From ee8de7381466ad917d1d2cab49830325230b4e5c Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 26 Apr 2020 13:22:35 +0300
Subject: [PATCH 001/215] gnu: python-scanpy: Update to 1.4.6.

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6.
[arguments]: Add another network based test to skip.
[propagated-inputs]: Add python-tqdm.
---
 gnu/packages/bioinformatics.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b9be0c1918..6c5b49e37e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13365,14 +13365,14 @@ in RNA-seq data.")
 (define-public python-scanpy
   (package
     (name "python-scanpy")
-    (version "1.4.5.1")
+    (version "1.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "scanpy" version))
        (sha256
         (base32
-         "14kh1ji70xxhmri5q8sgcibsidhr6f221wxrcw8a5xvibj5da17j"))))
+         "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -13382,6 +13382,7 @@ in RNA-seq data.")
              ;; These tests require Internet access.
              (delete-file-recursively "scanpy/tests/notebooks")
              (delete-file "scanpy/tests/test_clustering.py")
+             (delete-file "scanpy/tests/test_datasets.py")
 
              ;; TODO: I can't get the plotting tests to work, even with Xvfb.
              (delete-file "scanpy/tests/test_plotting.py")
@@ -13398,8 +13399,8 @@ in RNA-seq data.")
        ("python-h5py" ,python-h5py)
        ("python-igraph" ,python-igraph)
        ("python-joblib" ,python-joblib)
-       ("python-louvain" ,python-louvain)
        ("python-legacy-api-wrap" ,python-legacy-api-wrap)
+       ("python-louvain" ,python-louvain)
        ("python-matplotlib" ,python-matplotlib)
        ("python-natsort" ,python-natsort)
        ("python-networkx" ,python-networkx)
@@ -13412,6 +13413,7 @@ in RNA-seq data.")
        ("python-seaborn" ,python-seaborn)
        ("python-statsmodels" ,python-statsmodels)
        ("python-tables" ,python-tables)
+       ("python-tqdm" ,python-tqdm)
        ("python-umap-learn" ,python-umap-learn)))
     (native-inputs
      `(("python-pytest" ,python-pytest)

From ca4b55882a0f6b4ba46253485afb82ec000f8fc2 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 2 Apr 2020 14:10:40 -0400
Subject: [PATCH 002/215] gnu: Add rav1e.

* gnu/packages/video.scm (rav1e): New variable.
* gnu/packages/rust-apps.scm (rust-cbindgen-0.12, rust-cargo-c): New
variables.
* gnu/packages/crates-io.scm: Various new packages and upgrades.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/crates-io.scm | 3771 +++++++++++++++++++++++++++++++++---
 gnu/packages/rust-apps.scm |   51 +-
 gnu/packages/video.scm     |   87 +
 3 files changed, 3660 insertions(+), 249 deletions(-)

diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index a42661e3f8..d318a05d71 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020 John Soo <jsoo1@asu.edu>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
+;;; Copyright © 2020 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,6 +41,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages video)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg))
@@ -72,8 +74,46 @@
 library in Rust.")
     (license license:expat)))
 
+(define-public rust-addr2line-0.11
+  (package
+    (name "rust-addr2line")
+    (version "0.11.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "addr2line" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0sk5g8cb2yynlcm0wcqff9l9c9ml69rqgfrrbii0ybgdc236jkhw"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Not all test files included.
+       #:cargo-inputs
+       (("rust-rustc-demangle" ,rust-rustc-demangle-0.1)
+        ("rust-object" ,rust-object-0.17)
+        ("rust-fallible-iterator" ,rust-fallible-iterator-0.2)
+        ("rust-cpp-demangle" ,rust-cpp-demangle-0.2)
+        ("rust-gimli" ,rust-gimli-0.20)
+        ("rust-smallvec" ,rust-smallvec-1)
+        ("rust-lazycell" ,rust-lazycell-1.2))
+       #:cargo-development-inputs
+       (("rust-backtrace" ,rust-backtrace-0.3)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-findshlibs" ,rust-findshlibs-0.5)
+        ("rust-memmap" ,rust-memmap-0.7)
+        ("rust-rustc-test" ,rust-rustc-test-0.3))))
+    (home-page "https://github.com/gimli-rs/addr2line")
+    (synopsis "Symbolication library written in Rust, using gimli")
+    (description
+     "This package provides a cross-platform symbolication library written in
+Rust, using gimli.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-addr2line-0.9
   (package
+    (inherit rust-addr2line-0.11)
     (name "rust-addr2line")
     (version "0.9.0")
     (source
@@ -85,7 +125,6 @@ library in Rust.")
        (sha256
         (base32
          "17rlf04nx3g3rcy661v24ksnmpk6vqn680g5b5sp8lk20iih2xnx"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
@@ -100,15 +139,9 @@ library in Rust.")
        #:cargo-development-inputs
        (("rust-backtrace" ,rust-backtrace-0.3)
         ("rust-clap" ,rust-clap-2)
-        ("rust-findshlibs" ,rust-findshlibs-0.5)
+        ;("rust-findshlibs" ,rust-findshlibs-0.4)
         ("rust-memmap" ,rust-memmap-0.7)
-        ("rust-rustc-test" ,rust-rustc-test-0.3))))
-    (home-page "https://github.com/gimli-rs/addr2line")
-    (synopsis "Symbolication library written in Rust, using gimli")
-    (description
-     "This package provides a cross-platform symbolication library written in
-Rust, using gimli.")
-    (license (list license:asl2.0 license:expat))))
+        ("rust-rustc-test" ,rust-rustc-test-0.3))))))
 
 (define-public rust-adler32-1.0
   (package
@@ -136,6 +169,34 @@ the Rust programming language.")
     (license (list license:bsd-3
                    license:zlib))))
 
+(define-public rust-afl-0.5
+  (package
+    (name "rust-afl")
+    (version "0.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "afl" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0azpi917l8nhvx25n2v670nvkxkrhcwmddfi85qnr6kchmi6y946"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rustc-version" ,rust-rustc-version-0.2)
+        ("rust-cc" ,rust-cc-1.0)
+        ("rust-xdg" ,rust-xdg-2.2)
+        ("rust-clap" ,rust-clap-2))))
+    (home-page "https://github.com/rust-fuzz/afl.rs")
+    (synopsis
+     "Fuzzing Rust code with american-fuzzy-lop")
+    (description
+     "Fuzz Rust code with american-fuzzy-lop.")
+    (license license:asl2.0)))
+
 (define-public rust-afl-0.4
   (package
     (name "rust-afl")
@@ -156,9 +217,6 @@ the Rust programming language.")
        (("rust-cc" ,rust-cc-1.0)
         ("rust-clap" ,rust-clap-2)
         ("rust-rustc-version" ,rust-rustc-version-0.2)
-        ("rust-xdg" ,rust-xdg-2.2))
-       #:cargo-development-inputs
-       (("rust-rustc-version" ,rust-rustc-version-0.2)
         ("rust-xdg" ,rust-xdg-2.2))))
     (home-page "https://github.com/rust-fuzz/afl.rs")
     (synopsis
@@ -170,7 +228,7 @@ the Rust programming language.")
 (define-public rust-aho-corasick-0.7
   (package
     (name "rust-aho-corasick")
-    (version "0.7.8")
+    (version "0.7.10")
     (source
      (origin
        (method url-fetch)
@@ -179,10 +237,10 @@ the Rust programming language.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "048q5vr1qac4lf90z80lw8kcya6qmlxw857xhwxsssk832jdafkl"))))
+         "1nka9509afjgal6lpymn8w2lq11dmjwxs8yjcmzys966if5l05l7"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:cargo-inputs (("rust-memchr" ,rust-memchr-2.2))
+     `(#:cargo-inputs (("rust-memchr" ,rust-memchr-2.3))
        #:cargo-development-inputs
        (("rust-doc-comment" ,rust-doc-comment-0.3))))
     (home-page "https://github.com/BurntSushi/aho-corasick")
@@ -450,6 +508,44 @@ text or blue underlined text, on ANSI terminals.")
 @code{std::error::Error}.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-aom-sys-0.1
+  (package
+    (name "rust-aom-sys")
+    (version "0.1.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "aom-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ix3djcf84kk53h6fac73n7jc614745n7kbmikxwi3s73b6vzgsr"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(;#:skip-build? #t
+       #:cargo-inputs
+       (("rust-bindgen" ,rust-bindgen-0.51)
+        ("rust-metadeps" ,rust-metadeps-1.1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-environmental-variable
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((clang (assoc-ref inputs "libclang")))
+               (setenv "LIBCLANG_PATH"
+                       (string-append clang "/lib")))
+             #t)))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libaom" ,libaom)
+       ("libclang" ,clang)
+       ("llvm" ,llvm)))
+    (home-page "https://github.com/rust-av/aom-rs")
+    (synopsis "FFI bindings to aom")
+    (description "This package provides FFI bindings to aom.")
+    (license license:expat)))
+
 (define-public rust-approx-0.3
   (package
     (name "rust-approx")
@@ -492,6 +588,26 @@ text or blue underlined text, on ANSI terminals.")
          "153awzwywmb61xg857b80l63b1x6hifx2pha7lxf6fck9qxwraq8"))))
     (arguments '())))
 
+(define-public rust-arbitrary-0.2
+  (package
+    (name "rust-arbitrary")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "arbitrary" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1i3fhcdyjq4isn22xx2svmpfr5hwyzi0wavbm07fs8i2dv5pdkv4"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/nagisa/rust_arbitrary/")
+    (synopsis "Trait for generating structured data from unstructured data")
+    (description
+     "The trait for generating structured data from unstructured data.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-arc-swap-0.4
   (package
     (name "rust-arc-swap")
@@ -547,6 +663,32 @@ text or blue underlined text, on ANSI terminals.")
         ("rust-proptest" ,rust-proptest-0.9)
         ("rust-version-sync" ,rust-version-sync-0.8))))))
 
+(define-public rust-arg-enum-proc-macro-0.3
+  (package
+    (name "rust-arg-enum-proc-macro")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "arg_enum_proc_macro" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "021rr6j3n031ynfbm7kwb3j3bxvbsz40n0nqi78k47d3p92rihcv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/lu-zero/arg_enum_proc_macro")
+    (synopsis "Procedural macro compatible with clap arg_enum")
+    (description
+     "This package provides a procedural macro compatible with clap's
+@code{arg_enum}.")
+    (license license:expat)))
+
 (define-public rust-argon2rs-0.2
   (package
     (name "rust-argon2rs")
@@ -638,7 +780,7 @@ ArrayVec and ArrayString.")
   (package
     (inherit rust-arrayvec-0.5)
     (name "rust-arrayvec")
-    (version "0.4.10")
+    (version "0.4.12")
     (source
      (origin
        (method url-fetch)
@@ -647,7 +789,7 @@ ArrayVec and ArrayString.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0wcch3ca9qvkixgdbd2afrv1xa27l83vpraf7frsh9l8pivgpiwj"))))
+         "1fdiv5m627gh6flp4mpmi1mh647imm9x423licsr11psz97d97yd"))))
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
@@ -658,10 +800,38 @@ ArrayVec and ArrayString.")
         ("rust-matches" ,rust-matches-0.1)
         ("rust-serde-test" ,rust-serde-test-1.0))))))
 
-(define-public rust-ascii-0.9
+(define-public rust-ascii-1.0
   (package
     (name "rust-ascii")
-    (version "0.9.1")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ascii" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0281gc828q4j692gb66jfdr5k16gyszgqflylh0pp30rllv63xdv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-test" ,rust-serde-test-1.0))))
+    (home-page "https://github.com/tomprogrammer/rust-ascii")
+    (synopsis "ASCII-only equivalents to `char`, `str` and `String`.")
+    (description
+     "A rust library that provides ASCII-only string and character types,
+equivalent to the @code{char}, @code{str} and @code{String} types in the
+standard library.")
+    (license (list license:asl2.0 license:expat))))
+
+(define-public rust-ascii-0.9
+  (package
+    (inherit rust-ascii-1.0)
+    (name "rust-ascii")
+    (version "0.9.3")
     (source
      (origin
        (method url-fetch)
@@ -670,20 +840,12 @@ ArrayVec and ArrayString.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0dck6rsjnxlczyjnncn8hf16bxj42m1vi6s2n32c1jg2ijd9dz55"))))
-    (build-system cargo-build-system)
+         "0km3zzkhrr22drf9p1zcblqirlxkdc7zra25acpi0h8qax5c1cga"))))
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
-       (("rust-quickcheck" ,rust-quickcheck-0.8)
+     `(#:cargo-inputs
+       (("rust-quickcheck" ,rust-quickcheck-0.6)
         ("rust-serde" ,rust-serde-1.0)
-        ("rust-serde-test" ,rust-serde-test-1.0))))
-    (home-page "https://github.com/tomprogrammer/rust-ascii")
-    (synopsis
-     "ASCII-only equivalents to char, str and String")
-    (description
-     "ASCII-only equivalents to @code{char}, @code{str} and @code{String}.")
-    (license (list license:expat license:asl2.0))))
+        ("rust-serde-test" ,rust-serde-test-1.0))))))
 
 (define-public rust-assert-matches-1.3
   (package
@@ -733,7 +895,7 @@ ArrayVec and ArrayString.")
 (define-public rust-atty-0.2
   (package
     (name "rust-atty")
-    (version "0.2.13")
+    (version "0.2.14")
     (source
       (origin
         (method url-fetch)
@@ -741,12 +903,13 @@ ArrayVec and ArrayString.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "140sswp1bwqwc4zk80bxkbnfb3g936hgrb77g9g0k1zcld3wc0qq"))))
+          "1s7yslcs6a28c5vz7jwj63lkfgyx8mx99fdirlhi9lbhhzhrpcyr"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-libc" ,rust-libc-0.2)
+       (("rust-hermit-abi" ,rust-hermit-abi-0.1)
+        ("rust-libc" ,rust-libc-0.2)
         ("rust-winapi" ,rust-winapi-0.3))))
     (home-page "https://github.com/softprops/atty")
     (synopsis "Simple interface for querying atty")
@@ -827,7 +990,7 @@ in Rust.")
 (define-public rust-backtrace-0.3
   (package
     (name "rust-backtrace")
-    (version "0.3.32")
+    (version "0.3.46")
     (source
      (origin
        (method url-fetch)
@@ -836,18 +999,18 @@ in Rust.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1rgsaha3b6wxh564s4jqn5hl5pkmg214blyjjs1svafib190zd8q"))))
+         "17hh1vrhfd01qpjilrdpy7q0lf2j2qv36achpg37q92rff4r5rmi"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-addr2line" ,rust-addr2line-0.9)
+       (("rust-addr2line" ,rust-addr2line-0.11)
         ("rust-backtrace-sys" ,rust-backtrace-sys-0.1)
         ("rust-cfg-if" ,rust-cfg-if-0.1)
         ("rust-compiler-builtins" ,rust-compiler-builtins-0.1)
         ("rust-cpp-demangle" ,rust-cpp-demangle-0.2)
         ("rust-findshlibs" ,rust-findshlibs-0.5)
-        ("rust-goblin" ,rust-goblin-0.0)
+        ("rust-goblin" ,rust-goblin-0.2)
         ("rust-libc" ,rust-libc-0.2)
         ("rust-memmap" ,rust-memmap-0.7)
         ("rust-rustc-demangle" ,rust-rustc-demangle-0.1)
@@ -866,7 +1029,7 @@ trace (backtrace) at runtime in a Rust program.")
 (define-public rust-backtrace-sys-0.1
   (package
     (name "rust-backtrace-sys")
-    (version "0.1.32")
+    (version "0.1.35")
     (source
       (origin
         (method url-fetch)
@@ -874,16 +1037,14 @@ trace (backtrace) at runtime in a Rust program.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "14c406z8bdmms8a5l8cv79jfkz1mk10qk5p97izf4vai53qparax"))))
+          "066iviphi72mx9hd3njzsplk5v45jhi10mrccbbyij391ahsps3x"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
+     `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
         ("rust-compiler-builtins" ,rust-compiler-builtins-0.1)
-        ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0))
-       #:cargo-development-inputs
-       (("rust-cc" ,rust-cc-1.0))))
+        ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0)
+        ("rust-cc" ,rust-cc-1.0))))
     (home-page "https://github.com/rust-lang/backtrace-rs")
     (synopsis "Bindings to the libbacktrace gcc library")
     (description
@@ -983,26 +1144,50 @@ and no more (caveat: black_box is still missing!).")
     (license (list license:asl2.0
                    license:expat))))
 
