1cqf8nr9fc3sa4"))))
+         "0x845ngfl6vf65fnpb5mm3wj0ql45pz11bnm0x4gxc4ybd9c52ij"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: testing libraries are missing.
     (inputs
@@ -623,7 +666,7 @@ be used to extend Hspec's functionality.")
 (define-public ghc-hspec-meta
   (package
     (name "ghc-hspec-meta")
-    (version "2.2.0")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
@@ -633,7 +676,7 @@ be used to extend Hspec's functionality.")
              ".tar.gz"))
        (sha256
         (base32
-         "1fmqmgrzp135cxhmxxbaswkk4bqbpgfml00cmcz0d39n11vzpa5z"))))
+         "1m1pkrxiglxzwv8gdj5jr1bdbhxvvg6sbl9m61w4565d7k1m8yxa"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
@@ -653,7 +696,7 @@ used to test the in-development version of Hspec.")
 (define-public ghc-hspec
   (package
     (name "ghc-hspec")
-    (version "2.2.0")
+    (version "2.2.4")
     (source
      (origin
        (method url-fetch)
@@ -663,7 +706,7 @@ used to test the in-development version of Hspec.")
              ".tar.gz"))
        (sha256
         (base32
-         "0zqisxznlbszivsgy3irvf566zhcr6ipqqj3x9i7pj5hy913jwqf"))))
+         "1cf90gqvg1iknja6ymxqxyabpahcxni3blqllh81ywbir3whljvj"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hspec-core" ,ghc-hspec-core)
@@ -726,3 +769,27 @@ Haskell, inspired by the Ruby library RSpec.")
     (description "This library provides catchy combinators for HUnit, see
 @uref{https://github.com/sol/hspec-expectations#readme, the README}.")
     (license license:expat)))
+
+(define-public ghc-nanospec
+  (package
+    (name "ghc-nanospec")
+    (version "0.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "nanospec/nanospec-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1rcmhl9bhyfvanalnf1r86wkx6rq6wdvagnw1h011jcnnb1cq56g"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("ghc-silently" ,ghc-silently)))
+    (home-page "https://github.com/hspec/nanospec#readme")
+    (synopsis "Lightweight implementation of a subset of Hspec's API")
+    (description
+     "Nanospec is a lightweight implementation of a subset of Hspec's API with
+minimal dependencies.")
+    (license license:expat)))

gnu/packages/haskell-crypto.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
-;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2017 rsiddharth <s@ricketyspace.net>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -257,7 +257,7 @@ the C implementation.")
 (define-public ghc-cryptonite
   (package
     (name "ghc-cryptonite")
-    (version "0.19")
+    (version "0.20")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -265,7 +265,7 @@ the C implementation.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1rw5k34vpn4134yrzdhf0rsshsrkixfbv9ap18di2n00z2cw1shw"))))
+                "0m63np0affci7ba9mrkvw2flzxn0s2mk930xldc4dwijw32gl6r6"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-memory" ,ghc-memory)
@@ -419,14 +419,14 @@ libraries, like OpenSSL.")
 (define-public ghc-x509
   (package
     (name "ghc-x509")
-    (version "1.6.3")
+    (version "1.6.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "x509/x509-" version ".tar.gz"))
               (sha256
                (base32
-                "1pmsby29abn485fvnymsgipvb3p1ch9c591xj5ncszkf0ivjiiin"))))
+                "0hixx76wpb4qxida017ka5zr6lrsycahrqyw8z90q9mxvndpy3my"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-memory" ,ghc-memory)
@@ -449,7 +449,7 @@ libraries, like OpenSSL.")
 (define-public ghc-x509-store
   (package
     (name "ghc-x509-store")
-    (version "1.6.1")
+    (version "1.6.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -457,7 +457,7 @@ libraries, like OpenSSL.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "01abx528i9f7djq2772xyna8x2mykrnwqkcfrapcx7z3bhprvml3"))))
+                "0yw09nwkvr324qz4sc27c0p28bz2h6gns6lkaz9mz92mgqf2dza9"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-mtl" ,ghc-mtl)
@@ -476,7 +476,7 @@ collections, certificates, revocation lists, and exception lists.")
 (define-public ghc-x509-validation
   (package
     (name "ghc-x509-validation")
-    (version "1.6.3")
+    (version "1.6.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -484,7 +484,7 @@ collections, certificates, revocation lists, and exception lists.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1qr1v561hdlhjgqjv9pj9mbk0q1xf2mr1j67ghy93nlxxyzd7dw0"))))
+                "190w1sr3w6w49v3yvqz4grb0v09ym4gll3n8bxwijvbvcybk3xyi"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-memory" ,ghc-memory)
@@ -508,7 +508,7 @@ list validation.")
 (define-public ghc-x509-system
   (package
     (name "ghc-x509-system")
-    (version "1.6.1")
+    (version "1.6.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -516,7 +516,7 @@ list validation.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "10qf60d2f9jqwnbrhsb2cwpi86xg66m6dxndlxw967v1cdb3h6gf"))))
+                "0k7zc0xp7r6kqmi39rpiicvq78xb0pr2cq6q5s3kmmsshllg13nr"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-mtl" ,ghc-mtl)