-(define-public rust-bincode-1.1
+(define-public rust-better-panic-0.2
   (package
-    (name "rust-bincode")
-    (version "1.1.4")
+    (name "rust-better-panic")
+    (version "0.2.0")
     (source
-     (origin
-       (method url-fetch)
-       (uri (crate-uri "bincode" version))
-       (file-name
-        (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1xx6bp39irvsndk6prnmmq8m1l9p6q2qj21j6mfks2y81pjsa14z"))))
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "better-panic" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0xl48v6pd9ys7wp0ni62i6q73xpd1nhf92z09sjc9n3lrj0ac4ix"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
-       (("rust-autocfg" ,rust-autocfg-0.1)
-        ("rust-byteorder" ,rust-byteorder-1.3)
-        ("rust-serde" ,rust-serde-1.0))
+     `(#:cargo-inputs
+       (("rust-backtrace" ,rust-backtrace-0.3)
+        ("rust-console" ,rust-console-0.9)
+        ("rust-syntect" ,rust-syntect-3.3))))
+    (home-page "https://github.com/mitsuhiko/better-panic")
+    (synopsis "Pretty backtraces inspired by Python's tracebacks")
+    (description
+     "This package provides pretty panic backtraces inspired by Python's
+tracebacks.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-bincode-1.2
+  (package
+    (name "rust-bincode")
+    (version "1.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bincode" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1gvxm3n67xv1874fwxmnlircdlphlk1hcw75ykrrnw9l2nky4lsp"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-serde" ,rust-serde-1.0)
+        ("rust-byteorder" ,rust-byteorder-1.3))
        #:cargo-development-inputs
        (("rust-serde-bytes" ,rust-serde-bytes-0.11)
         ("rust-serde-derive" ,rust-serde-derive-1.0))))
@@ -1014,10 +1199,127 @@ and no more (caveat: black_box is still missing!).")
 that uses Serde for transforming structs into bytes and vice versa!")
     (license license:expat)))
 
-(define-public rust-bindgen-0.50
+(define-public rust-bincode-1.1
+  (package
+    (inherit rust-bincode-1.2)
+    (name "rust-bincode")
+    (version "1.1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "bincode" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1xx6bp39irvsndk6prnmmq8m1l9p6q2qj21j6mfks2y81pjsa14z"))))
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-autocfg" ,rust-autocfg-0.1)
+        ("rust-byteorder" ,rust-byteorder-1.3)
+        ("rust-serde" ,rust-serde-1.0))
+       #:cargo-development-inputs
+       (("rust-serde-bytes" ,rust-serde-bytes-0.11)
+        ("rust-serde-derive" ,rust-serde-derive-1.0))))))
+
+(define-public rust-bindgen-0.52
   (package
     (name "rust-bindgen")
-    (version "0.50.0")
+    (version "0.52.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bindgen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0mzy2gjiaggl602yn4a11xzrxfj18kl7pwqa5yv32njkxd257j7i"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-shlex" ,rust-shlex-0.1)
+        ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-peeking-take-while"
+         ,rust-peeking-take-while-0.1)
+        ("rust-clang-sys" ,rust-clang-sys-0.28)
+        ("rust-cexpr" ,rust-cexpr-0.3)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-env-logger" ,rust-env-logger-0.7)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-quote" ,rust-quote-1.0)
+        ("rust-rustc-hash" ,rust-rustc-hash-1.1)
+        ("rust-bitflags" ,rust-bitflags-1)
+        ("rust-lazycell" ,rust-lazycell-1.2)
+        ("rust-regex" ,rust-regex-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-which" ,rust-which-3.1))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-diff" ,rust-diff-0.1)
+        ("rust-shlex" ,rust-shlex-0.1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-environmental-variable
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((clang (assoc-ref inputs "libclang")))
+               (setenv "LIBCLANG_PATH"
+                       (string-append clang "/lib")))
+             #t)))))
+    (inputs
+     `(("libclang" ,clang)))
+    (home-page "https://rust-lang.github.io/rust-bindgen/")
+    (synopsis
+     "Automatically generates Rust FFI bindings to C and C++ libraries")
+    (description
+     "Automatically generates Rust FFI bindings to C and C++ libraries.")
+    (license license:bsd-3)))
+
+(define-public rust-bindgen-0.51
+  (package
+    (inherit rust-bindgen-0.52)
+    (name "rust-bindgen")
+    (version "0.51.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bindgen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0x9gndlnwmxsihxvsc3izyyss7g8b2djn0daafshj1gcy69i7mzb"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-shlex" ,rust-shlex-0.1)
+        ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-peeking-take-while"
+         ,rust-peeking-take-while-0.1)
+        ("rust-clang-sys" ,rust-clang-sys-0.28)
+        ("rust-cexpr" ,rust-cexpr-0.3)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-env-logger" ,rust-env-logger-0.6)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-quote" ,rust-quote-1.0)
+        ("rust-rustc-hash" ,rust-rustc-hash-1.1)
+        ("rust-bitflags" ,rust-bitflags-1)
+        ("rust-regex" ,rust-regex-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-which" ,rust-which-3.1))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-diff" ,rust-diff-0.1)
+        ("rust-shlex" ,rust-shlex-0.1))))
+    (inputs `())))
+
+(define-public rust-bindgen-0.50
+  (package
+    (inherit rust-bindgen-0.51)
+    (name "rust-bindgen")
+    (version "0.50.1")
     (source
      (origin
        (method url-fetch)
@@ -1026,8 +1328,7 @@ that uses Serde for transforming structs into bytes and vice versa!")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1k4n1d002vrfn1mlpww3ib7f275yn4rpxfwkqpr9bym27zg17ab5"))))
-    (build-system cargo-build-system)
+         "1fp98x0k4cawil3rqxsfrb58pq3mb5mn37rp745zxfmjfigml3nb"))))
     (arguments
      `(#:cargo-inputs
        (("rust-bitflags" ,rust-bitflags-1)
@@ -1041,22 +1342,49 @@ that uses Serde for transforming structs into bytes and vice versa!")
         ("rust-log" ,rust-log-0.4)
         ("rust-peeking-take-while" ,rust-peeking-take-while-0.1)
         ("rust-proc-macro2" ,rust-proc-macro2-0.4)
-        ("rust-quote" ,rust-quote-1.0)
+        ("rust-quote" ,rust-quote-0.6)
         ("rust-regex" ,rust-regex-1.1)
         ("rust-shlex" ,rust-shlex-0.1)
         ("rust-which" ,rust-which-2.0))
        #:cargo-development-inputs
        (("rust-clap" ,rust-clap-2)
         ("rust-diff" ,rust-diff-0.1)
-        ("rust-shlex" ,rust-shlex-0.1))))
-    (home-page
-     "https://rust-lang.github.io/rust-bindgen/")
-    (synopsis
-     "Automatically generates FFI bindings to C and C++ libraries")
-    (description
-     "Automatically generates Rust FFI bindings to C and C++
-libraries.")
-    (license license:bsd-3)))
+        ("rust-shlex" ,rust-shlex-0.1))))))
+
+(define-public rust-bindgen-0.37
+  (package
+    (inherit rust-bindgen-0.50)
+    (name "rust-bindgen")
+    (version "0.37.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bindgen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "08f2cyzr8fc027mzj2lhmn5j3w318g2ql7yfw5ngxa3yhy1an98v"))))
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-peeking-take-while"
+         ,rust-peeking-take-while-0.1)
+        ("rust-cexpr" ,rust-cexpr-0.2)
+        ("rust-clang-sys" ,rust-clang-sys-0.23)
+        ("rust-proc-macro2" ,rust-proc-macro2-0.3)  ; 0.3.5
+        ("rust-log" ,rust-log-0.4)
+        ("rust-env-logger" ,rust-env-logger-0.5)
+        ("rust-quote" ,rust-quote-0.5)
+        ("rust-which" ,rust-which-1.0)
+        ("rust-regex" ,rust-regex-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-clap" ,rust-clap-2))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-diff" ,rust-diff-0.1)
+        ("rust-shlex" ,rust-shlex-0.1))))))
 
 (define-public rust-bindgen-0.33
   (package
@@ -1193,6 +1521,29 @@ behave like a set of bitflags.")
         (base32
          "0v8hh6wdkpk9my8z8442g4hqrqf05h0qj53dsay6mv18lqvqklda"))))))
 
+(define-public rust-bitstream-io-0.8
+  (package
+    (name "rust-bitstream-io")
+    (version "0.8.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bitstream-io" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "00a6wy54s1dmadm5xz8k2cbsd7ixvm48mlc45bk0fdy0pbra6jk1"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/tuffy/bitstream-io")
+    (synopsis
+      "Library for reading/writing un-aligned values from/to streams in big-endian and little-endian formats.")
+    (description
+      "Library for reading/writing un-aligned values from/to streams in big-endian and little-endian formats.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-blake2-0.8
   (package
     (name "rust-blake2")
@@ -1428,7 +1779,7 @@ Bresenham's line algorithm.")
 (define-public rust-bstr-0.2
   (package
     (name "rust-bstr")
-    (version "0.2.1")
+    (version "0.2.12")
     (source
      (origin
        (method url-fetch)
@@ -1437,7 +1788,7 @@ Bresenham's line algorithm.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0prq6yk3da0k5bg2czcgg1i4ynsq1l59xc89ycsv6v7p08p5gh3c"))))
+         "0hazfback6i2k3vhhwyj8h46id3y58zxqh22pz46hj9r1zayd298"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -1567,6 +1918,34 @@ UTF-8.")
 in a byte slice, fast.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-bytecount-0.4
+  (package
+    (name "rust-bytecount")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bytecount" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "13qpy38z5wx0rzcdvr2h0ixbfgi1dbrif068il3hwn3k2mah88mr"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-packed-simd" ,rust-packed-simd-0.3))
+       #:cargo-development-inputs
+       (("rust-criterion" ,rust-criterion-0.2)
+        ("rust-quickcheck" ,rust-quickcheck-0.6)
+        ("rust-rand" ,rust-rand-0.4))))
+    (home-page "https://github.com/llogiq/bytecount")
+    (synopsis "Counting bytes really fast")
+    (description
+     "This package counts occurrences of a given byte, or the number of UTF-8
+code points, in a byte slice, fast.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-byteorder-1.3
   (package
     (name "rust-byteorder")
@@ -1910,6 +2289,64 @@ exposed as Reader/Writer streams.")
 capabilities")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-cargo-metadata-0.9
+  (package
+    (name "rust-cargo-metadata")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cargo_metadata" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "00pjms89lghvizh4d55lz80hvrih9r55xv9m5wd9vcsgc163gqs6"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f
+       #:cargo-inputs
+       (("rust-semver" ,rust-semver-0.9)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-serde-json" ,rust-serde-json-1.0))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-docopt" ,rust-docopt-1.1)
+        ("rust-structopt" ,rust-structopt-0.2))))
+    (home-page "https://github.com/oli-obk/cargo_metadata")
+    (synopsis "Structured access to the output of `cargo metadata`")
+    (description
+     "This package provides structured access to the output of @code{cargo
+metadata}.")
+    (license license:expat)))
+
+(define-public rust-cargo-metadata-0.6
+  (package
+    (inherit rust-cargo-metadata-0.9)
+    (name "rust-cargo-metadata")
+    (version "0.6.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cargo_metadata" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1givpi2w7iwqqnl87x5yc15zcm5hs6yw490sb6abkfp1h39v9lg5"))))
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-error-chain" ,rust-error-chain-0.12)
+        ("rust-semver" ,rust-semver-0.9)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-serde-json" ,rust-serde-json-1.0))
+       #:cargo-development-inputs
+       (;("rust-docopt" ,rust-docopt-0.8)
+        ("rust-clap" ,rust-clap-2))))))
+
 (define-public rust-cargon-0.0
   (package
     (name "rust-cargon")
@@ -1936,7 +2373,7 @@ used in argon2rs' bench suite.")
 (define-public rust-cast-0.2
   (package
     (name "rust-cast")
-    (version "0.2.2")
+    (version "0.2.3")
     (source
      (origin
        (method url-fetch)
@@ -1945,12 +2382,14 @@ used in argon2rs' bench suite.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "09yl2700crxa4n860b080msij25klvs1kfzazhp2aihchvr16q4j"))))
+         "1c5z7zryj0zwnhdgs6rw5dfvnlwc1vm19jzrlgx5055alnwk952b"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rustc-version" ,rust-rustc-version-0.2))
        #:cargo-development-inputs
-       (("rust-quickcheck" ,rust-quickcheck-0.8))))
+       (("rust-quickcheck" ,rust-quickcheck-0.9))))
     (home-page "https://github.com/japaric/cast.rs")
     (synopsis
      "Ergonomic, checked cast functions for primitive types")
@@ -2012,7 +2451,7 @@ archive to be linked into Rustcode.")
 (define-public rust-cexpr-0.3
   (package
     (name "rust-cexpr")
-    (version "0.3.5")
+    (version "0.3.6")
     (source
      (origin
        (method url-fetch)
@@ -2021,7 +2460,7 @@ archive to be linked into Rustcode.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1by64ini3f058pwad3immx5cc12wr0m0kwgaxa8apzym03mj9ym7"))))
+         "07fdfj4ff2974y33yixrb657riq9zl9b9h9lr0h7ridhhvxvbrgw"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -2197,7 +2636,7 @@ for computer graphics.")
 (define-public rust-chrono-0.4
   (package
     (name "rust-chrono")
-    (version "0.4.7")
+    (version "0.4.11")
     (source
      (origin
        (method url-fetch)
@@ -2206,23 +2645,26 @@ for computer graphics.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1glam3iqhshbamzgf0npn7hgghski92r31lm7gg8841hnxc1zn3p"))))
+         "1cmmxamkzzs36zncqjjr7qm7xkb6zyrkjslnlj3axdgqki84y2c0"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-libc" ,rust-libc-0.2)
-        ("rust-num-integer" ,rust-num-integer-0.1)
+       (("rust-num-integer" ,rust-num-integer-0.1)
         ("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-js-sys" ,rust-js-sys-0.3)
         ("rust-rustc-serialize" ,rust-rustc-serialize-0.3)
         ("rust-serde" ,rust-serde-1.0)
-        ("rust-time" ,rust-time-0.1))
+        ("rust-time" ,rust-time-0.1)
+        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2))
        #:cargo-development-inputs
-       (("rust-bincode" ,rust-bincode-1.1)
+       (;("rust-bincode" ,rust-bincode-0.8)
+        ("rust-criterion" ,rust-criterion-0.2)
         ("rust-doc-comment" ,rust-doc-comment-0.3)
         ("rust-num-iter" ,rust-num-iter-0.1)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
-        ("rust-serde-json" ,rust-serde-json-1.0))))
+        ("rust-serde-json" ,rust-serde-json-1.0)
+        ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.2))))
     (home-page
      "https://github.com/chronotope/chrono")
     (synopsis "Date and time library for Rust")
@@ -2315,6 +2757,21 @@ for computer graphics.")
                        (string-append clang "/lib")))
              #t)))))))
 
+(define-public rust-clang-sys-0.23
+  (package
+    (inherit rust-clang-sys-0.26)
+    (name "rust-clang-sys")
+    (version "0.23.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "clang-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1hjr333izzhs6bic84qwnyzy5xzmvasib8f3zkzj4ln3a97c1xyp"))))))
+
 (define-public rust-clang-sys-0.22
   (package
     (inherit rust-clang-sys-0.26)
@@ -2512,6 +2969,35 @@ pitfalls in Rust.")
      "Low level interface to CloudABI.  Contains all syscalls and related types.")
     (license license:bsd-2)))
 
+(define-public rust-cloudflare-zlib-sys-0.2
+  (package
+    (name "rust-cloudflare-zlib-sys")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cloudflare-zlib-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "01lwfd15ijw4d8jsqp87yv4wpmzcp84qm0qqwy3yxmm0fjr5q6by"))))
+    ;; This crate bundles cloudflare's fork of zlib, so we don't unbundle it.
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-cc" ,rust-cc-1.0))))
+    (home-page "https://github.com/cloudflare/zlib")
+    (synopsis
+     "Cloudflare fork of zlib with massive performance improvements")
+    (description
+     "Cloudflare fork of zlib with massive performance improvements.")
+    (license
+      (list license:expat
+            license:asl2.0
+            license:zlib))))
+
 (define-public rust-cmake-0.1
   (package
     (name "rust-cmake")
@@ -2602,12 +3088,42 @@ CMAKE environmental variable is set.")
      "Color quantization library to reduce n colors to 256 colors.")
     (license license:expat)))
 