gnu/packages/haskell-web.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 rsiddharth <s@ricketyspace.net>
@@ -36,7 +36,7 @@
 (define-public ghc-tagsoup
   (package
     (name "ghc-tagsoup")
-    (version "0.14")
+    (version "0.14.3")
     (source
      (origin
        (method url-fetch)
@@ -46,11 +46,12 @@
              ".tar.gz"))
        (sha256
         (base32
-         "07pax7i0bl79dmqqz58zy09yrgpnyyr2ya0z183hv96kp65jv0lh"))))
+         "00j2rm2sx0syn16kg2402fz4k8yqfl9knmi367jsiycds1q9zzf9"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-text" ,ghc-text)))
-    (home-page
+    (native-inputs
-     "http://community.haskell.org/~ndm/tagsoup/")
+     `(("ghc-quickcheck" ,ghc-quickcheck)))
+    (home-page "http://community.haskell.org/~ndm/tagsoup/")
     (synopsis
      "Parsing and extracting information from (possibly malformed) HTML/XML
 documents")
@@ -126,7 +127,7 @@ both client and server code).")
 (define-public ghc-http
   (package
     (name "ghc-http")
-    (version "4000.2.20")
+    (version "4000.3.3")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -137,7 +138,7 @@ both client and server code).")
              ".tar.gz"))
        (sha256
         (base32
-         "0nyqdxr5ls2dxkf4a1f3x15xzwdm46ppn99nkcbhswlr6s3cq1s4"))))
+         "1wlvvqcxsnd2is3khsla0vd8i9cy12v1pg6d6i13ihcd131a7bdv"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)))
@@ -391,7 +392,7 @@ communication between web applications and web servers.")
 (define-public ghc-wai-logger
   (package
     (name "ghc-wai-logger")
-    (version "2.2.4.1")
+    (version "2.3.0")
     (source
      (origin
        (method url-fetch)
@@ -401,7 +402,7 @@ communication between web applications and web servers.")
              ".tar.gz"))
        (sha256
         (base32
-         "1s6svvy3ci4j1dj1jaw8hg628miwj8f5gpy9n8d8hpsaxav6nzgk"))))
+         "1w0b0vinsyqr37wciljkz8g5dcmfi2r210lq194a0wkycly9kkch"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: Tests cannot find libraries exported
                                ; by propagated-inputs.
@@ -424,7 +425,7 @@ communication between web applications and web servers.")
 (define-public ghc-wai-extra
   (package
     (name "ghc-wai-extra")
-    (version "3.0.13.1")
+    (version "3.0.18")
     (source
      (origin
        (method url-fetch)
@@ -434,7 +435,7 @@ communication between web applications and web servers.")
              ".tar.gz"))
        (sha256
         (base32
-         "0mh761a1bayr4ydwqmh3h8ndpi19zqw34mmy49lp2abr70r0nm1p"))))
+         "0r079mqqdv14fp97w0rigdpwk6b88grpjlqsjc5y8bbc0skf5za2"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-ansi-terminal" ,ghc-ansi-terminal)
@@ -578,17 +579,16 @@ a WAI handler, via the native Haskell TLS implementation.")
 (define-public ghc-xss-sanitize
   (package
     (name "ghc-xss-sanitize")
-    (version "0.3.5.6")
+    (version "0.3.5.7")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://hackage.haskell.org/package/xss-sanitize/xss-sanitize-"
-             version
+             version ".tar.gz"))
-             ".tar.gz"))
        (sha256
         (base32
-         "1j2qrn2dbfx01m7zyk9ilgnp9zjwq9mk62b0rdal4zkg4vh212h0"))))
+         "005cmhaw9xbzkcn42jmhvcvk63bzmg4lml368xwmqdvh7r0mcn4m"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-tagsoup" ,ghc-tagsoup)
@@ -610,7 +610,7 @@ attacks.")
 (define-public ghc-css-text
   (package
     (name "ghc-css-text")
-    (version "0.1.2.1")
+    (version "0.1.3.0")
     (source
      (origin
        (method url-fetch)
@@ -620,7 +620,7 @@ attacks.")
              ".tar.gz"))
        (sha256
         (base32
-         "1xi1n2f0g8y43p95lynhcg50wxbq7hqfzbfzm7fy8mn7gvd920nw"))))
+         "0ynd9f4hn2sfwqzbsa0y7phmxq8za7jiblpjwx0ry8b372zhgxaz"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-text" ,ghc-text)
@@ -636,7 +636,7 @@ Haskell.")
 (define-public ghc-mime-types
   (package
     (name "ghc-mime-types")
-    (version "0.1.0.6")
+    (version "0.1.0.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -644,7 +644,7 @@ Haskell.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "090z3dp928243amnc6s8g10rk2h2bprk9y138q6wj3cpflzr72pw"))))
+                "1fg9cqpp5lswk8ajlq4f41n12c2v2naz179l8dsz6zisjqj4l5l3"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-text" ,ghc-text)))
@@ -702,23 +702,29 @@ Strict, Transitional and Frameset variants.")
 (define-public ghc-blaze-html
   (package
     (name "ghc-blaze-html")
-    (version "0.8.1.1")
+    (version "0.9.0.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
+       (uri (string-append "https://hackage.haskell.org/package/"
-             "https://hackage.haskell.org/package/blaze-html/blaze-html-"
+                           "blaze-html/blaze-html-"
-             version
+                           version ".tar.gz"))
-             ".tar.gz"))
        (sha256
         (base32
-         "1dnw50kh0s405cg9i2y4a8awanhj3bqzk21jwgfza65kcjby7lpq"))))
+         "0r0acv47nh75bmf7kjyfvhcwz8f02rn9x0a1l80pzgyczfrsmkmf"))))
     (build-system haskell-build-system)
-    (arguments `(#:tests? #f)) ; FIXME: testing libraries are missing.
+    (arguments
+     `(#:configure-flags (list "--allow-newer=QuickCheck")))
     (inputs
      `(("ghc-blaze-builder" ,ghc-blaze-builder)
        ("ghc-text" ,ghc-text)
        ("ghc-blaze-markup" ,ghc-blaze-markup)))
+    (native-inputs
+     `(("ghc-hunit" ,ghc-hunit)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
     (home-page "http://jaspervdj.be/blaze")
     (synopsis "Fast HTML combinator library")
     (description "This library provides HTML combinators for Haskell.")
@@ -727,7 +733,7 @@ Strict, Transitional and Frameset variants.")
 (define-public ghc-aeson
   (package
     (name "ghc-aeson")
-    (version "0.10.0.0")
+    (version "1.2.4.0")
     (source
      (origin
        (method url-fetch)
@@ -737,21 +743,33 @@ Strict, Transitional and Frameset variants.")
              ".tar.gz"))
        (sha256
         (base32
-         "19kp33rfivr4d3myyr8xn803wd7p8x5nc4wb3qvlgjwgyqjaxvrz"))))
+         "16zwpd07cmhs58wwsqbhxy3b58gqw8w5nr7nf6lwi4nvznjdn09l"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: testing libraries are missing.
     (inputs
      `(("ghc-attoparsec" ,ghc-attoparsec)
+       ("ghc-base-compat" ,ghc-base-compat)
        ("ghc-dlist" ,ghc-dlist)
-       ("ghc-mtl" ,ghc-mtl)
-       ("ghc-scientific" ,ghc-scientific)
-       ("ghc-syb" ,ghc-syb)
-       ("ghc-unordered-containers" ,ghc-unordered-containers)
-       ("ghc-vector" ,ghc-vector)
        ("ghc-hashable" ,ghc-hashable)
+       ("ghc-scientific" ,ghc-scientific)
+       ("ghc-tagged" ,ghc-tagged)
        ("ghc-text" ,ghc-text)
+       ("ghc-th-abstraction" ,ghc-th-abstraction)
+       ("ghc-time-locale-compat" ,ghc-time-locale-compat)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-uuid-types" ,ghc-uuid-types)
+       ("ghc-vector" ,ghc-vector)
        ("ghc-hunit" ,ghc-hunit)
-       ("ghc-quickcheck" ,ghc-quickcheck)))
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-integer-logarithms" ,ghc-integer-logarithms)
+       ("ghc-base-orphans" ,ghc-base-orphans)
+       ("ghc-base16-bytestring" ,ghc-base16-bytestring)
+       ("ghc-generic-deriving" ,ghc-generic-deriving)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
+       ("ghc-quickcheck-instances" ,ghc-quickcheck-instances)
+       ("ghc-hashable-time" ,ghc-hashable-time)))
     (home-page "https://github.com/bos/aeson")
     (synopsis "Fast JSON parsing and encoding")
     (description "This package provides a JSON parsing and encoding library
@@ -762,7 +780,7 @@ naming: in Greek mythology, Aeson was the father of Jason.)")
 (define-public ghc-aeson-pretty
   (package
     (name "ghc-aeson-pretty")
-    (version "0.7.2")
+    (version "0.8.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -770,14 +788,15 @@ naming: in Greek mythology, Aeson was the father of Jason.)")
                     version ".tar.gz"))
               (sha256
                (base32
-                "03ap81853qi8yd9kdgczllrrni23a6glsfxrwj8zab6ipjrbh234"))))
+                "1yd98972srlbkn0f2jhrb3f443j9wnq2fnw5gbxjxzmkcinfh5yx"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-aeson" ,ghc-aeson)
+       ("ghc-base-compat" ,ghc-base-compat)
+       ("ghc-scientific" ,ghc-scientific)
        ("ghc-vector" ,ghc-vector)
        ("ghc-text" ,ghc-text)
-       ("ghc-unordered-containers"
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
-        ,ghc-unordered-containers)
        ("ghc-attoparsec" ,ghc-attoparsec)
        ("ghc-cmdargs" ,ghc-cmdargs)))
     (home-page "https://github.com/informatikr/aeson-pretty")

gnu/packages/kde-frameworks.scm

@@ -766,6 +766,57 @@ but also for getting notified upon idle time events, such as custom timeouts,
 or user activity.")
     (license (list license:gpl2+ license:lgpl2.1+))))
 
+(define-public kirigami
+  ;; Kirigami is listed as tier 1 framework, but optionally includes
+  ;; plasma-framework which is tier 3.
+  (package
+    (name "kirigami")
+    (version "5.39.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://kde/stable/frameworks/"
+                    (version-major+minor version) "/"
+                    "kirigami2-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0spgylk4yjy74rs5d5b28qv72qz5ra9j3wfmk6vx2b6cvf1fw517"))))
+    (properties `((upstream-name . "kirigami2")))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("qttools" ,qttools)))
+    (inputs
+     `(("kwindowsystem" ,kwindowsystem)
+       ;; TODO: Find a way to activate this optional include without
+       ;; introducing a recursive dependency.
+       ;;("plasma-frameworks" ,plasma-framework) ;; Tier 3!
+       ("qtbase" ,qtbase)
+       ("qtdeclarative" ,qtdeclarative)
+       ("qtquickcontrols2" ,qtquickcontrols2)
+       ("qtsvg" ,qtsvg)
+       ;; Run-time dependency
+       ("qtgraphicaleffects" ,qtgraphicaleffects)))
+    (arguments
+     `(#:tests? #f ;; FIXME: Test suite is broken,
+       ;; see https://bugs.kde.org/show_bug.cgi?id=386456
+       ;; Note for when enabling the tests: The test-suite is meant to be run
+       ;; without prior installation, see
+       ;; https://cgit.kde.org/kirigami.git/commit/?id=24ad2c9
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'check-setup
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; make Qt render "offscreen", required for tests
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t)))))
+    (home-page "https://community.kde.org/Frameworks")
+    (synopsis "QtQuick components for mobile user interfaces")
+    (description "Kirigami is a set of high level QtQuick components looking
+and feeling well on both mobile and desktop devices.  They ease the creation
+of applications that follow the Kirigami Human Interface Guidelines.")
+    (license license:lgpl2.1+)))
+
 (define-public kitemmodels
   (package
     (name "kitemmodels")

gnu/packages/libcanberra.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Fabian Harfert <fhmgufs@web.de>
-;;; Copyright © 2017 ng0 <ng0@infotropique.org>
+;;; Copyright © 2017, 2018 ng0 <ng0@crash.cx>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -139,7 +139,7 @@ sounds for various system events.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://d.n0.is/releases/pycanberra/"
+       (uri (string-append "https://files.crash.cx/releases/"
                            "pycanberra-" version ".tar.xz"))
        (sha256
         (base32
@@ -152,5 +152,5 @@ sounds for various system events.")
     (synopsis "Ctypes wrapper for the libcanberra API")
     (description
      "Pycanberra is a basic Python wrapper for libcanberra.")
-    (home-page "https://c.n0.is/pycanberra/")
+    (home-page "https://code.crash.cx/pycanberra/log.html")
     (license lgpl2.1+)))

gnu/packages/libreoffice.scm

@@ -7,7 +7,7 @@
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -54,6 +54,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gperf)
+  #:use-module (gnu packages gnupg)
   #:use-module (gnu packages gnuzilla)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages gtk)
@@ -839,22 +840,10 @@ and to return information on pronunciations, meanings and synonyms.")
     (license (non-copyleft "file://COPYING"
                            "See COPYING in the distribution."))))
 