+(define-public rust-colored-1.9
+  (package
+    (name "rust-colored")
+    (version "1.9.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "colored" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0nbc1czs512h1k696y7glv1kjrb2b914zpxraic6q5fgv80wizzl"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-atty" ,rust-atty-0.2)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-lazy-static" ,rust-lazy-static-1))
+       #:cargo-development-inputs
+       (("rust-ansi-term" ,rust-ansi-term-0.12)
+        ;("rust-rspec" ,rust-rspec-1.0)
+        )))
+    (home-page "https://github.com/mackwic/colored")
+    (synopsis "Add colors in your terminal")
+    (description
+     "The most simple way to add colors in your terminal.")
+    (license license:mpl2.0)))
+
 ;; This package requires features which are unavailable
 ;; on the stable releases of Rust.
 (define-public rust-compiler-builtins-0.1
   (package
     (name "rust-compiler-builtins")
-    (version "0.1.23")
+    (version "0.1.26")
     (source
       (origin
         (method url-fetch)
@@ -2615,14 +3131,13 @@ CMAKE environmental variable is set.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0m8rfikg08av2plyp32drjfsv7i10nf2kwzajjjkvl13yhj9s5fn"))))
+          "1rhj6ccmfkh9gcxnxgjq4fg257yi4f9325nfzsphbmxwkrg06sq3"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0))
-       #:cargo-development-inputs
-       (("rust-cc" ,rust-cc-1.0))))
+       (("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0)
+        ("rust-cc" ,rust-cc-1.0))))
     (home-page "https://github.com/rust-lang/compiler-builtins")
     (synopsis "Compiler intrinsics used by the Rust compiler")
     (description
@@ -2711,6 +3226,36 @@ harness.")
         ("rust-rustc-serialize" ,rust-rustc-serialize-0.3)
         ("rust-tempdir" ,rust-tempdir-0.3))))))
 
+(define-public rust-console-0.9
+  (package
+    (name "rust-console")
+    (version "0.9.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "console" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h765951c9mywff534f0191slazykmif4290g2yarcwhd2cg7q25"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-unicode-width" ,rust-unicode-width-0.1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-termios" ,rust-termios-0.3)
+        ("rust-encode-unicode" ,rust-encode-unicode-0.3)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-clicolors-control" ,rust-clicolors-control-1.0)
+        ("rust-regex" ,rust-regex-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1))))
+    (home-page "https://github.com/mitsuhiko/console")
+    (synopsis "Terminal and console abstraction for Rust")
+    (description
+     "This package provides a terminal and console abstraction for Rust")
+    (license license:expat)))
+
 (define-public rust-console-0.7
   (package
     (name "rust-console")
@@ -3010,7 +3555,7 @@ intrinsics.")
 (define-public rust-cpp-demangle-0.2
   (package
     (name "rust-cpp-demangle")
-    (version "0.2.12")
+    (version "0.2.14")
     (source
      (origin
        (method url-fetch)
@@ -3019,17 +3564,17 @@ intrinsics.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0a4hqsfc0sfdwy7pcr0rc1fjp2j47fxbkqfc2lfrbi4zlm5hq36k"))))
+         "1mm064x84868q06r4m4b7byf999nrkbhx7iyc4nchyssaxpsy5a1"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-afl" ,rust-afl-0.4)
-        ("rust-cfg-if" ,rust-cfg-if-0.1))
+        ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-glob" ,rust-glob-0.3))
        #:cargo-development-inputs
        (("rust-clap" ,rust-clap-2)
-        ("rust-diff" ,rust-diff-0.1)
-        ("rust-glob" ,rust-glob-0.3))))
+        ("rust-diff" ,rust-diff-0.1))))
     (home-page "https://github.com/gimli-rs/cpp_demangle")
     (synopsis "Demangle C++ symbols")
     (description
@@ -3101,7 +3646,7 @@ intrinsics.")
 (define-public rust-criterion-0.3
   (package
     (name "rust-criterion")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
@@ -3110,7 +3655,7 @@ intrinsics.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1iig7r9c6bkn5qb6axxkblc1amif6k49lix35rhqs728cphh71wk"))))
+         "1lgpr82rlmg6rm4gr3c3pla2xgxnakbf8w9sabjsig8jkikmbiqz"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -3122,15 +3667,14 @@ intrinsics.")
         ("rust-itertools" ,rust-itertools-0.8)
         ("rust-lazy-static" ,rust-lazy-static-1)
         ("rust-num-traits" ,rust-num-traits-0.2)
-        ("rust-rand-core" ,rust-rand-core-0.5)
-        ("rust-rand-os" ,rust-rand-os-0.2)
-        ("rust-rand-xoshiro" ,rust-rand-xoshiro-0.3)
-        ("rust-rayon" ,rust-rayon-1.1)
+        ("rust-oorandom" ,rust-oorandom-11.1)
+        ("rust-plotters" ,rust-plotters-0.2)
+        ("rust-rayon" ,rust-rayon-1.3)
         ("rust-serde" ,rust-serde-1.0)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
         ("rust-serde-json" ,rust-serde-json-1.0)
         ("rust-tinytemplate" ,rust-tinytemplate-1.0)
-        ("rust-walkdir" ,rust-walkdir-2.2))
+        ("rust-walkdir" ,rust-walkdir-2.3))
        #:cargo-development-inputs
        (("rust-approx" ,rust-approx-0.3)
         ("rust-quickcheck" ,rust-quickcheck-0.9)
@@ -3478,7 +4022,7 @@ intrinsics.")
 (define-public rust-crossbeam-utils-0.7
   (package
     (name "rust-crossbeam-utils")
-    (version "0.7.0")
+    (version "0.7.2")
     (source
      (origin
        (method url-fetch)
@@ -3487,7 +4031,7 @@ intrinsics.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1x1rn35q2v05qif14ijfg7800d3rf3ji2cg79awnacfw5jq6si6f"))))
+         "1a31wbrda1320gj2a6az1lin2d34xfc3xf88da4c17qy5lxcgiy3"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -3621,7 +4165,7 @@ Code} (MAC) algorithms.")
 (define-public rust-csv-1.1
   (package
     (name "rust-csv")
-    (version "1.1.0")
+    (version "1.1.3")
     (source
      (origin
        (method url-fetch)
@@ -3630,7 +4174,7 @@ Code} (MAC) algorithms.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0qxvzq030hi915dszazv6a7f0apzzi7gn193ni0g2lzkawjxck55"))))
+         "0yd2z55m2pg4al4yng4nl2y7c9dw2v7yhg5ynihxyrmmd9zzxbq0"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -3672,7 +4216,7 @@ Code} (MAC) algorithms.")
 (define-public rust-csv-core-0.1
   (package
     (name "rust-csv-core")
-    (version "0.1.6")
+    (version "0.1.10")
     (source
      (origin
        (method url-fetch)
@@ -3681,11 +4225,11 @@ Code} (MAC) algorithms.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0k5zs0x0qmmn27pa5kcg86lg84s29491fw5sh3zswxswnavasp4v"))))
+         "145wcc3560v1kmysqqspvddppiysr2rifqzy4nnlh3r6kxanc91b"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
-       (("rust-memchr" ,rust-memchr-2.2))
+       (("rust-memchr" ,rust-memchr-2.3))
        #:cargo-development-inputs
        (("rust-arrayvec" ,rust-arrayvec-0.4))))
     (home-page "https://github.com/BurntSushi/rust-csv")
@@ -3695,6 +4239,34 @@ Code} (MAC) algorithms.")
      "Bare bones CSV parsing with no_std support.")
     (license (list license:unlicense license:expat))))
 
+(define-public rust-ctor-0.1
+  (package
+    (name "rust-ctor")
+    (version "0.1.13")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ctor" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1qgwkwyxishpp3wkbwq5i27zdxz539ii0sz129xj061ffnnfbia7"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))
+       ;#:cargo-development-inputs
+       ;(("rust-libc-print" ,rust-libc-print-0.1))
+       ))
+    (home-page "https://github.com/mmastrac/rust-ctor")
+    (synopsis "__attribute__((constructor)) for Rust")
+    (description
+     "This package provides an @code{__attribute__((constructor))} for Rust.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-ctrlc-3.1
   (package
     (name "rust-ctrlc")
@@ -3862,6 +4434,43 @@ hexadecimal, base32, and base64.")
 and arithmetic.")
     (license license:expat)))
 
+(define-public rust-dav1d-sys-0.3
+  (package
+    (name "rust-dav1d-sys")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "dav1d-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1022czzp3s54r42x6rhr870w1fwzyp7b6qn0zirpz55zmqjpgnwa"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-pkg-config" ,rust-pkg-config-0.3)
+        ("rust-bindgen" ,rust-bindgen-0.52)
+        ("rust-metadeps" ,rust-metadeps-1.1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-environmental-variable
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((clang (assoc-ref inputs "libclang")))
+               (setenv "LIBCLANG_PATH"
+                       (string-append clang "/lib")))
+             #t)))))
+    (inputs
+     `(("dav1d" ,dav1d)
+       ("pkg-config" ,pkg-config)
+       ("libclang" ,clang)
+       ("llvm" ,llvm)))
+    (home-page "https://github.com/rust-av/dav1d-rs")
+    (synopsis "FFI bindings to dav1d")
+    (description "FFI bindings to dav1d")
+    (license license:expat)))
+
 (define-public rust-decimal-2.0
   (package
     (name "rust-decimal")
@@ -4109,7 +4718,7 @@ Windows, and the Standard Directory guidelines on macOS.")
   (package
     (inherit rust-dirs-2.0)
     (name "rust-dirs")
-    (version "1.0.3")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -4117,11 +4726,12 @@ Windows, and the Standard Directory guidelines on macOS.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "02vigc566z5i6n9wr2x8sch39qp4arn89xhhrh18fhpm3jfc0ygn"))))
+          "009rrhzj9pxyncmm2vhlj70npg0cgggv2hjbbkiwdl9vccq8kmrz"))))
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
+        ("rust-redox-users" ,rust-redox-users-0.3)
         ("rust-winapi" ,rust-winapi-0.3))))))
 
 (define-public rust-dirs-sys-0.3
@@ -4348,6 +4958,29 @@ from macros.")
 parameters, associated types, and type constraints.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-draw-state-0.8
+  (package
+    (name "rust-draw-state")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "draw_state" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0lfng4fz9x7bwsmzv9r20ply10w0iid6vfcrhx292s6hw8vrbkrk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-serde" ,rust-serde-1.0)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "https://github.com/gfx-rs/draw_state")
+    (synopsis "Graphics state blocks for gfx-rs")
+    (description "Graphics state blocks for gfx-rs.")
+    (license license:asl2.0)))
+
 (define-public rust-dtoa-0.4
   (package
     (name "rust-dtoa")
@@ -4494,7 +5127,7 @@ floating-point primitives to an @code{io::Write}.")
 (define-public rust-either-1.5
   (package
     (name "rust-either")
-    (version "1.5.2")
+    (version "1.5.3")
     (source
      (origin
        (method url-fetch)
@@ -4503,7 +5136,7 @@ floating-point primitives to an @code{io::Write}.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0yyggfd5yq9hyyp0bd5jj0fgz3rwws42d19ri0znxwwqs3hcy9sm"))))
+         "1qyz1b1acad6w0k5928jw5zaq900zhsk7p8dlcp4hh61w4f6n7xv"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -4545,7 +5178,7 @@ inclusion of Windows resources in the most resilient fashion imaginable.")
 (define-public rust-encode-unicode-0.3
   (package
     (name "rust-encode-unicode")
-    (version "0.3.5")
+    (version "0.3.6")
     (source
      (origin
        (method url-fetch)
@@ -4554,12 +5187,12 @@ inclusion of Windows resources in the most resilient fashion imaginable.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1g8a8pixkxz6r927f4sc4r15qyc0szxdxb1732v8q7h0di4wkclh"))))
+         "07w3vzrhxh9lpjgsg2y5bwzfar2aq35mdznvcp3zjl0ssj7d4mx3"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-ascii" ,rust-ascii-0.9)
+       (("rust-ascii" ,rust-ascii-1.0)
         ("rust-clippy" ,rust-clippy-0.0))
        #:cargo-development-inputs
        (("rust-lazy-static" ,rust-lazy-static-1))))
@@ -4946,7 +5579,7 @@ is configured via an environment variable.")
 (define-public rust-erased-serde-0.3
   (package
     (name "rust-erased-serde")
-    (version "0.3.9")
+    (version "0.3.11")
     (source
      (origin
        (method url-fetch)
@@ -4955,14 +5588,14 @@ is configured via an environment variable.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0q7bnxs5zskfq5iillig55g7891dllcxh2p8y8k1p2j72syf9viv"))))
+         "1lgkpkk7nx6f24gmr3psyj8d2avc9701r9jyw1i4ssp10lbnv2yq"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-serde" ,rust-serde-1.0))
        #:cargo-development-inputs
-       (("rust-serde-cbor" ,rust-serde-cbor-0.10)
+       (;("rust-serde-cbor" ,rust-serde-cbor-0.9)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
         ("rust-serde-json" ,rust-serde-json-1.0))))
     (home-page "https://github.com/dtolnay/erased-serde")
@@ -4971,6 +5604,37 @@ is configured via an environment variable.")
      "Type-erased Serialize and Serializer traits.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-err-derive-0.2
+  (package
+    (name "rust-err-derive")
+    (version "0.2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "err-derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0v6wxrshfpg7mwaxzq8jwxbfiyn7zk5rlm4m8kkrwh7dpf8nrx42"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-synstructure" ,rust-synstructure-0.12)
+        ("rust-skeptic" ,rust-skeptic-0.13)
+        ("rust-proc-macro-error" ,rust-proc-macro-error-0.4)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-rustversion" ,rust-rustversion-1.0)
+        ("rust-quote" ,rust-quote-1.0))
+       #:cargo-development-inputs
+       (("rust-skeptic" ,rust-skeptic-0.13))))
+    (home-page "https://gitlab.com/torkleyy/err-derive")
+    (synopsis "Derive macro for `std::error::Error`")
+    (description
+     "Derive macro for @code{std::error::Error}.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-errno-0.2
   (package
     (name "rust-errno")
@@ -5025,7 +5689,7 @@ is configured via an environment variable.")
 (define-public rust-error-chain-0.12
   (package
     (name "rust-error-chain")
-    (version "0.12.1")
+    (version "0.12.2")
     (source
      (origin
        (method url-fetch)
@@ -5034,23 +5698,60 @@ is configured via an environment variable.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1ndpw1ny2kxqpw6k1shq8k56z4vfpk4xz9zr8ay988k0rffrxd1s"))))
+         "1ka5y0fmymxzx3gz2yrd7rpz2i555m1iw4fpmcggpzcgr1n10wfk"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-backtrace" ,rust-backtrace-0.3)
-        ("rust-version-check" ,rust-version-check-0.1))))
+        ("rust-version-check" ,rust-version-check-0.9))))
     (home-page "https://github.com/rust-lang-nursery/error-chain")
     (synopsis "Yet another error boilerplate library")
     (description
      "Yet another error boilerplate library.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-error-chain-0.11
+  (package
+    (inherit rust-error-chain-0.12)
+    (name "rust-error-chain")
+    (version "0.11.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "error-chain" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1wykkr0naizbkwxjwia1rch8xhwvgij9khqvjzs07mrmqifislgz"))))
+    (arguments
+     `(#:tests? #f      ; Not all test files included.
+       #:cargo-inputs
+       (("rust-backtrace" ,rust-backtrace-0.3))))))
+
+(define-public rust-error-chain-0.10
+  (package
+    (inherit rust-error-chain-0.11)
+    (name "rust-error-chain")
+    (version "0.10.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "error-chain" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1y1gyj9g5c3k1nzkvxrgry8v9k86kcc585mczrm3qz019s35shyr"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-backtrace" ,rust-backtrace-0.3))))))
+
 (define-public rust-euclid-0.20
   (package
     (name "rust-euclid")
-    (version "0.20.7")
+    (version "0.20.10")
     (source
      (origin
        (method url-fetch)
@@ -5059,7 +5760,7 @@ is configured via an environment variable.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0pa8kxblvc0s9gia9n0966w7169aswpg7knw2pmwrqa204r2v19z"))))
+         "0c3hbl0kvc53k6nws0v9d46hi0giza1j079sqx2bgl4wfw65nshc"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -5127,7 +5828,7 @@ is configured via an environment variable.")
 (define-public rust-failure-0.1
   (package
     (name "rust-failure")
-    (version "0.1.5")
+    (version "0.1.7")
     (source
      (origin
        (method url-fetch)
@@ -5136,7 +5837,7 @@ is configured via an environment variable.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1qppmgv4i5jj6vrss91qackqnl0a12h7lnby4l7j5fdy78yxhnvr"))))
+         "0js6i6mb42q1g6q3csfbmi6q40s64k96705xbim0d8zg44j9qlmq"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -5152,7 +5853,7 @@ is configured via an environment variable.")
 (define-public rust-failure-derive-0.1
   (package
     (name "rust-failure-derive")
-    (version "0.1.5")
+    (version "0.1.7")
     (source
      (origin
        (method url-fetch)
@@ -5161,15 +5862,15 @@ is configured via an environment variable.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1q97n7dp51j5hndzic9ng2fgn6f3z5ya1992w84l7vypby8n647a"))))
+         "0cfjz0c9szqpxn43b2r722p6m3swzxj7aj6xhqw23ml7h8y762h3"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-proc-macro2" ,rust-proc-macro2-0.4)
-        ("rust-quote" ,rust-quote-0.6)
-        ("rust-syn" ,rust-syn-0.15)
-        ("rust-synstructure" ,rust-synstructure-0.10))
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-quote" ,rust-quote-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-synstructure" ,rust-synstructure-0.12))
        #:cargo-development-inputs
        (("rust-failure" ,rust-failure-0.1))))
     (home-page "https://rust-lang-nursery.github.io/failure/")
@@ -5190,7 +5891,6 @@ is configured via an environment variable.")
          (base32
           "1xq759lsr8gqss7hva42azn3whgrbrs2sd9xpn92c5ickxm1fhs4"))))
     (build-system cargo-build-system)
-    (arguments '(#:skip-build? #t))
     (home-page "https://github.com/sfackler/rust-fallible-iterator")
     (synopsis "Fallible iterator traits")
     (description "If the @code{std} or @code{alloc} features are enabled, this
@@ -5200,6 +5900,38 @@ provides implementations for @code{HashMap} and @code{HashSet}.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-fern-0.5
+  (package
+    (name "rust-fern")
+    (version "0.5.9")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fern" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1anslk0hx9an4ypcaxqff080hgbcxm7ji7d4qf4f6qx1mkav16p6"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-reopen" ,rust-reopen-0.3)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-colored" ,rust-colored-1.9)
+        ("rust-syslog" ,rust-syslog-3.3)
+        ("rust-syslog" ,rust-syslog-4.0))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-tempdir" ,rust-tempdir-0.3))))
+    (home-page "https://github.com/daboross/fern")
+    (synopsis "Simple, efficient logging")
+    (description
+     "This package provides a simple, efficient logging system for Rust.")
+    (license license:expat)))
+
 (define-public rust-filetime-0.2
   (package
     (name "rust-filetime")
@@ -5334,7 +6066,7 @@ cross platform API.")
 (define-public rust-flate2-1.0
   (package
     (name "rust-flate2")
-    (version "1.0.9")
+    (version "1.0.14")
     (source
      (origin
        (method url-fetch)
@@ -5343,22 +6075,25 @@ cross platform API.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1n639gc7sbmrkir6pif608xqpwcv60kigmp5cn9x7m8892nk82am"))))
+         "0hlb2zmn5ixrgr0i1qvrd3a7j4fpp002d0kddn2hm7hjj49z9zrc"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-crc32fast" ,rust-crc32fast-1.2)
+       (("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-cloudflare-zlib-sys"
+         ,rust-cloudflare-zlib-sys-0.2)
+        ("rust-crc32fast" ,rust-crc32fast-1.2)
         ("rust-futures" ,rust-futures-0.1)
         ("rust-libc" ,rust-libc-0.2)
         ("rust-libz-sys" ,rust-libz-sys-1.0)
         ("rust-miniz-sys" ,rust-miniz-sys-0.1)
-        ("rust-miniz-oxide-c-api" ,rust-miniz-oxide-c-api-0.2)
+        ("rust-miniz-oxide" ,rust-miniz-oxide-0.3)
         ("rust-tokio-io" ,rust-tokio-io-0.1))
        #:cargo-development-inputs
        (("rust-futures" ,rust-futures-0.1)
-        ("rust-quickcheck" ,rust-quickcheck-0.8)
-        ("rust-rand" ,rust-rand-0.4)
+        ("rust-quickcheck" ,rust-quickcheck-0.9)
+        ("rust-rand" ,rust-rand-0.7)
         ("rust-tokio-io" ,rust-tokio-io-0.1)
         ("rust-tokio-tcp" ,rust-tokio-tcp-0.1)
         ("rust-tokio-threadpool" ,rust-tokio-threadpool-0.1))))
@@ -5454,6 +6189,48 @@ implementation that is more efficient for smaller hash keys.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-font-kit-0.4
+  (package
+    (name "rust-font-kit")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "font-kit" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1fmg1jmqdvsjxjbyz8chpx1mhp544mwq128ns1shhrha5a6zzdqp"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-lyon-path" ,rust-lyon-path-0.14)
+        ("rust-core-graphics" ,rust-core-graphics-0.17)
+        ("rust-float-ord" ,rust-float-ord-0.2)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-euclid" ,rust-euclid-0.20)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-servo-fontconfig"
+         ,rust-servo-fontconfig-0.4)
+        ("rust-freetype" ,rust-freetype-0.4)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-core-foundation"
+         ,rust-core-foundation-0.6)
+        ("rust-memmap" ,rust-memmap-0.7)
+        ("rust-dwrote" ,rust-dwrote-0.9)
+        ("rust-dirs" ,rust-dirs-1.0)
+        ("rust-byteorder" ,rust-byteorder-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-core-text" ,rust-core-text-13)
+        ("rust-walkdir" ,rust-walkdir-2.3))))
+    (home-page "https://github.com/servo/font-kit")
+    (synopsis "Cross-platform font loading library")
+    (description
+     "This package provides a cross-platform font loading library.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-foreign-types-0.5
   (package
     (name "rust-foreign-types")
@@ -5606,6 +6383,31 @@ implementation that is more efficient for smaller hash keys.")
 values to other threads.")
     (license license:asl2.0)))
 