-;; LibreOffice requires an xmlsec source tarball; it does not even check
-;; for the presence of an externally compiled library.
-(define xmlsec-src-libreoffice
-  (origin
-    (method url-fetch)
-    (uri
-      (string-append
-       "http://dev-www.libreoffice.org/src/"
-       "86b1daaa438f5a7bea9a52d7b9799ac0-xmlsec1-1.2.23.tar.gz"))
-    (sha256 (base32
-             "17qfw5crkqn4v6xbkjxrjvcccfc00dy053892wrwv54qdk8n7m21"))))
-
 (define-public libreoffice
   (package
     (name "libreoffice")
-    (version "5.3.7.2")
+    (version "5.4.5.1")
     (source
      (origin
       (method url-fetch)
@@ -863,16 +852,11 @@ and to return information on pronunciations, meanings and synonyms.")
           "https://download.documentfoundation.org/libreoffice/src/"
           (version-prefix version 3) "/libreoffice-" version ".tar.xz"))
       (sha256 (base32
-               "0z7fssp0jcj09wxad1wmhy69n71a2mwl933lxp9dz5sdvzncxmy3"))))
+               "167bh6jgyhfcvn3g7xghkg4nb99h91diypdlry5df21xs8bis5gb"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(;; autoreconf is run by the LibreOffice build system, since after
+     `(("bison" ,bison)
-       ;; unpacking the external xmlsec tarball, it applies a series of
+       ("cppunit" ,cppunit-1.14)
-       ;; patches to Makefile.am, configure.in, config.guess and config.sub.
-       ("autoconf" ,autoconf)
-       ("automake" ,automake)
-       ("bison" ,bison)
-       ("cppunit" ,cppunit)
        ("flex" ,flex)
        ("pkg-config" ,pkg-config)
        ("python" ,python-wrapper)
@@ -888,6 +872,7 @@ and to return information on pronunciations, meanings and synonyms.")
        ("glew" ,glew)
        ("glm" ,glm)
        ("gperf" ,gperf)
+       ("gpgme" ,gpgme)
        ("graphite2" ,graphite2)
        ("gst-plugins-base" ,gst-plugins-base)
        ("gtk+" ,gtk+)
@@ -897,12 +882,14 @@ and to return information on pronunciations, meanings and synonyms.")
        ("libabw" ,libabw)
        ("libcdr" ,libcdr)
        ("libcmis" ,libcmis)
-       ("libjpeg" ,libjpeg)
+       ("libjpeg-turbo" ,libjpeg-turbo)
        ("libe-book" ,libe-book)
        ("libetonyek" ,libetonyek)
        ("libexttextcat" ,libexttextcat)
        ("libfreehand" ,libfreehand)
        ("liblangtag" ,liblangtag)
+       ;; XXX: Perhaps this should be propagated from xmlsec.
+       ("libltdl" ,libltdl)
        ("libmspub" ,libmspub)
        ("libmwaw" ,libmwaw)
        ("libodfgen" ,libodfgen)
@@ -935,7 +922,7 @@ and to return information on pronunciations, meanings and synonyms.")
        ("unixodbc" ,unixodbc)
        ("unzip" ,unzip)
        ("vigra" ,vigra)
-       ("xmlsec-src" ,xmlsec-src-libreoffice)
+       ("xmlsec" ,xmlsec-nss)
        ("zip" ,zip)))
     (arguments
      `(#:tests? #f ; Building the tests already fails.
@@ -944,7 +931,7 @@ and to return information on pronunciations, meanings and synonyms.")
          (modify-phases %standard-phases
            (add-before 'configure 'prepare-src
              (lambda* (#:key inputs #:allow-other-keys)
-               (let ((xmlsec (assoc-ref inputs "xmlsec-src")))
+               (let ((gpgme (assoc-ref inputs "gpgme")))
                  (substitute*
                    "sdext/source/pdfimport/xpdfwrapper/pdfioutdev_gpl.cxx"
                    ;; This header was renamed in Poppler 0.62.0.
@@ -956,20 +943,21 @@ and to return information on pronunciations, meanings and synonyms.")
                          "solenv/gbuild/gbuild.mk"
                          "solenv/gbuild/platform/unxgcc.mk")
                    (("/bin/sh") (which "sh")))
-                 (mkdir "external/tarballs")
+
-                 (symlink
+                 ;; GPGME++ headers are installed in a gpgme++ subdirectory,
-                   xmlsec
+                 ;; but files in "xmlsecurity/source/gpg/" expect to find them
-                   (string-append "external/tarballs/"
+                 ;; on the include path without a prefix.
-                                  "86b1daaa438f5a7bea9a52d7b9799ac0-"
+                 (substitute* "xmlsecurity/Library_xsec_xmlsec.mk"
-                                  "xmlsec1-1.2.23.tar.gz"))
+                   (("\\$\\$\\(INCLUDE\\)")
-                 ;; The following is required for building xmlsec from the
+                    (string-append "$$(INCLUDE) -I" gpgme "/include/gpgme++")))
-                 ;; unpatched external tarball; since "configure" starts with
+
-                 ;; "/bin/sh", it needs to be executed by a command invoking
+                 ;; XXX: When GTK2 is disabled, one header file is not included.
-                 ;; the shell.
+                 ;; This is likely fixed in later versions.  See also
-                 (setenv "SHELL" (which "bash"))
+                 ;; <https://bugs.gentoo.org/641812>.
-                 (setenv "CONFIG_SHELL" (which "bash"))
+                 (substitute* "vcl/unx/gtk3/gtk3gtkframe.cxx"
-                 (substitute* "external/libxmlsec/ExternalProject_xmlsec.mk"
+                   (("#include <unx/gtk/gtkgdi.hxx>")
-                   (("./configure") "$(CONFIG_SHELL) ./configure" ))
+                    "#include <unx/gtk/gtkgdi.hxx>\n#include <unx/gtk/gtksalmenu.hxx>"))
+
                  #t)))
            (add-after 'install 'bin-and-desktop-install
              ;; Create 'soffice' and 'libreoffice' symlinks to the executable
@@ -1043,6 +1031,10 @@ and to return information on pronunciations, meanings and synonyms.")
           "--disable-coinmp"
           "--disable-firebird-sdbc" ; embedded firebird
           "--disable-gltf"
+          ;; XXX: PDFium support requires fetching an external tarball and
+          ;; patching the build scripts to work with GCC5.  Try enabling this
+          ;; when our default compiler is >=GCC 6.
+          "--disable-pdfium"
           "--disable-gtk" ; disable use of GTK+ 2
           "--without-doxygen")))
     (home-page "https://www.libreoffice.org/")

gnu/packages/libusb.scm

@@ -287,14 +287,14 @@ proposed for standardization.")
 (define-public gmtp
   (package
     (name "gmtp")
-    (version "1.3.10")
+    (version "1.3.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/gmtp/gMTP-" version
                                   "/gmtp-" version ".tar.gz"))
               (sha256
                (base32
-                "0fyi3pdl2g57vr0p46ip2wwzyap3l0by7iqaqygv0yxfcs79l6xj"))))
+                "04q6byyq002fhzkc2rkkahwh5b6272xakaj4m3vwm8la8jf0r0ss"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      '(#:configure-flags

gnu/packages/linux.scm

@@ -24,7 +24,7 @@
 ;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
-;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 nee <nee-git@hidamari.blue>
 ;;; Copyright © 2017 Dave Love <fx@gnu.org>
 ;;;
@@ -382,8 +382,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.15.2")
+(define %linux-libre-version "4.15.3")
-(define %linux-libre-hash "0rzncbk513a8q60z9psb9yz7liadsb7nghj12s1kmwn441z1zv93")
+(define %linux-libre-hash "1svn7v0gdqh7mi1f139g3nhf18g4vr9958x1zh24zww0lyic8l27")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
@@ -391,8 +391,8 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.18")
+(define %linux-libre-4.14-version "4.14.19")
-(define %linux-libre-4.14-hash "1kl6zc9dzi02hzxwmzskxb4cqh5lph4afy94677bj5ribanmizn5")
+(define %linux-libre-4.14-hash "1zns8nxx1j1fxpgqgsm9z0kffn0ji1pcsav1r77gxqllsn49wa8m")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -401,8 +401,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.80"
+  (make-linux-libre "4.9.81"
-                    "094c66sh4h1n46as20n0ip2clp89khsn91ngxwg5p85gf3jqk1h9"
+                    "1x89llah2hklh36rgx7cywacdmvbs9334101qhpycicdi5sv7mnn"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
@@ -3065,7 +3065,7 @@ is flexible, efficient and uses a modular implementation.")
 (define-public fuse-exfat
   (package
     (name "fuse-exfat")
-    (version "1.2.7")
+    (version "1.2.8")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3073,7 +3073,7 @@ is flexible, efficient and uses a modular implementation.")
                     version "/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0df0ccnd0dgwc6rvk9qmrz0nfb8whc5s3wg9qnw1mzbrh4rcvhw2"))))
+                "1jwnxw0bg9v5ij8xvbg4xpjr50nykq8a1lmc2xkblz204rq7wd8z"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

gnu/packages/maths.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
@@ -698,7 +698,9 @@ incompatible with HDF5.")
        #:configure-flags '("--enable-cxx"
                            "--enable-fortran"
                            "--enable-fortran2003")
-
+       ;; Use -fPIC to allow the R bindings to link with the static libraries
+       #:make-flags (list "CFLAGS=-fPIC"
+                          "CXXFLAGS=-fPIC")
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'patch-configure
@@ -1893,12 +1895,12 @@ programming problems.")
 (define-public r-pracma
   (package
     (name "r-pracma")
-    (version "2.1.1")
+    (version "2.1.4")
     (source (origin
       (method url-fetch)
       (uri (cran-uri "pracma" version))
       (sha256
-        (base32 "1mylrrkyycaw9m01mmg6xkn5wgdlabs5l0qyws60r0n2ycblp897"))))
+        (base32 "1ygm81i7mqvh229dp9935djjyb120p3bqvaf4k572sa4q63fzjhc"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-quadprog" ,r-quadprog)))

gnu/packages/patches/mpv-CVE-2018-6360-1.patch

@@ -1,138 +0,0 @@
-Fix CVE-2018-6360:
-
-https://github.com/mpv-player/mpv/issues/5456
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-6360
-https://security-tracker.debian.org/tracker/CVE-2018-6360
-
-Patch copied from upstream source repository:
-
-https://github.com/mpv-player/mpv/commit/e6e6b0dcc7e9b0dbf35154a179b3dc1fcfcaff43
-
-To apply the patch to mpv 0.28.0 release tarball, hunk #4 is removed. Hunk #4
-checks if 'mpd_url' is safe, but the support for 'mpd_url' is not available
-for the 0.28.0 release. So it should be safe to remove hunk #4.
-
-From e6e6b0dcc7e9b0dbf35154a179b3dc1fcfcaff43 Mon Sep 17 00:00:00 2001
-From: Ricardo Constantino <wiiaboo@gmail.com>
-Date: Fri, 26 Jan 2018 01:19:04 +0000
-Subject: [PATCH] ytdl_hook: whitelist protocols from urls retrieved from
- youtube-dl
-
-Not very clean since there's a lot of potential unsafe urls that youtube-dl
-can give us, depending on whether it's a single url, split tracks,
-playlists, segmented dash, etc.
----
- player/lua/ytdl_hook.lua | 54 +++++++++++++++++++++++++++++++++++++++++-------
- 1 file changed, 47 insertions(+), 7 deletions(-)
-
-diff --git a/player/lua/ytdl_hook.lua b/player/lua/ytdl_hook.lua
-index dd96ecc01d..b480c21625 100644
---- a/player/lua/ytdl_hook.lua
-+++ b/player/lua/ytdl_hook.lua
-@@ -16,6 +16,18 @@ local ytdl = {
- 
- local chapter_list = {}
- 
-+function Set (t)
-+    local set = {}
-+    for _, v in pairs(t) do set[v] = true end
-+    return set
-+end
-+
-+local safe_protos = Set {
-+    "http", "https", "ftp", "ftps",
-+    "rtmp", "rtmps", "rtmpe", "rtmpt", "rtmpts", "rtmpte",
-+    "data"
-+}
-+
- local function exec(args)
-     local ret = utils.subprocess({args = args})
-     return ret.status, ret.stdout, ret
-@@ -183,6 +195,9 @@ local function edl_track_joined(fragments, protocol, is_live, base)
- 
-     for i = offset, #fragments do
-         local fragment = fragments[i]
-+        if not url_is_safe(join_url(base, fragment)) then
-+            return nil
-+        end
-         table.insert(parts, edl_escape(join_url(base, fragment)))
-         if fragment.duration then
-             parts[#parts] =
-@@ -208,6 +223,15 @@ local function proto_is_dash(json)
-            or json["protocol"] == "http_dash_segments"
- end
- 
-+local function url_is_safe(url)
-+    local proto = type(url) == "string" and url:match("^(.+)://") or nil
-+    local safe = proto and safe_protos[proto]
-+    if not safe then
-+        msg.error(("Ignoring potentially unsafe url: '%s'"):format(url))
-+    end
-+    return safe
-+end
-+
- local function add_single_video(json)
-     local streamurl = ""
-     local max_bitrate = 0
-@@ -238,14 +264,18 @@ local function add_single_video(json)
-             edl_track = edl_track_joined(track.fragments,
-                 track.protocol, json.is_live,
-                 track.fragment_base_url)
-+            local url = edl_track or track.url
-+            if not url_is_safe(url) then
-+                return
-+            end
-             if track.acodec and track.acodec ~= "none" then
-                 -- audio track
-                 mp.commandv("audio-add",
--                    edl_track or track.url, "auto",
-+                    url, "auto",
-                     track.format_note or "")
-             elseif track.vcodec and track.vcodec ~= "none" then
-                 -- video track
--                streamurl = edl_track or track.url
-+                streamurl = url
-             end
-         end
- 
-@@ -264,7 +294,13 @@ local function add_single_video(json)
- 
-     msg.debug("streamurl: " .. streamurl)
- 
--    mp.set_property("stream-open-filename", streamurl:gsub("^data:", "data://", 1))
-+    streamurl = streamurl:gsub("^data:", "data://", 1)
-+
-+    if not url_is_safe(streamurl) then
-+        return
-+    end
-+
-+    mp.set_property("stream-open-filename", streamurl)
- 
-     mp.set_property("file-local-options/force-media-title", json.title)
- 
-@@ -526,14 +562,18 @@ mp.add_hook(o.try_ytdl_first and "on_load" or "on_load_fail", 10, function ()
-                         site = entry["webpage_url"]
-                     end
- 
--                    if not (site:find("https?://") == 1) then
--                        site = "ytdl://" .. site
-+                    -- links with only youtube id as returned by --flat-playlist
-+                    if not site:find("://") then
-+                        table.insert(playlist, "ytdl://" .. site)
-+                    elseif url_is_safe(site) then
-+                        table.insert(playlist, site)
-                     end
--                    table.insert(playlist, site)
- 
-                 end
- 
--                mp.set_property("stream-open-filename", "memory://" .. table.concat(playlist, "\n"))
-+                if #playlist > 0 then
-+                    mp.set_property("stream-open-filename", "memory://" .. table.concat(playlist, "\n"))
-+                end
-             end
- 
-         else -- probably a video
--- 
-2.16.1
-

gnu/packages/patches/mpv-CVE-2018-6360-2.patch

@@ -1,59 +0,0 @@
-Fix CVE-2018-6360:
-
-https://github.com/mpv-player/mpv/issues/5456
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-6360
-https://security-tracker.debian.org/tracker/CVE-2018-6360
-
-Patch copied from upstream source repository:
-
-https://github.com/mpv-player/mpv/commit/f8263e82cc74a9ac6530508bec39c7b0dc02568f
-
-From f8263e82cc74a9ac6530508bec39c7b0dc02568f Mon Sep 17 00:00:00 2001
-From: Ricardo Constantino <wiiaboo@gmail.com>
-Date: Fri, 26 Jan 2018 11:26:27 +0000
-Subject: [PATCH] ytdl_hook: move url_is_safe earlier in code
-
-lua isn't javascript.
----
- player/lua/ytdl_hook.lua | 18 +++++++++---------
- 1 file changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/player/lua/ytdl_hook.lua b/player/lua/ytdl_hook.lua
-index b480c21625..458c94af38 100644
---- a/player/lua/ytdl_hook.lua
-+++ b/player/lua/ytdl_hook.lua
-@@ -84,6 +84,15 @@ local function edl_escape(url)
-     return "%" .. string.len(url) .. "%" .. url
- end
- 
-+local function url_is_safe(url)
-+    local proto = type(url) == "string" and url:match("^(.+)://") or nil
-+    local safe = proto and safe_protos[proto]
-+    if not safe then
-+        msg.error(("Ignoring potentially unsafe url: '%s'"):format(url))
-+    end
-+    return safe
-+end
-+
- local function time_to_secs(time_string)
-     local ret
- 
-@@ -223,15 +232,6 @@ local function proto_is_dash(json)
-            or json["protocol"] == "http_dash_segments"
- end
- 
--local function url_is_safe(url)
--    local proto = type(url) == "string" and url:match("^(.+)://") or nil
--    local safe = proto and safe_protos[proto]
--    if not safe then
--        msg.error(("Ignoring potentially unsafe url: '%s'"):format(url))
--    end
--    return safe
--end
--
- local function add_single_video(json)
-     local streamurl = ""
-     local max_bitrate = 0
--- 
-2.16.1
-