+(define-public rust-freetype-0.4
+  (package
+    (name "rust-freetype")
+    (version "0.4.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "freetype" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0a70x03n68997f08bi3n47q9wyi3pv5s9v4rjc79sihb84mnp4hi"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-servo-freetype-sys" ,rust-servo-freetype-sys-4))))
+    (home-page "https://github.com/servo/rust-freetype")
+    (synopsis "Bindings for Freetype used by Servo")
+    (description
+     "Bindings for Freetype used by Servo.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-freetype-rs-0.23
   (package
     (name "rust-freetype-rs")
@@ -5764,6 +6566,31 @@ for file changes notifications")
 macOS API for file changes notifications")
     (license license:expat)))
 
+(define-public rust-fst-0.4
+  (package
+    (name "rust-fst")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fst" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ybmdzkknhv1wx6ws86iyixfyzc04l4nm71b9va7953r1m3i6z1z"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-utf8-ranges" ,rust-utf8-ranges-1.0))))
+    (home-page "https://github.com/BurntSushi/fst")
+    (synopsis "Represent sets or maps of large numbers of strings.")
+    (description
+     "Use finite state transducers to compactly represent sets or maps of many
+strings (> 1 billion is possible).")
+    (license (list license:unlicense license:expat))))
+
 (define-public rust-fuchsia-cprng-0.1
   (package
     (name "rust-fuchsia-cprng")
@@ -6616,7 +7443,7 @@ API library @code{gdi32}.")
 (define-public rust-getrandom-0.1
   (package
     (name "rust-getrandom")
-    (version "0.1.6")
+    (version "0.1.14")
     (source
      (origin
        (method url-fetch)
@@ -6625,16 +7452,19 @@ API library @code{gdi32}.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0macrjfkgsjn6ikr94agapp4fkxmr8w7y2g7qis4icc4a17cwp76"))))
+         "1sq30li71h19rhnhs1h6576ja68insajx8wvh1nn088r8pc8vg3s"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-lazy-static" ,rust-lazy-static-1)
+       (("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-compiler-builtins" ,rust-compiler-builtins-0.1)
+        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
         ("rust-libc" ,rust-libc-0.2)
         ("rust-log" ,rust-log-0.4)
         ("rust-stdweb" ,rust-stdweb-0.4)
-        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2))))
+        ("rust-wasi" ,rust-wasi-0.9)
+        ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0))))
     (home-page "https://github.com/rust-random/getrandom")
     (synopsis "Retrieve random data from system source")
     (description
@@ -6642,6 +7472,109 @@ API library @code{gdi32}.")
 retrieving random data from system source.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-gfx-0.18
+  (package
+    (name "rust-gfx")
+    (version "0.18.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfx" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0nqmxqi3x4ni0g78g77a6aldrv8cfvzhnpqhxyd2ap4aa3wldph1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-mint" ,rust-mint-0.5)
+        ("rust-draw-state" ,rust-draw-state-0.8)
+        ("rust-gfx-core" ,rust-gfx-core-0.9))))
+    (home-page "https://github.com/gfx-rs/gfx")
+    (synopsis "High-performance, bindless graphics API")
+    (description
+     "This package provides a high-performance, bindless graphics API.")
+    (license license:asl2.0)))
+
+(define-public rust-gfx-core-0.9
+  (package
+    (name "rust-gfx-core")
+    (version "0.9.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfx_core" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0haldr99n12d90vqgvl77n59hywlklhdff85j2aljaz1yapdvyvm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-mint" ,rust-mint-0.5)
+        ("rust-draw-state" ,rust-draw-state-0.8)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "https://github.com/gfx-rs/gfx")
+    (synopsis "Core library of Gfx-rs")
+    (description "This package is a core library of Gfx-rs.")
+    (license license:asl2.0)))
+
+(define-public rust-gfx-device-gl-0.16
+  (package
+    (name "rust-gfx-device-gl")
+    (version "0.16.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfx_device_gl" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1g5yg19jvxdmviljyakhd6253bnb2qg7v8iscf48ihc0ldgki70h"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-gfx-gl" ,rust-gfx-gl-0.6)
+        ("rust-gfx-core" ,rust-gfx-core-0.9))))
+    (home-page "https://github.com/gfx-rs/gfx")
+    (synopsis "OpenGL backend for gfx-rs")
+    (description "This package provides the openGL backend for gfx-rs.")
+    (license license:asl2.0)))
+
+(define-public rust-gfx-gl-0.6
+  (package
+    (name "rust-gfx-gl")
+    (version "0.6.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfx_gl" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ppzj4bgjawdqz3fvnscqk8lnmgh95pwzh0v96vwy809cxj83lzj"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gl-generator" ,rust-gl-generator-0.14))))
+    (home-page "https://github.com/gfx-rs/gfx_gl")
+    (synopsis "OpenGL bindings for gfx, based on gl-rs")
+    (description
+     "This package provides OpenGL bindings for gfx, based on gl-rs.")
+    (license license:asl2.0)))
+
 (define-public rust-gif-0.10
   (package
     (name "rust-gif")
@@ -6669,6 +7602,37 @@ retrieving random data from system source.")
     (description "This package provides a GIF decoder and encoder in Rust.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-gimli-0.20
+  (package
+    (name "rust-gimli")
+    (version "0.20.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gimli" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0cz6wg1niwfqf0mk28igsdnsm92cs57cai9jpzdmvw6hma863pc1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-fallible-iterator"
+         ,rust-fallible-iterator-0.2)
+        ("rust-arrayvec" ,rust-arrayvec-0.5)
+        ("rust-stable-deref-trait"
+         ,rust-stable-deref-trait-1.1)
+        ("rust-smallvec" ,rust-smallvec-1)
+        ("rust-indexmap" ,rust-indexmap-1.3)
+        ("rust-byteorder" ,rust-byteorder-1.3))))
+    (home-page "https://github.com/gimli-rs/gimli")
+    (synopsis "Library for reading and writing the DWARF debugging format")
+    (description
+     "This package provides a library for reading and writing the DWARF debugging format.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-gimli-0.18
   (package
     (name "rust-gimli")
@@ -6868,6 +7832,29 @@ reading and writing git repositories.")
         ("rust-thread-id" ,rust-thread-id-3.3)
         ("rust-time" ,rust-time-0.1))))))
 
+(define-public rust-gl-0.11
+  (package
+    (name "rust-gl")
+    (version "0.11.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gl" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1wcqpyhck0xriffkmgmldy33lwk2044hb4l02d44vm4fbvicin6p"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gl-generator" ,rust-gl-generator-0.10))))
+    (home-page "https://github.com/brendanzab/gl-rs/")
+    (synopsis "OpenGL bindings for rust")
+    (description "This package provides OpenGL bindings for rust.")
+    (license license:asl2.0)))
+
 (define-public rust-gl-generator-0.14
   (package
     (name "rust-gl-generator")
@@ -6923,6 +7910,33 @@ reading and writing git repositories.")
        (base32
         "1gdchvay0k0g931b2ki33mkfixcw4radk5b8sqsm29rahxg3v8ir"))))))
 
+(define-public rust-gl-generator-0.10
+  (package
+    (name "rust-gl-generator")
+    (version "0.10.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gl_generator" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0146yd4i9wbgfrhnkc04w7n7civbanznc0q87skp6v7p7hbszzx0"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-xml-rs" ,rust-xml-rs-0.8)
+        ("rust-khronos-api" ,rust-khronos-api-3))))
+    (home-page "https://github.com/brendanzab/gl-rs/")
+    (synopsis
+     "Code generators for creating bindings to the Khronos OpenGL APIs")
+    (description
+     "Code generators for creating bindings to the Khronos OpenGL APIs.")
+    (license license:asl2.0)))
+
 (define-public rust-gleam-0.6
   (package
     (name "rust-gleam")
@@ -7365,6 +8379,53 @@ path simultaneously, and returning all of the globs that matched.")
     (description "This package provides FFI bindings to libgobject-2.0.")
     (license license:expat)))
 
+(define-public rust-goblin-0.2
+  (package
+    (name "rust-goblin")
+    (version "0.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "goblin" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1j38fkqadbsjxawr3wnj9m0qaihcwp6pmfakmhsar881509y7mfx"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-scroll" ,rust-scroll-0.10)
+        ("rust-plain" ,rust-plain-0.2)
+        ("rust-log" ,rust-log-0.4))))
+    (home-page "https://github.com/m4b/goblin")
+    (synopsis "ELF, Mach-o, and PE binary parsing and loading crate")
+    (description "This package provides an ELF, Mach-o, and PE binary parsing
+and loading crate.")
+    (license license:expat)))
+
+(define-public rust-goblin-0.1
+  (package
+    (inherit rust-goblin-0.2)
+    (name "rust-goblin")
+    (version "0.1.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "goblin" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nn0aa2jf207gbyccxnrzm7n217di025z5y1ybblp7nkk11j309h"))))
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-scroll" ,rust-scroll-0.10)
+        ("rust-plain" ,rust-plain-0.2)
+        ("rust-log" ,rust-log-0.4))))))
+
 (define-public rust-goblin-0.0
   (package
     (name "rust-goblin")
@@ -7845,7 +8906,7 @@ consistent, and reasonably well performing.")
 (define-public rust-hermit-abi-0.1
   (package
     (name "rust-hermit-abi")
-    (version "0.1.6")
+    (version "0.1.10")
     (source
       (origin
         (method url-fetch)
@@ -7854,7 +8915,7 @@ consistent, and reasonably well performing.")
          (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-         "0wippj5nkw9q5yyyaqpdrgdhag3l3nbrwja7149cwn7ii1nnbwpg"))))
+          "0blmmzik5cs79ivq70s9gal8ypgzj50wnl2hwsaam46gjjbz2p3j"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -8364,6 +9425,38 @@ for the most common image formats.")
         ("rust-num-complex" ,rust-num-complex-0.2)
         ("rust-quickcheck" ,rust-quickcheck-0.6))))))
 
+(define-public rust-indexmap-1.3
+  (package
+    (name "rust-indexmap")
+    (version "1.3.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "indexmap" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "14i2gmq9pwaafvlxmsc12j6539hjgqk4j4jz40fz763vbcn08vq7"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-autocfg" ,rust-autocfg-1.0)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-rayon" ,rust-rayon-1.3))))
+    (home-page "https://github.com/bluss/indexmap")
+    (synopsis "Hash table with consistent order and fast iteration.")
+    (description
+     "This package provides a hash table with consistent order and fast iteration.
+
+The indexmap is a hash table where the iteration order of the key-value
+pairs is independent of the hash values of the keys.  It has the usual
+hash table functionality, it preserves insertion order except after
+removals, and it allows lookup of its elements by either hash table key
+or numerical index.  A corresponding hash set type is also provided.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-indexmap-1.0
   (package
     (name "rust-indexmap")
@@ -8546,6 +9639,53 @@ in Rust.")
 that works on WASM too.")
     (license license:bsd-3)))
 