gnu/packages/patches/mpv-CVE-2018-6360-3.patch

@@ -1,84 +0,0 @@
-Fix CVE-2018-6360:
-
-https://github.com/mpv-player/mpv/issues/5456
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-6360
-https://security-tracker.debian.org/tracker/CVE-2018-6360
-
-Patch copied from upstream source repository:
-
-https://github.com/mpv-player/mpv/commit/ce42a965330dfeb7d2f6c69ea42d35454105c828
-
-From ce42a965330dfeb7d2f6c69ea42d35454105c828 Mon Sep 17 00:00:00 2001
-From: Ricardo Constantino <wiiaboo@gmail.com>
-Date: Fri, 26 Jan 2018 18:54:17 +0000
-Subject: [PATCH] ytdl_hook: fix safe url checking with EDL urls
-
----
- player/lua/ytdl_hook.lua | 22 +++++++++++-----------
- 1 file changed, 11 insertions(+), 11 deletions(-)
-
-diff --git a/player/lua/ytdl_hook.lua b/player/lua/ytdl_hook.lua
-index 458c94af38..6c8e78657d 100644
---- a/player/lua/ytdl_hook.lua
-+++ b/player/lua/ytdl_hook.lua
-@@ -264,18 +264,17 @@ local function add_single_video(json)
-             edl_track = edl_track_joined(track.fragments,
-                 track.protocol, json.is_live,
-                 track.fragment_base_url)
--            local url = edl_track or track.url
--            if not url_is_safe(url) then
-+            if not edl_track and not url_is_safe(track.url) then
-                 return
-             end
-             if track.acodec and track.acodec ~= "none" then
-                 -- audio track
-                 mp.commandv("audio-add",
--                    url, "auto",
-+                    edl_track or track.url, "auto",
-                     track.format_note or "")
-             elseif track.vcodec and track.vcodec ~= "none" then
-                 -- video track
--                streamurl = url
-+                streamurl = edl_track or track.url
-             end
-         end
- 
-@@ -284,6 +283,9 @@ local function add_single_video(json)
-         edl_track = edl_track_joined(json.fragments, json.protocol,
-             json.is_live, json.fragment_base_url)
- 
-+        if not edl_track and not url_is_safe(json.url) then
-+            return
-+        end
-         -- normal video or single track
-         streamurl = edl_track or json.url
-         set_http_headers(json.http_headers)
-@@ -294,13 +296,7 @@ local function add_single_video(json)
- 
-     msg.debug("streamurl: " .. streamurl)
- 
--    streamurl = streamurl:gsub("^data:", "data://", 1)
--
--    if not url_is_safe(streamurl) then
--        return
--    end
--
--    mp.set_property("stream-open-filename", streamurl)
-+    mp.set_property("stream-open-filename", streamurl:gsub("^data:", "data://", 1))
- 
-     mp.set_property("file-local-options/force-media-title", json.title)
- 
-@@ -499,6 +495,10 @@ mp.add_hook(o.try_ytdl_first and "on_load" or "on_load_fail", 10, function ()
- 
-                 msg.debug("EDL: " .. playlist)
- 
-+                if not playlist then
-+                    return
-+                end
-+
-                 -- can't change the http headers for each entry, so use the 1st
-                 if json.entries[1] then
-                     set_http_headers(json.entries[1].http_headers)
--- 
-2.16.1
-