+(define-public rust-interpolate-name-0.2
+  (package
+    (name "rust-interpolate-name")
+    (version "0.2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "interpolate_name" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05vzsiqb69d1mbpaphcg4ifjsjs6g03b8pacskfcydqhh555zcxl"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/lu-zero/interpolate_name")
+    (synopsis "Simple procedural macro attribute for repetitive tests")
+    (description
+     "Simple procedural macro attribute for repetitive tests.")
+    (license license:expat)))
+
+(define-public rust-interpolation-0.2
+  (package
+    (name "rust-interpolation")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "interpolation" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "00icvvgc72zdgyrwwg2p0wad4hry4d2vd6l9iqpyjpmw5dykbdyk"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page "https://github.com/pistondevelopers/interpolation")
+    (synopsis "Library for interpolation")
+    (description
+     "This package provides a library for interpolation.")
+    (license license:expat)))
+
 (define-public rust-intervaltree-0.2
   (package
     (name "rust-intervaltree")
@@ -8620,7 +9760,7 @@ immutable interval tree.")
 (define-public rust-itertools-0.8
   (package
     (name "rust-itertools")
-    (version "0.8.0")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
@@ -8629,7 +9769,7 @@ immutable interval tree.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0n2k13b6w4x2x6np2lykh9bj3b3z4hwh2r4cn3z2dgnfq7cng12v"))))
+         "1154j48aw913v5jnyhpxialxhdn2sfpl4d7bwididyb1r05jsspm"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -8637,8 +9777,8 @@ immutable interval tree.")
        (("rust-either" ,rust-either-1.5))
        #:cargo-development-inputs
        (("rust-permutohedron" ,rust-permutohedron-0.2)
-        ("rust-quickcheck" ,rust-quickcheck-0.8)
-        ("rust-rand" ,rust-rand-0.4))))
+        ("rust-quickcheck" ,rust-quickcheck-0.7)
+        ("rust-rand" ,rust-rand-0.6))))
     (home-page
      "https://github.com/rust-itertools/itertools")
     (synopsis
@@ -8700,7 +9840,7 @@ and functions.")
 (define-public rust-itoa-0.4
   (package
     (name "rust-itoa")
-    (version "0.4.4")
+    (version "0.4.5")
     (source
       (origin
         (method url-fetch)
@@ -8708,7 +9848,7 @@ and functions.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0zvg2d9qv3avhf3d8ggglh6fdyw8kkwqg3r4622ly5yhxnvnc4jh"))))
+          "13nxqrfnh83a7x5rw4wq2ilp8nxvwy74dxzysdg59dbxqk0agdxq"))))
     (build-system cargo-build-system)
     (home-page "https://github.com/dtolnay/itoa")
     (synopsis "Fast functions for printing integer primitives")
@@ -8746,6 +9886,29 @@ primitives to an @code{io::Write}.")
         (base32
          "18g7p2hrb3dk84z3frfgmszfc9hjb4ps9vp99qlb1kmf9gm8hc5f"))))))
 
+(define-public rust-ivf-0.1
+  (package
+    (name "rust-ivf")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ivf" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1wfjf3rilqavrhvwagzinvng9dg28wcjk3c6c6p5qmc1xy65qfh1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-bitstream-io" ,rust-bitstream-io-0.8))))
+    (home-page "https://github.com/xiph/rav1e")
+    (synopsis "Simple ivf muxer")
+    (description "This package provides a simple ivf muxer.")
+    (license license:bsd-2)))
+
 (define-public rust-jemalloc-sys-0.3
   (package
     (name "rust-jemalloc-sys")
@@ -8919,7 +10082,7 @@ primitives to an @code{io::Write}.")
 (define-public rust-js-sys-0.3
   (package
     (name "rust-js-sys")
-    (version "0.3.35")
+    (version "0.3.37")
     (source
      (origin
        (method url-fetch)
@@ -8928,7 +10091,7 @@ primitives to an @code{io::Write}.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1ybwazllkbif71i195dadgrsw64k6l04ggk5yimiy5c2cb1wg2bq"))))
+         "0mbhpbw3zjjl51m24qx3ilq4y8xipm5sfa5hsavaabqs6wsx89va"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -9181,7 +10344,7 @@ requires non-const function calls to be computed.")
 (define-public rust-libc-0.2
   (package
     (name "rust-libc")
-    (version "0.2.66")
+    (version "0.2.68")
     (source
      (origin
        (method url-fetch)
@@ -9189,7 +10352,7 @@ requires non-const function calls to be computed.")
        (file-name (string-append name "-" version ".crate"))
        (sha256
         (base32
-         "0n0mwry21fxfwc063k33mvxk8xj7ia5ar8m42c9ymbam2ksb25fm"))))
+         "1w6z9krcqn7p200sb80dxx76iyvw3jdz949zxr1sgfr3a50c186y"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -9462,6 +10625,30 @@ known as zlib).")
 graphics and video games.")
     (license license:expat)))
 
+(define-public rust-line-wrap-0.1
+  (package
+    (name "rust-line-wrap")
+    (version "0.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "line-wrap" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ffa2whkyh9mwvdlpk6v8pjkg8p8mlzyjfymq5adll9a18sl80zk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-safemem" ,rust-safemem-0.3))))
+    (home-page "https://bitbucket.org/marshallpierce/line-wrap-rs/src")
+    (synopsis "Efficiently insert line separators")
+    (description
+     "Efficiently insert line separators.")
+    (license license:asl2.0)))
+
 (define-public rust-linked-hash-map-0.5
   (package
     (name "rust-linked-hash-map")
@@ -9717,7 +10904,7 @@ by inspecting the system for user preference.")
   (package
     (inherit rust-log-0.4)
     (name "rust-log")
-    (version "0.3.8")
+    (version "0.3.9")
     (source
       (origin
         (method url-fetch)
@@ -9725,7 +10912,10 @@ by inspecting the system for user preference.")
         (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "0nsn28syc49vvjhxcfc8261rd1frhjc0r4bn9v3mqvps3ra7f3w8"))))))
+          "0jq23hhn5h35k7pa8r7wqnsywji6x3wn1q5q7lif5q536if8v7p1"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-log" ,rust-log-0.4))))))
 
 (define-public rust-loom-0.1
   (package
@@ -9780,6 +10970,58 @@ by inspecting the system for user preference.")
      "Colorize paths using the LS_COLORS environment variable.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-lyon-geom-0.14
+  (package
+    (name "rust-lyon-geom")
+    (version "0.14.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "lyon_geom" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "178z4cqqmyw0rsabbgx9phkjxjzcnq0604062lqjlq87k063216a"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-euclid" ,rust-euclid-0.20)
+        ("rust-arrayvec" ,rust-arrayvec-0.4)
+        ("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://github.com/nical/lyon")
+    (synopsis "2D graphics rendering on the GPU using tessellation")
+    (description
+     "This package provides 2D graphics rendering on the GPU using tessellation.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-lyon-path-0.14
+  (package
+    (name "rust-lyon-path")
+    (version "0.14.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "lyon_path" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0qk8x46w0sf6j04l6gvhgn9kr4ymcqkmkh67w8wqahm54jn5gjqb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-lyon-geom" ,rust-lyon-geom-0.14)
+        ("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://github.com/nical/lyon")
+    (synopsis "Types and utilities to store, build and iterate over 2D paths")
+    (description
+     "Types and utilities to store, build and iterate over 2D paths.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-lzma-sys-0.1
   (package
     (name "rust-lzma-sys")
@@ -10082,6 +11324,30 @@ parallelize and optimize.")
         (base32
          "0j2s8aqdkhwhy7awga2bmv5n8qq8bgy8672iha9f3y871dm6vibr"))))))
 
+(define-public rust-memchr-2.3
+  (package
+    (name "rust-memchr")
+    (version "2.3.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "memchr" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0074pvsfl938ndl5js14ibc7i9q0k3zp390z843w8nlyv4bxha1p"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2))))
+    (home-page "https://github.com/BurntSushi/rust-memchr")
+    (synopsis "Safe interface to memchr")
+    (description "The @code{memchr} crate provides heavily optimized routines
+for searching bytes.")
+    (license (list license:unlicense license:expat))))
+
 (define-public rust-memchr-2.2
   (package
     (name "rust-memchr")
@@ -10252,6 +11518,31 @@ for Rust structs.")
          "1cvm2z7dy138s302ii7wlzcxbka5a8yfl5pl5di7lbdnw9hw578g"))))
     (arguments `(#:skip-build? #t))))
 
+(define-public rust-metadeps-1.1
+  (package
+    (name "rust-metadeps")
+    (version "1.1.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "metadeps" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1hjla9ypycqw1snd2qf87cckcc0d5z5qvxpcijn5yrrs3f825cbk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-error-chain" ,rust-error-chain-0.10)
+        ("rust-toml" ,rust-toml-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))))
+    (home-page "https://github.com/joshtriplett/metadeps")
+    (synopsis "Run pkg-config from declarative dependencies in Cargo.toml")
+    (description "Run pkg-config from declarative dependencies in Cargo.toml.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-metal-0.14
   (package
     (name "rust-metal")
@@ -10311,14 +11602,15 @@ for Rust structs.")
 (define-public rust-miniz-oxide-0.3
   (package
     (name "rust-miniz-oxide")
-    (version "0.3.3")
+    (version "0.3.6")
     (source
       (origin
         (method url-fetch)
         (uri (crate-uri "miniz_oxide" version))
         (file-name (string-append name "-" version ".crate"))
         (sha256
-         (base32 "1bmanbbcdmssfbgik3fs323g7vljc5wkjz7s61jsbbz2kg0nckrh"))))
+         (base32
+          "198n4hfpq0qcxf275l6fpzh7b9cl7ck2xs6pjgpds74bazv9yrxa"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -10664,6 +11956,29 @@ checking.")
       "Chaining APIs for both self -> Self and &mut self methods.")
     (license license:expat)))
 
+(define-public rust-nasm-rs-0.1
+  (package
+    (name "rust-nasm-rs")
+    (version "0.1.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "nasm-rs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0r34hiy1pc0aksrfc02zsl0zyw33i9yi7kyx8l214l7nm0mzm97y"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rayon" ,rust-rayon-1.3))))
+    (home-page "https://github.com/medek/nasm-rs")
+    (synopsis "Run NASM during your Cargo build")
+    (description "Run NASM during your Cargo build.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-nalgebra-0.18
   (package
     (name "rust-nalgebra")
@@ -11081,6 +12396,29 @@ combinators library.")
       ;; This is an ancient version and all inputs are optional.
      `(#:skip-build? #t))))
 
+(define-public rust-noop-proc-macro-0.2
+  (package
+    (name "rust-noop-proc-macro")
+    (version "0.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "noop_proc_macro" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "0in1l0rjxzs4fylb6zad484z1c58jxyzchhc12k0cjrvm0y6zwsz"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/lu-zero/noop_proc_macro")
+    (synopsis
+      "No-op proc_macro, literally does nothing")
+    (description
+      "No-op proc_macro, literally does nothing")
+    (license license:expat)))
+
 (define-public rust-notify-4
   (package
     (name "rust-notify")
@@ -11318,6 +12656,31 @@ including bigint, complex, rational, range iterators, generic integers, and more
        #:cargo-development-inputs
        (("rust-doc-comment" ,rust-doc-comment-0.3))))))
 
+(define-public rust-num-derive-0.3
+  (package
+    (name "rust-num-derive")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "num-derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0imprwv8cs01k46g56ajlvc97dp8kz51y2vn6cp9jkw1c6r1b2qc"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/rust-num/num-derive")
+    (synopsis "Numeric syntax extensions")
+    (description "This package provides numeric syntax extensions.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-num-derive-0.2
   (package
     (name "rust-num-derive")
@@ -11671,6 +13034,37 @@ Foundation framework.")
      "This package provides utilities for testing Objective-C interop.")
     (license license:expat)))
 
+(define-public rust-object-0.17
+  (package
+    (name "rust-object")
+    (version "0.17.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "object" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1bmgbg4k0725lchfy9j1wnpfmywh5qhs0k4k6j2g7c0acvys8i7a"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-goblin" ,rust-goblin-0.1)
+        ("rust-target-lexicon" ,rust-target-lexicon-0.10)
+        ("rust-scroll" ,rust-scroll-0.10)
+        ("rust-parity-wasm" ,rust-parity-wasm-0.41)
+        ("rust-uuid" ,rust-uuid-0.8)
+        ("rust-flate2" ,rust-flate2-1.0)
+        ("rust-crc32fast" ,rust-crc32fast-1.2)
+        ("rust-indexmap" ,rust-indexmap-1.3))))
+    (home-page "https://github.com/gimli-rs/object")
+    (synopsis "Unified interface for reading and writing object file formats")
+    (description "This package provides a unified interface for reading and
+writing object file formats.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-object-0.12
   (package
     (name "rust-object")
@@ -11735,6 +13129,67 @@ slices (@code{.find()}, @code{RevSlice}), strings and other things.
 Things in odds may move to more appropriate crates if we find them.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-onig-5.0
+  (package
+    (name "rust-onig")
+    (version "5.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "onig" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ivr0wq1zlyjhhkxpsnmpncg92sjx3rha8pnp3m1mzvgk7y27rz4"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-bitflags" ,rust-bitflags-1)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-onig-sys" ,rust-onig-sys-69.2))))
+    (home-page "http://github.com/iwillspeak/rust-onig")
+    (synopsis
+     "Rust bindings for the Oniguruma regular expression library")
+    (description
+     "Rust-Onig is a set of Rust bindings for the Oniguruma regular expression
+library.  Oniguruma is a modern regex library with support for multiple
+character encodings and regex syntaxes.")
+    (license license:expat)))
+
+(define-public rust-onig-sys-69.2
+  (package
+    (name "rust-onig-sys")
+    (version "69.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "onig_sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0kjijq29yx05xxg9snvqnfn53dl52hchb4sk3zhfr77mypxlx38a"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-pkg-config" ,rust-pkg-config-0.3)
+        ("rust-bindgen" ,rust-bindgen-0.50)
+        ("rust-cc" ,rust-cc-1.0))))
+    (home-page "http://github.com/iwillspeak/rust-onig")
+    (synopsis
+     "Rust bindings to the oniguruma library.")
+    (description
+      "The @code{onig_sys} crate contains raw rust bindings to the oniguruma
+library.  This crate exposes a set of unsafe functions which can then be used by
+other crates to create safe wrappers around Oniguruma.
+You probably don't want to link to this crate directly; instead check out the
+@code{onig} crate.")
+    (license license:expat)))
+
 (define-public rust-once-cell-1.2
   (package
     (name "rust-once-cell")
@@ -11763,6 +13218,27 @@ Things in odds may move to more appropriate crates if we find them.")
      "Single assignment cells and lazy values.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-oorandom-11.1
+  (package
+    (name "rust-oorandom")
+    (version "11.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "oorandom" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "01clxfnz1zwg4maynvbgj09wlkj5m3c8kjqfrp3sqp59qb4wgkpb"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page "https://hg.sr.ht/~icefox/oorandom")
+    (synopsis "A tiny, robust PRNG implementation.")
+    (description
+      "This package provides a tiny, robust PRNG implementation.")
+    (license license:expat)))
+
 (define-public rust-opaque-debug-0.2
   (package
     (name "rust-opaque-debug")
@@ -12088,6 +13564,31 @@ under its new name.")
      "A cross-platform library for opening OS pipes.")
     (license license:expat)))
 
+(define-public rust-output-vt100-0.1
+  (package
+    (name "rust-output-vt100")
+    (version "0.1.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "output_vt100" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ygqplpxz4gg3i8f3rkan2q69pqll7gv65l2mmd8r9dphnvwbkak"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-winapi" ,rust-winapi-0.3))))
+    (home-page "https://github.com/Phundrak/output-vt100-rs")
+    (synopsis
+     "Utility to activate escape codes in Windows' CMD and PowerShell")
+    (description
+     "Utility to activate escape codes in Windows' CMD and PowerShell.")
+    (license license:expat)))
+
 (define-public rust-osmesa-sys-0.1
   (package
     (name "rust-osmesa-sys")
@@ -12187,6 +13688,61 @@ normally prevent moving a type that has been borrowed from.")
       "This package provides a library for padding strings at runtime.")
     (license license:expat)))
 