gnu/packages/statistics.scm

@@ -318,14 +318,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-47")
+    (version "7.3-48")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "1gy6z7ly9wn86rfn9xrmqiqq1ijw3pkasrr2299kbzsgx2mwsi7d"))))
+         "02q95ba909p2gxnzfp295ipxjnv14f7bm55nicxwn2kj8hizpzqd"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
@@ -511,14 +511,14 @@ nonlinear mixed-effects models.")
 (define-public r-mgcv
   (package
    (name "r-mgcv")
-   (version "1.8-22")
+   (version "1.8-23")
    (source
     (origin
      (method url-fetch)
      (uri (cran-uri "mgcv" version))
      (sha256
       (base32
-       "1546p6aflg3z6xl2mns1n2c3j8q2spr9cjggj9rn33vrrhsv4fss"))))
+       "1lsrhf1yzn25pfn3f5x8yxjqnfryim4jx3iqd7ah8aalh5asqwbp"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-matrix" ,r-matrix)
@@ -554,14 +554,14 @@ single hidden layer, and for multinomial log-linear models.")
 (define-public r-rpart
   (package
     (name "r-rpart")
-    (version "4.1-11")
+    (version "4.1-12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rpart" version))
        (sha256
         (base32
-         "165djqj7lk81jr7z5fwccq3h7ayys26hx1kj9hndvg2rkyaq1arq"))))
+         "177p03w4m0qshb3sqkdyixim3f44g2an31v3vlbjmpzjvd5ff6yq"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/rpart")
     (synopsis "Recursive partitioning and regression trees")
@@ -704,13 +704,13 @@ effects of different types of color-blindness.")
 (define-public r-digest
   (package
     (name "r-digest")
-    (version "0.6.13")
+    (version "0.6.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "digest" version))
        (sha256
-        (base32 "1bsgl07bvf4nk6bn7n3l2ilvk4qvn3nk7yxp22miil7x405xdks6"))))
+        (base32 "1ia4ak956gnn0f5aqhwgam6g9z6f1y57zz8jv45jc8h79yxp8bl8"))))
     (build-system r-build-system)
     ;; Vignettes require r-knitr, which requires r-digest, so we have to
     ;; disable them and the tests.
@@ -734,13 +734,13 @@ OpenSSL should be used.")
 (define-public r-estimability
   (package
     (name "r-estimability")
-    (version "1.2")
+    (version "1.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "estimability" version))
               (sha256
                (base32
-                "13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h"))))
+                "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/estimability")
     (synopsis "Tools for assessing estimability of linear predictions")
@@ -1347,17 +1347,16 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
 (define-public r-knitr
   (package
     (name "r-knitr")
-    (version "1.17")
+    (version "1.19")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "knitr" version))
               (sha256
                (base32
-                "00gljbz57n9lkvbd6az4n37gpbs8vg3fxx5p9biamhmhqyra514l"))))
+                "1gyj9bw90h4h9rc9k1iqrnzirm2f8mj45zi8bkjc6rp610vlh63j"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-evaluate" ,r-evaluate)
-       ("r-digest" ,r-digest)
        ("r-highr" ,r-highr)
        ("r-markdown" ,r-markdown)
        ("r-stringr" ,r-stringr)
@@ -1398,16 +1397,14 @@ from knitr Rmarkdown.")
 (define-public r-microbenchmark
   (package
     (name "r-microbenchmark")
-    (version "1.4-2.1")
+    (version "1.4-4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "microbenchmark" version))
               (sha256
                (base32
-                "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
+                "0fv2w2vsiz18imf4115nd9chhmf275w2mb49pn7pkxi6z3bamc9c"))))
     (build-system r-build-system)
-    (propagated-inputs
-     `(("r-ggplot2" ,r-ggplot2)))
     (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
     (synopsis "Accurate timing functions for R")
     (description
@@ -1552,13 +1549,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
     (name "r-rlang")
-    (version "0.1.4")
+    (version "0.1.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rlang" version))
               (sha256
                (base32
-                "1x5rwwsx7xrlyspy41yl5nhyvfgzl73195nsdb4rc6z85ab6r6wd"))))
+                "1x62assn8m7cd0q75r809gxsdqmxmd2br1xz53ykzhrfz3j768kp"))))
     (build-system r-build-system)
     (home-page "http://rlang.tidyverse.org")
     (synopsis "Functions for base types, core R and Tidyverse features")
@@ -1570,18 +1567,20 @@ like tidy evaluation.")
 (define-public r-tibble
   (package
     (name "r-tibble")
-    (version "1.3.4")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tibble" version))
        (sha256
         (base32
-         "02vn6yqzcvmazy5jaqar3wwbrmh83a1bfgsqgk0hgz38i80zgvm7"))))
+         "05svbjkm1xqv56ybjgsqqg2pp8nn6hams1yxcr8aanbhzx9h6rqi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rlang" ,r-rlang)
-       ("r-rcpp" ,r-rcpp)))
+       ("r-cli" ,r-cli)
+       ("r-crayon" ,r-crayon)
+       ("r-pillar" ,r-pillar)))
     (home-page "https://github.com/hadley/tibble")
     (synopsis "Simple data frames")
     (description
@@ -1628,14 +1627,14 @@ database.")
 (define-public r-dbplyr
   (package
     (name "r-dbplyr")
-    (version "1.1.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbplyr" version))
        (sha256
         (base32
-         "17gn8vr4a6m9ynarjbm9xsrhcvgn5lnxhb2qhiiglmhh5mm4a7kv"))))
+         "17br61mhssi2pm6v8604f89ykglng3qp9ymfzmhw10cary6zm982"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -1645,7 +1644,8 @@ database.")
        ("r-purrr" ,r-purrr)
        ("r-r6" ,r-r6)
        ("r-rlang" ,r-rlang)
-       ("r-tibble" ,r-tibble)))
+       ("r-tibble" ,r-tibble)
+       ("r-tidyselect" ,r-tidyselect)))
     (home-page "https://github.com/tidyverse/dbplyr")
     (synopsis "Dplyr back end for databases")
     (description
@@ -1722,13 +1722,13 @@ and density estimation.")
 (define-public r-chron
   (package
     (name "r-chron")
-    (version "2.3-51")
+    (version "2.3-52")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "chron" version))
               (sha256
                (base32
-                "05aznigw9nwv3hbwjnjbvqhfjqkwsw2csgrjx8500gzr2fvla5w8"))))
+                "185lfp75cv3l4cavg64sccj8lgc5sivch13n6gkannv3pd5cyzy4"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/chron")
     (synopsis "Chronological R objects which can handle dates and times")
@@ -1923,20 +1923,22 @@ and environmental data in the framework of Euclidean exploratory methods.")
 (define-public r-xml2
   (package
     (name "r-xml2")
-    (version "1.1.1")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xml2" version))
        (sha256
         (base32
-         "05iifrcgzx53w5ciw8bbm4vdwc3giv4xsvazv8chqxkndfvf7wq0"))))
+         "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
     (build-system r-build-system)
     (inputs
-     `(("libxml2" ,libxml2)))
+     `(("libxml2" ,libxml2)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (propagated-inputs
-     `(("r-rcpp" ,r-rcpp)
+     `(("r-rcpp" ,r-rcpp)))
-       ("r-bh" ,r-bh)))
     (home-page "https://github.com/hadley/xml2")
     (synopsis "Parse XML with R")
     (description
@@ -2229,14 +2231,14 @@ collation, and NAMESPACE files.")
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "0.9.9")
+    (version "1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "1ir7ggs0rxgn83h40r6jg9dzhb7hbcwhkcj5nsdzj7jz61sfgv77"))))
+         "1j8smqrb79lnaf2n9icksjiy641fcazsbkhmgg916s3nnyjngjz3"))))
     (build-system r-build-system)
     (inputs
      `(("libressl" ,libressl)))
@@ -2284,13 +2286,13 @@ functions make it easy to control additional request components.")
 (define-public r-git2r
   (package
     (name "r-git2r")
-    (version "0.20.0")
+    (version "0.21.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "git2r" version))
               (sha256
                (base32
-                "1pqggijvsalb5cc2pr5gwfj3s713s63f4xii1xrd0qagfgbgz846"))))
+                "11xgddmxzh9cy85k8fb90il43qswpvryz0h9r0j1gbclfg2f9004"))))
     (build-system r-build-system)
     ;; This R package contains modified sources of libgit2.  This modified
     ;; version of libgit2 is built as the package is built.  Hence libgit2 is
@@ -2354,16 +2356,14 @@ tools to simplify the devolpment of R packages.")
 (define-public r-withr
   (package
     (name "r-withr")
-    (version "2.1.0")
+    (version "2.1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "withr" version))
               (sha256
                (base32
-                "12v263fj6l3ds9nrsj6q7h6zhbivp3w2jk7w9dpk1610d3nx9gf8"))))
+                "17pbllxv18gf1mli9mm5px4wzp364907a4wrl20r1y5q8qwawpxx"))))
     (build-system r-build-system)
-    (propagated-inputs
-     `(("r-lattice" ,r-lattice)))
     (home-page "https://github.com/jimhester/withr")
     (synopsis "Run code with temporarily modified global state")
     (description
@@ -2375,14 +2375,14 @@ were originally a part of the r-devtools package.")
 (define-public r-hms
   (package
     (name "r-hms")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hms" version))
        (sha256
         (base32
-         "07sh75flp15lx2b00s3nxh04xr9gk4qhlbh125qx25isf71zw6zl"))))
+         "0vr7k3a7k52a5yf67bwzl88lkjz09v1avw5axdk1y9v3nz33zl2h"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rlang" ,r-rlang)
@@ -2551,14 +2551,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
 (define-public r-rprojroot
   (package
     (name "r-rprojroot")
-    (version "1.3-1")
+    (version "1.3-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rprojroot" version))
        (sha256
         (base32
-         "1jigr2jh3hzy35h94im52yq81lyikw7nfvmbxij84a1b9c32r332"))))
+         "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)))
@@ -3023,18 +3023,19 @@ using the multicore functionality of the parallel package.")
 (define-public r-dt
   (package
     (name "r-dt")
-    (version "0.2")
+    (version "0.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DT" version))
               (sha256
                (base32
-                "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1"))))
+                "06gsqz7p2fv6hc3fm3759gaa50krcfrqrmy7qbxyam6a36w9daix"))))
     (properties
      `((upstream-name . "DT")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-htmltools" ,r-htmltools)
+     `(("r-crosstalk" ,r-crosstalk)
+       ("r-htmltools" ,r-htmltools)
        ("r-htmlwidgets" ,r-htmlwidgets)
        ("r-magrittr" ,r-magrittr)))
     (home-page "http://rstudio.github.io/DT")
@@ -3075,14 +3076,14 @@ flexible than the orphaned \"base64\" package.")
 (define-public r-irlba
   (package
     (name "r-irlba")
-    (version "2.3.1")
+    (version "2.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "irlba" version))
        (sha256
         (base32
-         "1dclzzkm75sbbqda5scj2hlqnw2sksgxbiqagxs4359fwfszi0k0"))))
+         "0f7wb12wa0zbyllk5adcf4f517wgjpkhsx4j176i9ax6xy7jvprz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -3261,19 +3262,20 @@ bigmemory and synchronicity packages.")
 (define-public r-synchronicity
   (package
     (name "r-synchronicity")
-    (version "1.1.9.1")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "synchronicity" version))
        (sha256
         (base32
-         "0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c"))))
+         "1idrjzl7nkamf1ip55s6qcf64s63xs9j8z9jv3r89p6r5lw7k5mv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
        ("r-bigmemory-sri" ,r-bigmemory-sri)
-       ("r-rcpp" ,r-rcpp)))
+       ("r-rcpp" ,r-rcpp)
+       ("r-uuid" ,r-uuid)))
     (home-page "http://www.bigmemory.org")
     (synopsis "Boost mutex functionality in R")
     (description "This package provides support for synchronization
@@ -3285,14 +3287,14 @@ message passing.")
 (define-public r-bigmemory
   (package
     (name "r-bigmemory")
-    (version "4.5.31")
+    (version "4.5.33")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bigmemory" version))
        (sha256
         (base32
-         "0wv0p746zz5a6r1yd0fgpj2kfcyzk2f4rxqz92p6lp9jzakv4lfs"))))
+         "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
@@ -3418,13 +3420,13 @@ developing R packages.")
 (define-public r-r-cache
   (package
     (name "r-r-cache")
-    (version "0.12.0")
+    (version "0.13.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.cache" version))
               (sha256
                (base32
-                "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
+                "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
     (properties `((upstream-name . "R.cache")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3444,17 +3446,18 @@ persistent (on the file system).")
 (define-public r-r-rsp
   (package
     (name "r-r-rsp")
-    (version "0.41.0")
+    (version "0.42.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.rsp" version))
               (sha256
                (base32
-                "01l430avj5ggmdsla2kiriix72g0dlzx9klniq321bs0za808v3c"))))
+                "1zcq0hzi0j7fvj2rs796a1i120wbr0387vck17rrd644awwbsbm0"))))
     (properties `((upstream-name . "R.rsp")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-r-cache" ,r-r-cache)
+     `(("r-digest" ,r-digest)
+       ("r-r-cache" ,r-r-cache)
        ("r-r-methodss3" ,r-r-methodss3)
        ("r-r-oo" ,r-r-oo)
        ("r-r-utils" ,r-r-utils)))
@@ -3475,13 +3478,13 @@ vignettes.")
 (define-public r-mvtnorm
   (package
     (name "r-mvtnorm")
-    (version "1.0-6")
+    (version "1.0-7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mvtnorm" version))
               (sha256
                (base32
-                "0i74s9dl4jf1gln6agra8h38qn9ifd5v0gi13caj1da5nrbmn0aa"))))
+                "0f7hzflygdnbwvzadr3knhybhanwg7agqddclj6mhbvwqpgb0qyh"))))
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))
@@ -3494,13 +3497,13 @@ t-probabilities, quantiles, random deviates and densities.")
 (define-public r-matrixstats
   (package
     (name "r-matrixstats")
-    (version "0.52.2")
+    (version "0.53.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "matrixStats" version))
               (sha256
                (base32
-                "19fjf19cr0p3j9pj17myz39zpi5bh7ci72db3la9my09n6k6mnir"))))
+                "0bkiz5fm09d3512mfr2ymj9qsb1b8aic5l5m6fkaf5j7nsgvqw6z"))))
     (properties `((upstream-name . "matrixStats")))
     (build-system r-build-system)
     (native-inputs
@@ -3518,13 +3521,13 @@ memory usage.")
 (define-public r-viridis
   (package
     (name "r-viridis")
-    (version "0.4.0")
+    (version "0.5.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "viridis" version))
               (sha256
                (base32
-                "03mha2935k1mw7mjjkq7mrx185hl0m3vq3967iiwbknpivbdxllk"))))
+                "1ka6amybgzqkg3cbwfxwwqzzzpfn6q5jcia5am0bw48y5hbpg97y"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -3545,14 +3548,14 @@ most common form of color blindness.")
 (define-public r-viridislite
   (package
     (name "r-viridislite")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "viridisLite" version))
        (sha256
         (base32
-         "1546h44ng4dxs130jkh6lkh990hmp90m1w45sq5p47n546gr0k9d"))))
+         "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
     (properties `((upstream-name . "viridisLite")))
     (build-system r-build-system)
     (home-page "https://github.com/sjmgarnier/viridisLite")
@@ -3596,14 +3599,14 @@ selection.")
 (define-public r-tidyr
   (package
     (name "r-tidyr")
-    (version "0.7.2")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyr" version))
        (sha256
         (base32
-         "1700fry2b3d3ksj7x2f09xl6agjrdnx1rqsc1r8gvzsp5cpflb06"))))
+         "1qjpbj1a2vw6nw4hdb6fgassnrxrdpqwf9a8i6wqnv3wxvjb6zqb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -3629,17 +3632,14 @@ and tidyr provides no margins or aggregation.")
 (define-public r-hexbin
   (package
     (name "r-hexbin")
-    ;; The package tarball was updated in place, resulting in a change in the
+    (version "1.27.2")
-    ;; hash value.  We decided to bump the version to 1.27.1-1 instead of
-    ;; keeping the version at upstream's 1.27.1.
-    (version "1.27.1-1")
     (source
      (origin
        (method url-fetch)
-       (uri (cran-uri "hexbin" "1.27.1"))
+       (uri (cran-uri "hexbin" version))
        (sha256
         (base32
-         "025d609z1nyy684hwvp34b9mjzkgvild7fvfr95f941dmsikan87"))))
+         "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -3877,14 +3877,14 @@ package instead.")
 (define-public r-hmisc
   (package
     (name "r-hmisc")
-    (version "4.0-3")
+    (version "4.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Hmisc" version))
        (sha256
         (base32
-         "1a7i7azag6pldgala85d8hh7wnx1shamyiriy4jfc65nxrr2lq8w"))))
+         "160l50ppjs69ipcaya1mlcz29zbn5rmqg91r09dvzzvkvwfb47cr"))))
     (properties `((upstream-name . "Hmisc")))
     (build-system r-build-system)
     (native-inputs
@@ -4158,13 +4158,13 @@ mechanism.")
 (define-public r-zoo
   (package
     (name "r-zoo")
-    (version "1.8-0")
+    (version "1.8-1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "zoo" version))
               (sha256
                (base32
-                "0mqklbx92ifwa0awm7gpm4r9dvwa09p55zjxjnypiqsxy532r4h9"))))
+                "16nc5jnpkf5j9vgq3pzssv7knj30mi055wj7q3sygz3l0d88hgfr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -4676,14 +4676,14 @@ regression methodology including model selections and multivariate statistics.")
 (define-public r-pcapp
   (package
     (name "r-pcapp")
-    (version "1.9-72")
+    (version "1.9-73")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pcaPP" version))
        (sha256
         (base32
-         "0i2822bv86dpqmk3q17x61nsp3gjjnn4nr8191rwvbiib7xhpgaq"))))
+         "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
     (properties `((upstream-name . "pcaPP")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4802,14 +4802,14 @@ of the points.")
 (define-public r-fpc
   (package
     (name "r-fpc")
-    (version "2.1-10")
+    (version "2.1-11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fpc" version))
        (sha256
         (base32
-         "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
+         "04alsqb5gbhsjg1000d8w52pmpnlwca29r0s12f7n7mdccdv6xar"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)
@@ -4836,14 +4836,14 @@ groupings.")
 (define-public r-vgam
   (package
     (name "r-vgam")
-    (version "1.0-4")
+    (version "1.0-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "VGAM" version))
        (sha256
         (base32
-         "0r59hyp3afmvms890b3v2yyckf8v0qkjf2w11rnqd2zgg1gri0g5"))))
+         "0ik3wyv6jj54bg34z0fzzk4xg0h6x98jqx4q2r7g1f0in0qgbb01"))))
     (properties `((upstream-name . "VGAM")))
     (build-system r-build-system)
     (inputs
@@ -4861,14 +4861,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.")
 (define-public r-pbapply
   (package
     (name "r-pbapply")
-    (version "1.3-3")
+    (version "1.3-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pbapply" version))
        (sha256
         (base32
-         "0iqhymf65jffh00qf056h1p76xf92bfmij6aymlmgnvn24fv4ybk"))))
+         "0lk5kxac09xzdv6vf7ix6r5bfrm7cnpyr2l5mkd4igpciadszzfd"))))
     (build-system r-build-system)
     (home-page "https://github.com/psolymos/pbapply")
     (synopsis "Adding progress bar to apply functions")
@@ -4925,14 +4925,14 @@ based on an interface to Fortran implementations by M. J. D. Powell.")
 (define-public r-rcppeigen
   (package
     (name "r-rcppeigen")
-    (version "0.3.3.3.1")
+    (version "0.3.3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppEigen" version))
        (sha256
         (base32
-         "093g2wmqyk86693l0lzh2va8119w3k7rvw5q24p842jdfv5x5z8l"))))
+         "1m6ssq6lvi36ggf26y4hhq996583pxxdb978jnn1x6r9gdb0q0hi"))))
     (properties `((upstream-name . "RcppEigen")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4994,14 +4994,14 @@ using modular prediction and response module classes.")
 (define-public r-quantreg
   (package
     (name "r-quantreg")
-    (version "5.34")
+    (version "5.35")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantreg" version))
        (sha256
         (base32
-         "0bmgfgnmzqwmwwaraliry682yb8kcr396q3rlzrd2qzaa9sgxxh4"))))
+         "18f3qxv1j1bqmq55hzssz8mnp5ww4flhy80rm2v1rk0mmg9paz7m"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -5048,14 +5048,14 @@ algorithms.")
 (define-public r-lme4
   (package
     (name "r-lme4")
-    (version "1.1-14")
+    (version "1.1-15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lme4" version))
        (sha256
         (base32
-         "1vars93604q7kyz6y1f8f886l05jkgj8bs78033l2czypvzki5la"))))
+         "0sc6rvhiizxxpkdc3wps200wg3pqc0d89crn29lzm75fk8qdd7vx"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -5274,14 +5274,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
 (define-public r-ranger
   (package
     (name "r-ranger")
-    (version "0.8.0")
+    (version "0.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ranger" version))
        (sha256
         (base32
-         "1fdbm879wx3hlng8s4c4f8f2x5yxz57llakcqnpa0lymybidw3vz"))))
+         "1pilj5pxl8jl0gsy9vsyqxqdqfcxzvphbgvrlp4hf7r9mrfw9v0p"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -5352,14 +5352,14 @@ is supported.")
 (define-public r-lubridate
   (package
     (name "r-lubridate")
-    (version "1.7.1")
+    (version "1.7.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lubridate" version))
        (sha256
         (base32
-         "0pzvazzybzvln3y676yims7whsc74g8i7kgf2nsfbxdq5943z349"))))
+         "0k417a1xp5gxf77ycbnx5apzpc5d25sjm83ss7wmqpbnhnr5dcav"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)