+(define-public rust-palette-0.5
+  (package
+    (name "rust-palette")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "palette" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0nfc4ycdsx2qgf2wkcpxqxc0vmx7188jjjx3ppgs8qlf8qs06p50"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-approx" ,rust-approx-0.3)
+        ("rust-palette-derive" ,rust-palette-derive-0.5)
+        ("rust-phf" ,rust-phf-0.8)
+        ("rust-phf-codegen" ,rust-phf-codegen-0.8)
+        ("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://github.com/Ogeon/palette")
+    (synopsis "Linear color calculations and conversion")
+    (description
+     "This package makes linear color calculations and conversion accessible.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-palette-derive-0.5
+  (package
+    (name "rust-palette-derive")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "palette_derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1x5icddb877923rpl27bg4cjsf1x0d3layxmgwa3mpb01rh5yjqb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/Ogeon/palette")
+    (synopsis "Automatically implement traits from the palette crate")
+    (description
+     "Automatically implement traits from the palette crate.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-pango-0.7
   (package
     (name "rust-pango")
@@ -12320,6 +13876,28 @@ normally prevent moving a type that has been borrowed from.")
     (description "This package provides FFI bindings to libgtk-3.")
     (license license:expat)))
 
+(define-public rust-parity-wasm-0.41
+  (package
+    (name "rust-parity-wasm")
+    (version "0.41.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "parity-wasm" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "0rfqgjyxrxrfjq5r5n81mdklahl8g4az6yhyyvw25nh0mj6qgz6x"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/paritytech/parity-wasm")
+    (synopsis "WebAssembly low-level format library")
+    (description
+      "WebAssembly low-level format library")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-parity-wasm-0.40
   (package
     (name "rust-parity-wasm")
@@ -12573,7 +14151,7 @@ synchronization primitives.")
 (define-public rust-paste-0.1
   (package
     (name "rust-paste")
-    (version "0.1.7")
+    (version "0.1.10")
     (source
      (origin
        (method url-fetch)
@@ -12582,12 +14160,15 @@ synchronization primitives.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0in0dqar8s16w6gbwyzwvckm80ala02pq87innx1w6yp73kszqb3"))))
+         "0yk4zbi7128dcrklsbwfa63d39x0dv8f7pdbrylvdlcj0s9v2kxb"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-paste-impl" ,rust-paste-impl-0.1)
-        ("rust-proc-macro-hack" ,rust-proc-macro-hack-0.5))))
+        ("rust-proc-macro-hack" ,rust-proc-macro-hack-0.5))
+       #:cargo-development-inputs
+       (("rust-rustversion" ,rust-rustversion-1.0)
+        ("rust-trybuild" ,rust-trybuild-1.0))))
     (home-page "https://github.com/dtolnay/paste")
     (synopsis "Macros for all your token pasting needs")
     (description
@@ -12597,7 +14178,7 @@ synchronization primitives.")
 (define-public rust-paste-impl-0.1
   (package
     (name "rust-paste-impl")
-    (version "0.1.7")
+    (version "0.1.10")
     (source
      (origin
        (method url-fetch)
@@ -12606,7 +14187,7 @@ synchronization primitives.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1fwj11j5lhya5fjr4gfljxfm74ahlr09c8xbb8f22hzpyskw8kbd"))))
+         "12jsm83dnsqnrcabfacnwcxh3h4kykl622vi7glv2wg527hqc956"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -12895,6 +14476,32 @@ algorithm.")
 algorithms.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-phf-0.8
+  (package
+    (name "rust-phf")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "04pyv8bzqvw69rd5dynd5nb85py1hf7wa4ixyhrvdz1l5qin3yrx"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro-hack" ,rust-proc-macro-hack-0.5)
+        ("rust-phf-shared" ,rust-phf-shared-0.8)
+        ("rust-phf-macros" ,rust-phf-macros-0.8))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "Runtime support for perfect hash function data structures")
+    (description "This package provides runtime support for perfect hash
+function data structures.")
+    (license license:expat)))
+
 (define-public rust-phf-0.7
   (package
     (name "rust-phf")
@@ -12920,6 +14527,30 @@ algorithms.")
      "Runtime support for perfect hash function data structures.")
     (license license:expat)))
 
+(define-public rust-phf-codegen-0.8
+  (package
+    (name "rust-phf-codegen")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf_codegen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05d8w7aqqjb6039pfm6404gk5dlwrrf97kiy1n21212vb1hyxzyb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-phf-generator" ,rust-phf-generator-0.8)
+        ("rust-phf-shared" ,rust-phf-shared-0.8))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "Codegen library for PHF types")
+    (description "Codegen library for PHF types.")
+    (license license:expat)))
+
 (define-public rust-phf-codegen-0.7
   (package
     (name "rust-phf-codegen")
@@ -12944,6 +14575,31 @@ algorithms.")
     (description "Codegen library for PHF types.")
     (license license:expat)))
 
+(define-public rust-phf-generator-0.8
+  (package
+    (name "rust-phf-generator")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf_generator" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "09i5338d1kixq6a60fcayz6awgxjlxcfw9ic5f02abbgr067ydhp"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-criterion" ,rust-criterion-0.3)
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-phf-shared" ,rust-phf-shared-0.8))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "PHF generation logic")
+    (description "PHF generation logic.")
+    (license license:expat)))
+
 (define-public rust-phf-generator-0.7
   (package
     (name "rust-phf-generator")
@@ -12967,6 +14623,35 @@ algorithms.")
     (description "PHF generation logic")
     (license license:expat)))
 
+(define-public rust-phf-macros-0.8
+  (package
+    (name "rust-phf-macros")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf_macros" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "170qm6yqn6b9mjlwb2xmm3iad9d5nzwgfawfwy7zr7s2zwcdwvvz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro-hack" ,rust-proc-macro-hack-0.5)
+        ("rust-phf-generator" ,rust-phf-generator-0.8)
+        ("rust-phf-shared" ,rust-phf-shared-0.8)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "Macros to generate types in the phf crate")
+    (description
+     "This package contains macros to generate types in the phf crate.")
+    (license license:expat)))
+
 (define-public rust-phf-macros-0.7
   (package
     (name "rust-phf-macros")
@@ -12999,6 +14684,31 @@ algorithms.")
      "Macros to generate types in the phf crate.")
     (license license:expat)))
 
+(define-public rust-phf-shared-0.8
+  (package
+    (name "rust-phf-shared")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf_shared" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1xssnqrrcn0nr9ayqrnm8xm37ac4xvwcx8pax7jxss7yxawzh360"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-siphasher" ,rust-siphasher-0.3)
+        ("rust-unicase" ,rust-unicase-2.6))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "Support code shared by PHF libraries")
+    (description
+     "This package provides support code shared by PHF libraries.")
+    (license license:expat)))
+
 (define-public rust-phf-shared-0.7
   (package
     (name "rust-phf-shared")
@@ -13062,6 +14772,368 @@ algorithms.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-piston-0.49
+  (package
+    (name "rust-piston")
+    (version "0.49.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1y0rbw92mzagqmwk79wv9axq0m7aid0s0d5cppyzh33wrxhdl3xj"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-pistoncore-input" ,rust-pistoncore-input-0.28)
+        ("rust-pistoncore-window" ,rust-pistoncore-window-0.44)
+        ("rust-pistoncore-event-loop" ,rust-pistoncore-event-loop-0.49))))
+    (home-page "https://github.com/PistonDevelopers/piston")
+    (synopsis "Piston game engine core libraries")
+    (description
+     "The Piston game engine core libraries.")
+    (license license:expat)))
+
+(define-public rust-piston-float-1.0
+  (package
+    (name "rust-piston-float")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-float" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "0r35aasycms79hf2vf1ap40kkp8ywgl4hmfkf762dq8jwd3vw07r"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/pistondevelopers/float")
+    (synopsis
+      "Traits for generic floats in game development")
+    (description
+      "Traits for generic floats in game development")
+    (license license:expat)))
+
+(define-public rust-piston-gfx-texture-0.40
+  (package
+    (name "rust-piston-gfx-texture")
+    (version "0.40.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-gfx_texture" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nr5awdgk3njfvfanszrv4gxz93f6skid1c8yijswccygripchqz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gfx" ,rust-gfx-0.18)
+        ("rust-image" ,rust-image-0.22)
+        ("rust-piston-texture" ,rust-piston-texture-0.8)
+        ("rust-gfx-core" ,rust-gfx-core-0.9))))
+    (home-page "https://github.com/pistondevelopers/gfx_texture")
+    (synopsis
+      "Gfx texture representation that works nicely with Piston libraries")
+    (description "This package provides a Gfx texture representation that works
+nicely with Piston libraries.")
+    (license license:expat)))
+
+(define-public rust-piston-graphics-api-version-0.2
+  (package
+    (name "rust-piston-graphics-api-version")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-graphics_api_version" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1b5p6s45jqv057lpbxkiq3yrdjjhvcynmi2vjf8292rf0yh4hky5"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/PistonDevelopers/graphics_api_version")
+    (synopsis
+      "A library for storing graphics API versions")
+    (description
+      "This package provides a library for storing graphics API versions")
+    (license license:expat)))
+
+(define-public rust-piston-shaders-graphics2d-0.3
+  (package
+    (name "rust-piston-shaders-graphics2d")
+    (version "0.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-shaders_graphics2d" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1dhh9bv4q19gdnj9d1nqq0yrvzs6gcn0c5j1p1f3xzyzq7d1gg4p"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/PistonDevelopers/shaders")
+    (synopsis "Shaders for 2D graphics in Rust")
+    (description "Shaders for 2D graphics in Rust")
+    (license license:expat)))
+
+(define-public rust-piston-texture-0.8
+  (package
+    (name "rust-piston-texture")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-texture" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1pcv5my49b8xzqcb87wqh2ndgvr4s9ipys96s0h9j2plxrj3bjb2"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/pistondevelopers/texture")
+    (synopsis "A generic library for textures")
+    (description
+      "This package provides a generic library for textures")
+    (license license:expat)))
+
+(define-public rust-piston-viewport-1.0
+  (package
+    (name "rust-piston-viewport")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-viewport" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "16378hcy41b7x3zj2z4har0wq6fl4r62kf9p106jjl8hg2dv3aq1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-float" ,rust-piston-float-1.0))))
+    (home-page "https://github.com/PistonDevelopers/viewport")
+    (synopsis "Library for storing viewport information")
+    (description
+     "This package provides a library for storing viewport information.")
+    (license license:expat)))
+
+(define-public rust-piston-window-0.105
+  (package
+    (name "rust-piston-window")
+    (version "0.105.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston_window" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05n2905gkp5ck25kbq95ia6pj1xz63dpp247jz3xcw1d41xpvi95"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gfx-device-gl" ,rust-gfx-device-gl-0.16)
+        ("rust-gfx" ,rust-gfx-0.18)
+        ("rust-piston2d-graphics" ,rust-piston2d-graphics-0.35)
+        ("rust-piston" ,rust-piston-0.49)
+        ("rust-shader-version" ,rust-shader-version-0.6)
+        ("rust-pistoncore-glutin-window" ,rust-pistoncore-glutin-window-0.63)
+        ("rust-piston2d-gfx-graphics" ,rust-piston2d-gfx-graphics-0.66)
+        ("rust-piston-texture" ,rust-piston-texture-0.8))))
+    (home-page "https://github.com/pistondevelopers/piston_window")
+    (synopsis "Official Piston window wrapper for the Piston game engine")
+    (description
+     "The official Piston window wrapper for the Piston game engine.")
+    (license license:expat)))
+
+(define-public rust-piston2d-gfx-graphics-0.66
+  (package
+    (name "rust-piston2d-gfx-graphics")
+    (version "0.66.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston2d-gfx_graphics" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1pmlkf5rl6pr0c1lqm0059xwj9pwlws7gaq9w6r9d916di6fzki1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gfx" ,rust-gfx-0.18)
+        ("rust-piston-shaders-graphics2d" ,rust-piston-shaders-graphics2d-0.3)
+        ("rust-piston-gfx-texture" ,rust-piston-gfx-texture-0.40)
+        ("rust-shader-version" ,rust-shader-version-0.6)
+        ("rust-draw-state" ,rust-draw-state-0.8))))
+    (home-page "https://github.com/PistonDevelopers/gfx_graphics")
+    (synopsis "Gfx 2D back-end for the Piston game engine")
+    (description
+     "This package provides a Gfx 2D back-end for the Piston game engine.")
+    (license license:expat)))
+
+(define-public rust-piston2d-graphics-0.35
+  (package
+    (name "rust-piston2d-graphics")
+    (version "0.35.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston2d-graphics" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1dx2fanxc2pj76hc5l72x0fh4qg9gchjlr8rmbhdk6jpggcmq56g"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-interpolation" ,rust-interpolation-0.2)
+        ("rust-rusttype" ,rust-rusttype-0.7)
+        ("rust-piston-texture" ,rust-piston-texture-0.8)
+        ("rust-piston-viewport" ,rust-piston-viewport-1.0)
+        ("rust-read-color" ,rust-read-color-1.0)
+        ("rust-vecmath" ,rust-vecmath-1.0)
+        ("rust-fnv" ,rust-fnv-1.0))))
+    (home-page "https://github.com/pistondevelopers/graphics")
+    (synopsis "Library for 2D graphics that works with multiple back-ends")
+    (description "This package provides a library for 2D graphics that works
+with multiple back-ends.")
+    (license license:expat)))
+
+(define-public rust-pistoncore-event-loop-0.49
+  (package
+    (name "rust-pistoncore-event-loop")
+    (version "0.49.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pistoncore-event_loop" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h9ij9vx42xg39198yxdlpk842pli5jqm2kwswiv3bqqcji0fwsm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-pistoncore-input" ,rust-pistoncore-input-0.28)
+        ("rust-pistoncore-window" ,rust-pistoncore-window-0.44))))
+    (home-page "https://github.com/PistonDevelopers/piston")
+    (synopsis "Piston event loop for games and interactive applications")
+    (description "This package provides a Piston event loop for games and
+interactive applications.")
+    (license license:expat)))
+
+(define-public rust-pistoncore-glutin-window-0.63
+  (package
+    (name "rust-pistoncore-glutin-window")
+    (version "0.63.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pistoncore-glutin_window" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0dhbyxarv5i742d400bmqdqq3f8c25kcgcg0xavrc18dc913rixc"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gl" ,rust-gl-0.11)
+        ("rust-glutin" ,rust-glutin-0.21)
+        ("rust-pistoncore-input" ,rust-pistoncore-input-0.28)
+        ("rust-pistoncore-window" ,rust-pistoncore-window-0.44)
+        ("rust-shader-version" ,rust-shader-version-0.6))))
+    (home-page "https://github.com/pistondevelopers/glutin_window")
+    (synopsis "Piston window back-end using the Glutin library")
+    (description
+     "This package provides a Piston window back-end using the Glutin library.")
+    (license license:expat)))
+
+(define-public rust-pistoncore-input-0.28
+  (package
+    (name "rust-pistoncore-input")
+    (version "0.28.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pistoncore-input" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1rrcz9px098m3nx98gvrvzirfdp3vg03cblfkcrp4wnvswc0hwq5"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-viewport" ,rust-piston-viewport-1.0)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "https://github.com/PistonDevelopers/piston")
+    (synopsis "Structure for user input")
+    (description
+     "This package provides a structure for user input.")
+    (license license:expat)))
+
+(define-public rust-pistoncore-window-0.44
+  (package
+    (name "rust-pistoncore-window")
+    (version "0.44.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pistoncore-window" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "18qy3nnpb9jczvkiyzzznamck0pzgiyi6073jrkldnci6b3in10q"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-graphics-api-version"
+         ,rust-piston-graphics-api-version-0.2)
+        ("rust-pistoncore-input" ,rust-pistoncore-input-0.28))))
+    (home-page "https://github.com/PistonDevelopers/piston")
+    (synopsis "Library for window abstraction")
+    (description
+     "This package provides a library for window abstraction.")
+    (license license:expat)))
+
 (define-public rust-pkg-config-0.3
   (package
     (name "rust-pkg-config")
@@ -13108,6 +15180,72 @@ used in Cargo build scripts.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-plist-0.4
+  (package
+    (name "rust-plist")
+    (version "0.4.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "plist" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0zqnxc5i4y6mj119vr0lzpb5j67vffpx2phhgh711533bw3ryajz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-line-wrap" ,rust-line-wrap-0.1)
+        ("rust-base64" ,rust-base64-0.10)
+        ("rust-xml-rs" ,rust-xml-rs-0.8)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-humantime" ,rust-humantime-1.3)
+        ("rust-byteorder" ,rust-byteorder-1.3))))
+    (home-page "https://github.com/ebarnard/rust-plist/")
+    (synopsis "Rusty plist parser")
+    (description
+     "This package provides a rusty plist parser.  Supports Serde serialization.")
+    (license license:expat)))
+
+(define-public rust-plotters-0.2
+  (package
+    (name "rust-plotters")
+    (version "0.2.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "plotters" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ssycy9an23vs9hq098c7kl1dvp5ych20d994lhsw9vx4kdbhfsf"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gif" ,rust-gif-0.10)
+        ("rust-piston-window" ,rust-piston-window-0.105)
+        ("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
+        ("rust-image" ,rust-image-0.22)
+        ("rust-js-sys" ,rust-js-sys-0.3)
+        ("rust-web-sys" ,rust-web-sys-0.3)
+        ("rust-font-kit" ,rust-font-kit-0.4)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-palette" ,rust-palette-0.5)
+        ("rust-cairo-rs" ,rust-cairo-rs-0.7)
+        ("rust-rusttype" ,rust-rusttype-0.8)
+        ("rust-lazy-static" ,rust-lazy-static-1))))
+    (home-page "https://github.com/38/plotters")
+    (synopsis "Rust drawing library focus on data plotting")
+    (description
+     "This package provides a Rust drawing library focus on data plotting for
+both WASM and native applications")
+    (license license:expat)))
+
 (define-public rust-plugin-0.2
   (package
     (name "rust-plugin")
@@ -13332,11 +15470,119 @@ for x86.")
 dependency to expose a precomputed hash.")
     (license license:expat)))
 
-;; Cyclic dependencies with rust-demo-hack.
+(define-public rust-pretty-assertions-0.6
+  (package
+    (name "rust-pretty-assertions")
+    (version "0.6.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pretty_assertions" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "09yl14gnmpygiqrdlsa64lcl4w6ydjl9m8jri6kgam0v9rjf309z"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-ctor" ,rust-ctor-0.1)
+        ("rust-output-vt100" ,rust-output-vt100-0.1)
+        ("rust-ansi-term" ,rust-ansi-term-0.11)
+        ("rust-difference" ,rust-difference-2.0))))
+    (home-page "https://github.com/colin-kiegel/rust-pretty-assertions")
+    (synopsis "Drop-in replacements for assert_eq! and assert_ne!")
+    (description
+     "Overwrite @code{assert_eq!} and @code{assert_ne!} with drop-in
+replacements, adding colorful diffs.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-pretty-env-logger-0.3
+  (package
+    (name "rust-pretty-env-logger")
+    (version "0.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pretty_env_logger" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0x4hyjlnvvhyk9m74iypzybm22w3dl2k8img4b956239n5vf8zki"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-env-logger" ,rust-env-logger-0.6))))
+    (home-page "https://github.com/seanmonstar/pretty-env-logger")
+    (synopsis "Visually pretty env_logger")
+    (description "This package provides a visually pretty env_logger.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-proc-macro-error-0.4
+  (package
+    (name "rust-proc-macro-error")
+    (version "0.4.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "proc-macro-error" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1rvpaadwv7vmsp142qqh2axqrr9v78f1nvdsi9nhmfhy10kk1wqq"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:skip-build? #t
+        #:cargo-inputs
+        (("rust-proc-macro-error-attr" ,rust-proc-macro-error-attr-0.4)
+         ("rust-version-check" ,rust-version-check-0.9)
+         ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+         ("rust-syn" ,rust-syn-1.0)
+         ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://gitlab.com/CreepySkeleton/proc-macro-error")
+    (synopsis "Almost drop-in replacement to panics in proc-macros")
+    (description
+     "Almost drop-in replacement to panics in proc-macros.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-proc-macro-error-attr-0.4
+  (package
+    (name "rust-proc-macro-error-attr")
+    (version "0.4.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "proc-macro-error-attr" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1pk9mwcfnpf8favgc2cl4sqlmi818p96hg8pfb51wg5nzmvlnnwa"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-syn-mid" ,rust-syn-mid-0.5)
+        ("rust-version-check" ,rust-version-check-0.9)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://gitlab.com/CreepySkeleton/proc-macro-error")
+    (synopsis "Attribute macro for proc-macro-error crate")
+    (description
+     "Attribute macro for proc-macro-error crate.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-proc-macro-hack-0.5
   (package
     (name "rust-proc-macro-hack")
-    (version "0.5.11")
+    (version "0.5.15")
     (source
      (origin
        (method url-fetch)
@@ -13345,15 +15591,15 @@ dependency to expose a precomputed hash.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1idz5vmnjjhvr51yvwyjb45mza18wa53fr05m1skqvbdyw15gm7c"))))
+         "0qqbfm1byabjkph56r2rlvv4cliz4960j6hav3ljazyjqvkryr8d"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:cargo-inputs
-       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
-        ("rust-quote" ,rust-quote-1.0)
-        ("rust-syn" ,rust-syn-1.0))
-       #:cargo-development-inputs
-       (("rust-demo-hack" ,rust-demo-hack-0.0)
+     `(#:cargo-development-inputs
+       (("rust-quote" ,rust-quote-1.0)
+        ("rust-rustversion" ,rust-rustversion-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-trybuild" ,rust-trybuild-1.0)
+        ("rust-demo-hack" ,rust-demo-hack-0.0)
         ("rust-demo-hack-impl" ,rust-demo-hack-impl-0.0))))
     (home-page "https://github.com/dtolnay/proc-macro-hack")
     (synopsis
@@ -13429,7 +15675,7 @@ dependency to expose a precomputed hash.")
 (define-public rust-proc-macro2-1.0
   (package
     (name "rust-proc-macro2")
-    (version "1.0.8")
+    (version "1.0.10")
     (source
       (origin
         (method url-fetch)
@@ -13437,7 +15683,7 @@ dependency to expose a precomputed hash.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0j45p176fnw0d02dzcky9sxyr4fadiggq07skmblwspqdxy33jrs"))))
+          "1qxbnl8i3a5b2nxb8kdxbq6kj3pd1ckhm35wm7z3jd7n5wlns96z"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -13465,11 +15711,39 @@ in terms of the upstream unstable API.")
          (base32
           "0nd71fl24sys066jrha6j7i34nfkjv44yzw8yww9742wmc8j0gfg"))))
     (arguments
-     `(#:cargo-inputs
+     `(#:tests? #f      ; doc tests fail
+       #:cargo-inputs
        (("rust-unicode-xid" ,rust-unicode-xid-0.1))
        #:cargo-development-inputs
        (("rust-quote" ,rust-quote-0.6))))))
 
+(define-public rust-proc-macro2-0.3
+  (package
+    (name "rust-proc-macro2")
+    (version "0.3.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "proc-macro2" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ryaynnaj39l4zphcg5w8wszndd80vsrv89m5d2293gl6pry41hv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-unicode-xid" ,rust-unicode-xid-0.1))))
+    (home-page "https://github.com/alexcrichton/proc-macro2")
+    (synopsis
+     "Substitute implementation of the compiler's `proc_macro` API")
+    (description
+     "This package provides a substitute implementation of the compiler's
+@code{proc_macro} API to decouple token-based libraries from the procedural
+macro use case.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-procedural-masquerade-0.1
   (package
     (name "rust-procedural-masquerade")
@@ -13617,6 +15891,31 @@ stack pointer and inspect the properties of the stack.")
      "This package provides a pull parser for CommonMark.")
     (license license:expat)))
 
+(define-public rust-pulldown-cmark-0.2
+  (package
+    (name "rust-pulldown-cmark")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pulldown-cmark" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05gfnqa0wzix5m17jrmgj0yyr9sflqm0knn79ndppsnhcan2zxgf"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-getopts" ,rust-getopts-0.2)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "https://github.com/raphlinus/pulldown-cmark")
+    (synopsis "Pull parser for CommonMark")
+    (description
+     "This package provides a pull parser for CommonMark.")
+    (license license:expat)))
+
 (define-public rust-quantiles-0.7
   (package
     (name "rust-quantiles")
@@ -13916,7 +16215,7 @@ integers, floats, tuples, booleans, lists, strings, options and results.")
 (define-public rust-quote-1.0
   (package
     (name "rust-quote")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
       (origin
         (method url-fetch)
@@ -13924,13 +16223,13 @@ integers, floats, tuples, booleans, lists, strings, options and results.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1zkc46ryacf2jdkc6krsy2z615xbk1x8kp1830rcxz3irj5qqfh5"))))
+          "0zwd6fp74xfg4jnnnwj4v84lkzif2giwj4ch1hka9g35ghc6rp1b"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-proc-macro2" ,rust-proc-macro2-1.0))
        #:cargo-development-inputs
-       (("rust-rustversion" ,rust-rustversion-0.1)
+       (("rust-rustversion" ,rust-rustversion-1.0)
         ("rust-trybuild" ,rust-trybuild-1.0))))
     (home-page "https://github.com/dtolnay/quote")
     (synopsis "Quasi-quoting macro quote!(...)")
@@ -13953,6 +16252,25 @@ integers, floats, tuples, booleans, lists, strings, options and results.")
     (arguments
      `(#:cargo-inputs (("rust-proc-macro2" ,rust-proc-macro2-0.4))))))
 
+(define-public rust-quote-0.5
+  (package
+    (inherit rust-quote-0.6)
+    (name "rust-quote")
+    (version "0.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "quote" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1s01fh0jl8qv4xggs85yahw0h507nzrxkjbf7vay3zw8d3kcyjcr"))))
+    (arguments
+      `(#:skip-build? #t
+        #:cargo-inputs
+        (("rust-proc-macro2" ,rust-proc-macro2-0.3))))))
+
 (define-public rust-quote-0.3
   (package
     (inherit rust-quote-0.6)
@@ -14107,7 +16425,7 @@ useful types and distributions, and some randomness-related algorithms.")
 (define-public rust-rand-chacha-0.2
   (package
     (name "rust-rand-chacha")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method url-fetch)
@@ -14116,7 +16434,7 @@ useful types and distributions, and some randomness-related algorithms.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0lv8imzzl4h2glm6sjj8mkvasgi8jym23ya48dakyln7m06sk8h3"))))
+         "00il36fkdbsmpr99p9ksmmp6dn1md7rmnwmz0rr77jbrca2yvj7l"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -14811,6 +17129,29 @@ reference counting.")
 @code{rdrand} and @code{rdseed} instructions")
     (license license:isc)))
 
+(define-public rust-read-color-1.0
+  (package
+    (name "rust-read-color")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "read_color" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1np0pk31ak7hni4hri3m75mbf8py1wdfjshmrj5krbd4p9c8hk4z"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/pistondevelopers/read_color")
+    (synopsis
+      "A simple library for reading hex colors")
+    (description
+      "This package provides a simple library for reading hex colors")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-recycler-0.1
   (package
     (name "rust-recycler")
@@ -14880,7 +17221,7 @@ system calls.")
 (define-public rust-redox-users-0.3
   (package
     (name "rust-redox-users")
-    (version "0.3.1")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
@@ -14889,15 +17230,14 @@ system calls.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0vdn688q9wg997b1x5abx2gf7406rn1lvd62ypcgh1gj7g5dpkjf"))))
+         "0cbl5w16l3bqm22i4vszclf6hzpljxicghmllw7j13az4s9k1ch9"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-failure" ,rust-failure-0.1)
-        ("rust-rand-os" ,rust-rand-os-0.1)
+       (("rust-getrandom" ,rust-getrandom-0.1)
         ("rust-redox-syscall" ,rust-redox-syscall-0.1)
-        ("rust-rust-argon2" ,rust-rust-argon2-0.5))))
+        ("rust-rust-argon2" ,rust-rust-argon2-0.7))))
     (home-page "https://gitlab.redox-os.org/redox-os/users")
     (synopsis "Access Redox users and groups")
     (description
@@ -15000,7 +17340,7 @@ functionality.")
 (define-public rust-regex-1.3
   (package
     (name "rust-regex")
-    (version "1.3.4")
+    (version "1.3.6")
     (source
      (origin
        (method url-fetch)
@@ -15009,12 +17349,12 @@ functionality.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1a1mh9mgr8jipnxdaykla6xlw4a6kjn2bzkq3cifx8xy4ivzjb1j"))))
+         "1cx4lcgy7vdi2kij2n1dp2whl33d7974g1kxwiklhs192nclcsbz"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-aho-corasick" ,rust-aho-corasick-0.7)
-        ("rust-memchr" ,rust-memchr-2.2)
+        ("rust-memchr" ,rust-memchr-2.3)
         ("rust-regex-syntax" ,rust-regex-syntax-0.6)
         ("rust-thread-local" ,rust-thread-local-1.0))
        #:cargo-development-inputs
@@ -15115,7 +17455,7 @@ uses finite automata and guarantees linear time matching on all inputs.")
 (define-public rust-regex-automata-0.1
   (package
     (name "rust-regex-automata")
-    (version "0.1.7")
+    (version "0.1.9")
     (source
      (origin
        (method url-fetch)
@@ -15124,21 +17464,22 @@ uses finite automata and guarantees linear time matching on all inputs.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "11hzn3rz02vdgvx3ykhrbzkvs5c5sm59fyi3xwljn9qc48br5l1y"))))
+         "1r3aqa9c0s9sfrmd2w0mli16ldjzbar0rzb1x7srfjkasrqys7df"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-byteorder" ,rust-byteorder-1.3)
-        ("rust-regex-syntax" ,rust-regex-syntax-0.6)
-        ("rust-utf8-ranges" ,rust-utf8-ranges-1.0))
+       (("rust-fst" ,rust-fst-0.4)
+        ("rust-byteorder" ,rust-byteorder-1.3)
+        ("rust-regex-syntax" ,rust-regex-syntax-0.6))
        #:cargo-development-inputs
-       (("rust-lazy-static" ,rust-lazy-static-1)
+       (("rust-bstr" ,rust-bstr-0.2)
+        ("rust-lazy-static" ,rust-lazy-static-1)
         ("rust-regex" ,rust-regex-1.1)
         ("rust-serde" ,rust-serde-1.0)
         ("rust-serde-bytes" ,rust-serde-bytes-0.11)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
-        ("rust-toml" ,rust-toml-0.5))))
+        ("rust-toml" ,rust-toml-0.5)))) ; 0.4
     (home-page "https://github.com/BurntSushi/regex-automata")
     (synopsis
      "Automata construction and matching using regular expressions")
@@ -15149,7 +17490,7 @@ uses finite automata and guarantees linear time matching on all inputs.")
 (define-public rust-regex-syntax-0.6
   (package
     (name "rust-regex-syntax")
-    (version "0.6.14")
+    (version "0.6.17")
     (source
       (origin
         (method url-fetch)
@@ -15157,7 +17498,7 @@ uses finite automata and guarantees linear time matching on all inputs.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "01myl8xqpbnird23xnsb92sjmz1cmp69r6m7y3dwbpmsx4zzx3dj"))))
+          "1blmlgzcg7in3kcxqabpfzzrbnamr2i671flbrmlqhfps5bvvrbz"))))
     (build-system cargo-build-system)
     (home-page "https://github.com/rust-lang/regex")
     (synopsis "Regular expression parser")
@@ -15230,6 +17571,30 @@ uses finite automata and guarantees linear time matching on all inputs.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-reopen-0.3
+  (package
+    (name "rust-reopen")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "reopen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "12b3mfxkwb8akdfa701nzvqr6lsc6n84vrq088gmjy8lxlmr4an6"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:skip-build? #t
+        #:cargo-inputs
+        (("rust-signal-hook" ,rust-signal-hook-0.1)
+         ("rust-libc" ,rust-libc-0.2))))
+    (home-page "https://github.com/vorner/reopen")
+    (synopsis "File reopening utility")
+    (description "File reopening utility.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-resolv-conf-0.6
   (package
     (name "rust-resolv-conf")
@@ -15284,6 +17649,35 @@ uses finite automata and guarantees linear time matching on all inputs.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-rust-argon2-0.7
+  (package
+    (name "rust-rust-argon2")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rust-argon2" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05xh5wfxgzq3b6jys8r34f3hmqqfs8ylvf934n9z87wfv95szj1b"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-constant-time-eq" ,rust-constant-time-eq-0.1)
+        ("rust-base64" ,rust-base64-0.11)
+        ("rust-blake2b-simd" ,rust-blake2b-simd-0.5)
+        ("rust-crossbeam-utils" ,rust-crossbeam-utils-0.7))))
+    (home-page "https://github.com/sru-systems/rust-argon2")
+    (synopsis
+     "Rust implementation of the Argon2 password hashing function")
+    (description
+     "This package provides a Rust implementation of the Argon2 password
+hashing function.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-rust-argon2-0.5
   (package
     (name "rust-rust-argon2")
@@ -15312,6 +17706,112 @@ uses finite automata and guarantees linear time matching on all inputs.")
 password hashing function.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-rust-hawktracer-0.7
+  (package
+    (name "rust-rust-hawktracer")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rust_hawktracer" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h9an3b73pmhhpzc2kk93nh93lplkvsffysj0rp6rxi7p4lhlj73"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rust-hawktracer-normal-macro"
+         ,rust-rust-hawktracer-normal-macro-0.4)
+        ("rust-rust-hawktracer-proc-macro"
+         ,rust-rust-hawktracer-proc-macro-0.4))))
+    (home-page "https://github.com/AlexEne/rust_hawktracer")
+    (synopsis "Rust bindings for hawktracer profiling library")
+    (description
+     "Rust bindings for hawktracer profiling library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-rust-hawktracer-proc-macro-0.4
+  (package
+    (name "rust-rust-hawktracer-proc-macro")
+    (version "0.4.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rust_hawktracer_proc_macro" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1qfksscfv8rbbzv2zb0i9sbbqmig0dr0vrma3c1kzsfmpsynlqnb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rust-hawktracer-sys" ,rust-rust-hawktracer-sys-0.4))))
+    (home-page "https://github.com/AlexEne/rust_hawktracer_proc_macro")
+    (synopsis
+     "Helper crate for hawktracer profiling library")
+    (description
+     "This package is a helper crate for hawktracer profiling library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-rust-hawktracer-normal-macro-0.4
+  (package
+    (name "rust-rust-hawktracer-normal-macro")
+    (version "0.4.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri
+               "rust_hawktracer_normal_macro"
+               version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1sfjmipdbb5s498c150czr6wihjlkwwgla2jyg3cs7cyjich0mwa"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rust-hawktracer-sys" ,rust-rust-hawktracer-sys-0.4))))
+    (home-page "https://github.com/AlexEne/rust_hawktracer_normal_macro")
+    (synopsis "Helper crate for hawktracer profiling library")
+    (description
+     "This package provides a helper crate for hawktracer profiling library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-rust-hawktracer-sys-0.4
+  (package
+    (name "rust-rust-hawktracer-sys")
+    (version "0.4.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rust_hawktracer_sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "15acrj881y2g7cwsgf1nr22cixrknp8m4x08dkx1an6zf4q8bk37"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-cmake" ,rust-cmake-0.1)
+        ("rust-pkg-config" ,rust-pkg-config-0.3)
+        ("rust-bindgen" ,rust-bindgen-0.37)
+        ("rust-itertools" ,rust-itertools-0.8))))
+    (home-page "https://github.com/AlexEne/rust_hawktracer_sys")
+    (synopsis
+     "Sys crate for the rust_hawktracer library")
+    (description
+     "This package provides a sys crate for the rust_hawktracer library.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-rustc-demangle-0.1
   (package
     (name "rust-rustc-demangle")
@@ -15337,6 +17837,29 @@ password hashing function.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-rustc-hash-1.1
+  (package
+    (name "rust-rustc-hash")
+    (version "1.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rustc-hash" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1qkc5khrmv5pqi5l5ca9p5nl5hs742cagrndhbrlk3dhlrx3zm08"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/rust-lang-nursery/rustc-hash")
+    (synopsis
+      "speed, non-cryptographic hash used in rustc")
+    (description
+      "speed, non-cryptographic hash used in rustc")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-rustc-hash-1.0
   (package
     (name "rust-rustc-hash")
@@ -15728,7 +18251,7 @@ using a fork-like interface.")
 (define-public rust-ryu-1.0
   (package
     (name "rust-ryu")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
       (origin
         (method url-fetch)
@@ -15736,14 +18259,15 @@ using a fork-like interface.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1j0h74f1xqf9hjkhanp8i20mqc1aw35kr1iq9i79q7713mn51a5z"))))
+          "0xlx9ybzncrb7d6r9533g8ydlg6mr252pfzl4g9cqaqkpvk24mjk"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-no-panic" ,rust-no-panic-0.1))
        #:cargo-development-inputs
        (("rust-num-cpus" ,rust-num-cpus-1.11)
-        ("rust-rand" ,rust-rand-0.5))))
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-rand-xorshift" ,rust-rand-xorshift-0.2))))
     (home-page "https://github.com/dtolnay/ryu")
     (synopsis "Fast floating point to string conversion")
     (description
@@ -15820,6 +18344,30 @@ paths point to the same file.")
        #:cargo-development-inputs
        (("rust-rand" ,rust-rand-0.3))))))
 