gnu/packages/version-control.scm

@@ -1602,7 +1602,7 @@ be served with a HTTP file server of your choice.")
 (define-public darcs
   (package
     (name "darcs")
-    (version "2.12.4")
+    (version "2.12.5")
     (source
      (origin
        (method url-fetch)
@@ -1610,7 +1610,7 @@ be served with a HTTP file server of your choice.")
                            "darcs-" version ".tar.gz"))
        (sha256
         (base32
-         "0jfwiwl5k8wspciq1kpmvh5yap4japrf97s9pvhcybxxhaj3ds28"))
+         "0lrm0sal5pl453mkqn8b9fc9l7lwinc140iqihya9g17bk408nrm"))
        (modules '((guix build utils)))
        ;; Remove time-dependent code for reproducibility.
        (snippet
@@ -1625,8 +1625,10 @@ be served with a HTTP file server of your choice.")
     (arguments
      `(#:configure-flags '("-fpkgconfig" "-fcurl" "-flibiconv" "-fthreaded"
                            "-fnetwork-uri" "-fhttp" "--flag=executable"
-                           "--flag=library")
+                           "--flag=library"
-       #:tests? #f)) ; 20 failing shell tests out of over 400
+                           "--allow-newer=shelly")
+       ;; FIXME: darcs is not compatible with the latest QuickCheck
+       #:tests? #f))
     (inputs
      `(("ghc-cmdargs" ,ghc-cmdargs)
        ("ghc-split" ,ghc-split)
@@ -1644,7 +1646,6 @@ be served with a HTTP file server of your choice.")
        ("ghc-bytestring-builder" ,ghc-bytestring-builder)
        ("ghc-cryptohash" ,ghc-cryptohash)
        ("ghc-data-ordlist" ,ghc-data-ordlist)
-       ("ghc-directory" ,ghc-directory)
        ("ghc-fgl" ,ghc-fgl)
        ("ghc-system-filepath" ,ghc-system-filepath)
        ("ghc-graphviz" ,ghc-graphviz)
@@ -1655,7 +1656,6 @@ be served with a HTTP file server of your choice.")
        ("ghc-mtl" ,ghc-mtl)
        ("ghc-old-time" ,ghc-old-time)
        ("ghc-parsec" ,ghc-parsec)
-       ("ghc-process" ,ghc-process)
        ("ghc-random" ,ghc-random)
        ("ghc-regex-applicative" ,ghc-regex-applicative)
        ("ghc-regex-compat-tdfa" ,ghc-regex-compat-tdfa)

gnu/packages/video.scm

@@ -21,7 +21,7 @@
 ;;; Copyright © 2017 Ethan R. Jones <doubleplusgood23@gmail.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Gregor Giesen <giesen@zaehlwerk.net>
-;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
@@ -1009,7 +1009,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.")
 (define-public mpv
   (package
     (name "mpv")
-    (version "0.28.0")
+    (version "0.28.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1017,10 +1017,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.")
                     ".tar.gz"))
               (sha256
                (base32
-                "1d2p6k3y9lqx8bpdal4grrj8ljy7pvd8qgdq8004fmr38afmbb7f"))
+                "1i1czric6dhbwvyxamzrnwjwsznrn9cpzp6m0m6aahiwpbfbl282"))
-              (patches (search-patches "mpv-CVE-2018-6360-1.patch"
-                                       "mpv-CVE-2018-6360-2.patch"
-                                       "mpv-CVE-2018-6360-3.patch"))
               (file-name (string-append name "-" version ".tar.gz"))))
     (build-system waf-build-system)
     (native-inputs

gnu/packages/vim.scm

@@ -717,7 +717,7 @@ refactor Vim in order to:
 (define-public vifm
   (package
     (name "vifm")
-    (version "0.9")
+    (version "0.9.1")
     (source
       (origin
         (method url-fetch)
@@ -728,7 +728,7 @@ refactor Vim in order to:
                               "vifm-" version ".tar.bz2")))
         (sha256
          (base32
-          "1zd72vcgir3g9rhs2iyca13qf5fc0b1f22y20f5gy92c3sfwj45b"))))
+          "1cz7vjjmghgdxd1lvsdwv85gvx4kz8idq14qijpwkpfrf2va9f98"))))
     (build-system gnu-build-system)
     (arguments
     '(#:configure-flags '("--disable-build-timestamp")

gnu/packages/w3m.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
-;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
@@ -36,7 +36,7 @@
 (define-public w3m
   (package
     (name "w3m")
-    (version "0.5.3+git20170102")
+    (version "0.5.3+git20180125")
     (source (origin
               (method git-fetch)
               ;; Debian's fork of w3m is the only one that is still
@@ -47,7 +47,7 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0p8csd49b550q69bk45ncs2y2x48xij7jj11xapp0s8dn1j7kcgx"))))
+                "0dafdfx1yhrvhbqzslkcapj09dvf64m2jadz3wl2icni0k4msq90"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f  ; no check target

gnu/packages/web.scm

@@ -3,7 +3,8 @@
 ;;; Copyright © 2013 Aljosha Papsch <misc@rpapsch.de>
 ;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
@@ -85,6 +86,7 @@
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages libidn)
   #:use-module (gnu packages libunistring)
+  #:use-module (gnu packages lisp)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages markup)
   #:use-module (gnu packages ncurses)
@@ -3881,13 +3883,13 @@ directory.")
 (define-public r-htmlwidgets
   (package
     (name "r-htmlwidgets")
-    (version "0.9")
+    (version "1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "htmlwidgets" version))
               (sha256
                (base32
-                "0plqkfqys1ca3ki7sb7yc6gwjpi7yy4g3mzh7hfy8s6qri0vam0i"))))
+                "09lkmzh35l1420sg0dyh4vgyishqx3g8xmgs2y9z7lbi09xgwwwr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-htmltools" ,r-htmltools)
@@ -3904,26 +3906,24 @@ applications.")
 (define-public r-htmltable
   (package
     (name "r-htmltable")
-    (version "1.11.0")
+    (version "1.11.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "htmlTable" version))
        (sha256
         (base32
-         "0x0qrzx6igg5z8jh901d2a8g2idpm5f4frwp1m02910scifcrxwf"))))
+         "1lbpi0kkk8b41w10scmlf27dg5azcv51a4q3p5bpqyphrnqp78k4"))))
     (properties `((upstream-name . "htmlTable")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-checkmate" ,r-checkmate)
-       ("r-dplyr" ,r-dplyr)
        ("r-htmltools" ,r-htmltools)
        ("r-htmlwidgets" ,r-htmlwidgets)
        ("r-knitr" ,r-knitr)
        ("r-magrittr" ,r-magrittr)
        ("r-rstudioapi" ,r-rstudioapi)
-       ("r-stringr" ,r-stringr)
+       ("r-stringr" ,r-stringr)))
-       ("r-tidyr" ,r-tidyr)))
     (home-page "http://gforge.se/packages/")
     (synopsis "Advanced tables for Markdown/HTML")
     (description
@@ -5418,6 +5418,47 @@ extensive prebuilt widgets make it possible to build beautiful,
 responsive, and powerful applications with minimal effort.")
     (license l:artistic2.0)))
 
+(define-public r-shinydashboard
+  (package
+    (name "r-shinydashboard")
+    (version "0.6.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "shinydashboard" version))
+              (sha256
+               (base32
+                "14zi7g5wrngy6lwi9xpvaid7727m6rfdijbb89al9likfhjqzqqy"))))
+    (build-system r-build-system)
+    ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
+    ;; Regenerate it from the included sources.
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build r-build-system)
+                  (ice-9 popen))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'generate-minified-javascript
+           (lambda _
+             (with-directory-excursion "inst/AdminLTE"
+               (delete-file "app.min.js")
+               (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
+                 (call-with-output-file "app.min.js"
+                   (lambda (port)
+                     (dump-port minified port))))))))))
+    (propagated-inputs
+     `(("r-htmltools" ,r-htmltools)
+       ("r-shiny" ,r-shiny)))
+    (native-inputs
+     `(("uglify-js" ,uglify-js)))
+    (home-page "http://rstudio.github.io/shinydashboard/")
+    (synopsis "Create dashboards with shiny")
+    (description "This package provides an extension to the Shiny web
+application framework for R, making it easy to create attractive dashboards.")
+    ;; This package includes software that was released under the Expat
+    ;; license, but the whole package is released under GPL version 2 or
+    ;; later.
+    (license l:gpl2+)))
+
 (define-public r-crosstalk
   (package
     (name "r-crosstalk")

gnu/packages/xml.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Raimon Grau <raimonster@gmail.com>
@@ -13,7 +13,7 @@
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016, 2017 ng0 <contact.ng0@cryptolab.net>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2016, 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Adriano Peluso <catonano@gmail.com>
 ;;; Copyright © 2017 Gregor Giesen <giesen@zaehlwerk.net>
 ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
@@ -41,6 +41,9 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages java)
+  #:use-module (gnu packages gnuzilla)
+  #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages perl-check)
   #:use-module (gnu packages python)
@@ -54,6 +57,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system haskell)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages pkg-config))
 
@@ -935,6 +939,15 @@ Libxml2).")
     (license (license:x11-style "file://COPYING"
                                 "See 'COPYING' in the distribution."))))
 
+(define-public xmlsec-nss
+  (package
+    (inherit xmlsec)
+    (name "xmlsec-nss")
+    (inputs
+     `(("nss" ,nss)
+       ("libltdl" ,libltdl)))
+    (synopsis "XML Security Library (using NSS instead of GnuTLS)")))
+
 (define-public minixml
   (package
     (name "minixml")
@@ -1958,3 +1971,109 @@ outputting XML data from Java code.")
     (description "XStream is a simple library to serialize Java objects to XML
 and back again.")
     (license license:bsd-3)))
+
+(define-public ghc-hxt-charproperties
+  (package
+    (name "ghc-hxt-charproperties")
+    (version "9.2.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "hxt-charproperties/hxt-charproperties-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1mml8wglvagqq891rchgli6r8rnkwrqhgsxfl6kb5403pzb18rp4"))))
+    (build-system haskell-build-system)
+    (home-page "https://github.com/UweSchmidt/hxt")
+    (synopsis "Character properties and classes for XML and Unicode")
+    (description
+     "The modules provided by this package contain predicates for Unicode
+blocks and char properties and character predicates defined by XML.  The
+supported Unicode version is 7.0.0")
+    (license license:expat)))
+
+(define-public ghc-hxt-unicode
+  (package
+    (name "ghc-hxt-unicode")
+    (version "9.0.2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/hxt-unicode/hxt-unicode-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0rj48cy8z4fl3zpg5bpa458kqr83adav6jnqv4i71dclpprj6n3v"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-hxt-charproperties" ,ghc-hxt-charproperties)))
+    (home-page
+     "http://www.fh-wedel.de/~si/HXmlToolbox/index.html https://github.com/UweSchmidt/hxt")
+    (synopsis
+     "Unicode en-/decoding functions for utf8, iso-latin-* and other encodings")
+    (description
+     "This package provides Unicode encoding and decoding functions for
+encodings used in the Haskell XML Toolbox.  ISO Latin 1-16, utf8, utf16, ASCII
+are supported. Decoding is done with lazy functions, errors may be detected or
+ignored.")
+    (license license:expat)))
+
+(define-public ghc-hxt-regex-xmlschema
+  (package
+    (name "ghc-hxt-regex-xmlschema")
+    (version "9.2.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "hxt-regex-xmlschema/hxt-regex-xmlschema-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1c4jr0439f5yc05h7iz53fa47g6l2wrvqp6gvwf01mlqajk3nx7l"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-hxt-charproperties" ,ghc-hxt-charproperties)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-text" ,ghc-text)
+       ("ghc-hunit" ,ghc-hunit)))
+    (home-page "http://www.haskell.org/haskellwiki/Regular_expressions_for_XML_Schema")
+    (synopsis "Regular expression library for W3C XML Schema regular expressions")
+    (description
+     "This library supports full W3C XML Schema regular expressions inclusive
+all Unicode character sets and blocks.  It is implemented by the technique of
+derivations of regular expressions.")
+    (license license:expat)))
+
+(define-public ghc-hxt
+  (package
+    (name "ghc-hxt")
+    (version "9.3.1.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/hxt/hxt-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1qq3ykgn355rx242xjcbqqksgvwr6k2fdj5phw4iv28qqxff6m8d"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-parsec" ,ghc-parsec)
+       ("ghc-mtl" ,ghc-mtl)
+       ("ghc-hxt-charproperties" ,ghc-hxt-charproperties)
+       ("ghc-hxt-unicode" ,ghc-hxt-unicode)
+       ("ghc-hxt-regex-xmlschema" ,ghc-hxt-regex-xmlschema)
+       ("ghc-network-uri" ,ghc-network-uri)))
+    (home-page "https://github.com/UweSchmidt/hxt")
+    (synopsis "Collection of tools for processing XML with Haskell")
+    (description
+     "The Haskell XML Toolbox bases on the ideas of HaXml and HXML, but
+introduces a more general approach for processing XML with Haskell.")
+    (license license:expat)))