+(define-public rust-scan-fmt-0.2
+  (package
+    (name "rust-scan-fmt")
+    (version "0.2.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scan_fmt" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1gmaa07z8bkkdv5xhq2lrgml6ri7fqyyrjpiks3phmpmq3p8d0i4"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-regex" ,rust-regex-1.3))))
+    (home-page "https://github.com/wlentz/scan_fmt")
+    (synopsis "Simple scanf()-like input for Rust")
+    (description
+     "This package provides a simple scanf()-like input for Rust")
+    (license license:expat)))
+
 (define-public rust-schannel-0.1
   (package
     (name "rust-schannel")
@@ -15949,6 +18497,31 @@ with one of the implemented strategies.")
          (base32
           "09sy9wbqp409pkwmqni40qmwa99ldqpl48pp95m1xw8sc19qy9cl"))))))
 
+(define-public rust-scroll-0.10
+  (package
+    (name "rust-scroll")
+    (version "0.10.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scroll" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1cbcns8538sqmfnmdbphqy0fd4j8z75z802pvmz3zlwmnln37cmb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-scroll-derive" ,rust-scroll-derive-0.10))))
+    (home-page "https://github.com/m4b/scroll")
+    (synopsis "Endian-aware Read/Write traits for byte buffers")
+    (description
+     "This package provides a suite of powerful, extensible, generic,
+endian-aware Read/Write traits for byte buffers.")
+    (license license:expat)))
+
 (define-public rust-scroll-0.9
   (package
     (name "rust-scroll")
@@ -15978,6 +18551,33 @@ with one of the implemented strategies.")
 endian-aware Read/Write traits for byte buffers.")
     (license license:expat)))
 
+(define-public rust-scroll-derive-0.10
+  (package
+    (name "rust-scroll-derive")
+    (version "0.10.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scroll_derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0a7f0xybi27p1njs4bqmxh9zyb2dqal4dbvgnhjjix4zkgm4wn7q"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/m4b/scroll")
+    (synopsis "Pread and Pwrite traits from the scroll crate")
+    (description
+     "This package provides a macros 1.1 derive implementation for Pread and
+Pwrite traits from the scroll crate.")
+    (license license:expat)))
+
 (define-public rust-scroll-derive-0.9
   (package
     (name "rust-scroll-derive")
@@ -16182,7 +18782,7 @@ proven statistical guarantees.")
 (define-public rust-serde-1.0
   (package
     (name "rust-serde")
-    (version "1.0.104")
+    (version "1.0.105")
     (source
       (origin
         (method url-fetch)
@@ -16190,7 +18790,7 @@ proven statistical guarantees.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0ja4mgw4p42syjk7jkzwhj2yg6llfrfm7vn8rvy7v3c1bzr1aha1"))))
+          "1zrj157dxvmymp5ii60anap2qqks4pkr3fwsp71wi3sv4nzzn1z7"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -16425,7 +19025,7 @@ for the serde framework.")
 (define-public rust-serde-derive-1.0
   (package
     (name "rust-serde-derive")
-    (version "1.0.104")
+    (version "1.0.105")
     (source
       (origin
         (method url-fetch)
@@ -16433,7 +19033,7 @@ for the serde framework.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0r7gjlwfry44b4ylz524ynjp9v3qiwdj4c588lh94aas78q9x3qj"))))
+          "1y5gzwpy8yjv9pwh1js11vr18nfz4gg1g2kmyr6p58hvavy00pdc"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -16480,7 +19080,7 @@ for the serde framework.")
 (define-public rust-serde-json-1.0
   (package
     (name "rust-serde-json")
-    (version "1.0.44")
+    (version "1.0.50")
     (source
       (origin
         (method url-fetch)
@@ -16488,18 +19088,21 @@ for the serde framework.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1mysl675nqhzzkbcrqy4x63cbbsrrx3gcc7k8ydx1gajrkh7bia8"))))
+          "0rs8rsk59kgkgsrw8hyyjrlhas9k1by2jwxxqcz3c2bq2qna39vq"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-indexmap" ,rust-indexmap-1.0)
+       (("rust-indexmap" ,rust-indexmap-1.3)
         ("rust-itoa" ,rust-itoa-0.4)
         ("rust-ryu" ,rust-ryu-1.0)
         ("rust-serde" ,rust-serde-1.0))
        #:cargo-development-inputs
-       (("rust-serde-bytes" ,rust-serde-bytes-0.11)
+       (;("rust-automod" ,rust-automod-0.1)
+        ("rust-rustversion" ,rust-rustversion-1.0)
+        ("rust-serde-bytes" ,rust-serde-bytes-0.11)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ;("rust-serde-stacker" ,rust-serde-stacker-0.1)
         ("rust-trybuild" ,rust-trybuild-1.0))))
     (home-page "https://github.com/serde-rs/json")
     (synopsis "JSON serialization file format")
@@ -16571,7 +19174,7 @@ for the serde framework.")
 (define-public rust-serde-test-1.0
   (package
     (name "rust-serde-test")
-    (version "1.0.101")
+    (version "1.0.105")
     (source
      (origin
        (method url-fetch)
@@ -16580,7 +19183,7 @@ for the serde framework.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0070ycbh47yhxb5vxwa15vi2wpdkw3v1m14v4mjryz1568fqkbsa"))))
+         "1vnp0wld20z1wjr8qp2hxcy6yh2zhicg1mfb0qrzxgwq2a4n6raa"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -16876,6 +19479,32 @@ for the serde framework.")
      "Assembly implementation of SHA-1 compression function.")
     (license license:expat)))
 
+(define-public rust-shader-version-0.6
+  (package
+    (name "rust-shader-version")
+    (version "0.6.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "shader_version" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1yk651xc9irl3pl0rlplypzyzy44d0j03ji0j7hjjdjknwzpi3j7"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-graphics-api-version"
+         ,rust-piston-graphics-api-version-0.2))))
+    (home-page "https://github.com/pistondevelopers/shader_version")
+    (synopsis
+     "Helper library for detecting and picking compatible shaders")
+    (description "This package provides a helper library for detecting and
+picking compatible shaders.")
+    (license license:expat)))
+
 (define-public rust-shared-child-0.3
   (package
     (name "rust-shared-child")
@@ -17097,6 +19726,54 @@ CPUs, as well as raw interfaces to platform-specific instructions.
        #:cargo-development-inputs
        (("rust-cfg-if" ,rust-cfg-if-0.1))))))
 
+(define-public rust-simd-helpers-0.1
+  (package
+    (name "rust-simd-helpers")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "simd_helpers" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "19idqicn9k4vhd04ifh2ff41wvna79zphdf2c81rlmpc7f3hz2cm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/lu-zero/simd_helpers")
+    (synopsis "Helpers to write more compact simd code")
+    (description
+     "This package provides helpers to write more compact simd code.")
+    (license license:expat)))
+
+(define-public rust-siphasher-0.3
+  (package
+    (name "rust-siphasher")
+    (version "0.3.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "siphasher" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "08xvk3yi4vawppm1f81s4zrkksf95psz8gczh36y808candgi24f"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://docs.rs/siphasher")
+    (synopsis "SipHash-2-4, SipHash-1-3 and 128-bit variants in pure Rust")
+    (description "This package provides SipHash-2-4, SipHash-1-3 and 128-bit
+variants in pure Rust.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-siphasher-0.2
   (package
     (name "rust-siphasher")
@@ -17117,6 +19794,37 @@ CPUs, as well as raw interfaces to platform-specific instructions.
      "SipHash functions from rust-core < 1.13.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-skeptic-0.13
+  (package
+    (name "rust-skeptic")
+    (version "0.13.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "skeptic" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0rai61hbs65nbvbhqlk1nap5hlav5qx3zmjjjzh9rhgxagc8xyyn"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-error-chain" ,rust-error-chain-0.12)
+        ("rust-pulldown-cmark" ,rust-pulldown-cmark-0.2)
+        ("rust-glob" ,rust-glob-0.2)
+        ("rust-tempdir" ,rust-tempdir-0.3)
+        ("rust-bytecount" ,rust-bytecount-0.4)
+        ("rust-cargo-metadata" ,rust-cargo-metadata-0.6)
+        ("rust-serde-json" ,rust-serde-json-1.0)
+        ("rust-walkdir" ,rust-walkdir-2.3))))
+    (home-page "https://github.com/budziq/rust-skeptic")
+    (synopsis "Test your Rust markdown documentation via Cargo")
+    (description
+     "Test your Rust markdown documentation via Cargo.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-slab-0.4
   (package
     (name "rust-slab")
@@ -17166,6 +19874,33 @@ data type.")
      "Rust FFI bindings to the SLEEF Vectorized Math Library.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-slog-2.5
+  (package
+    (name "rust-slog")
+    (version "2.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "slog" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "16bv6zrdn1sm315vbnia02g31xvsmbjyz5gv3z0vrgxdli0cdj8w"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-erased-serde" ,rust-erased-serde-0.3))))
+    (home-page "https://github.com/slog-rs/slog")
+    (synopsis "Structured, extensible, composable logging for Rust")
+    (description
+     "This package provides structured, extensible, composable logging for Rust.")
+    (license
+      (list license:mpl2.0
+            license:expat
+            license:asl2.0))))
+
 (define-public rust-slog-2.4
   (package
     (name "rust-slog")
@@ -17936,6 +20671,32 @@ and Jaro-Winkler.")
         (base32
          "0z3zzvmilfldp4xw42qbkjf901dcnbk58igrzsvivydjzd24ry37"))))))
 
+(define-public rust-structopt-0.3
+  (package
+    (name "rust-structopt")
+    (version "0.3.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "structopt" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "178m7wxnjyy9a8a961z74nazjsg79rfv3gv9g3bykfrrjmqs5yn8"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-structopt-derive" ,rust-structopt-derive-0.4)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-clap" ,rust-clap-2))))
+    (home-page "https://github.com/TeXitoi/structopt")
+    (synopsis "Parse command line argument by defining a struct")
+    (description
+     "Parse command line argument by defining a struct.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-structopt-0.2
   (package
     (name "rust-structopt")
@@ -17960,6 +20721,34 @@ and Jaro-Winkler.")
      "Parse command line arguments by defining a struct.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-structopt-derive-0.4
+  (package
+    (name "rust-structopt-derive")
+    (version "0.4.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "structopt-derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0c04bbzc5bmr2ns6qy35yz55nn3xvlq4dpwxdynnljb9ikhvi21z"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-heck" ,rust-heck-0.3)
+        ("rust-proc-macro-error" ,rust-proc-macro-error-0.4)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/TeXitoi/structopt")
+    (synopsis "Parse command line argument by defining a struct, derive crate")
+    (description
+     "Parse command line argument by defining a struct, derive crate.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-structopt-derive-0.2
   (package
     (name "rust-structopt-derive")
@@ -18008,10 +20797,61 @@ and Jaro-Winkler.")
 cryptographic implementations.")
     (license license:bsd-3)))
 
+(define-public rust-sval-0.4
+  (package
+    (name "rust-sval")
+    (version "0.4.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "sval" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1aljggx64481q4wp3wx9hxsfh2bs7d64nqsrwbb2zxcpmdnbn6yk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-sval-derive" ,rust-sval-derive-0.4)
+        ("rust-smallvec" ,rust-smallvec-0.6)
+        ("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://github.com/sval-rs/sval")
+    (synopsis "No-std, object-safe serialization framework")
+    (description
+     "This package provides a no-std, object-safe serialization framework.")
+    (license (list license:asl2.0 license:expat))))
+
+(define-public rust-sval-derive-0.4
+  (package
+    (name "rust-sval-derive")
+    (version "0.4.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "sval_derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "07s7jqsdczsg0wnydfnxyrsj8zyrjmiwl4is1dfgn8dfvyi8n2bj"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/sval-rs/sval")
+    (synopsis "Custom derive for sval")
+    (description "Custom derive for sval.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-syn-1.0
   (package
     (name "rust-syn")
-    (version "1.0.5")
+    (version "1.0.17")
     (source
       (origin
         (method url-fetch)
@@ -18019,12 +20859,28 @@ cryptographic implementations.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1gw03w7lzrlqmp2vislcybikgl5wkhrqi6sy70w93xss2abhx1b6"))))
+          "00xvf772ys4fj9fr8kplmsqb9if215dsipi3nv54aw9q7xkfpw0d"))))
     (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-unicode-xid" ,rust-unicode-xid-0.2)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-quote" ,rust-quote-1.0))
+       #:cargo-development-inputs
+       (("rust-anyhow" ,rust-anyhow-1.0)
+        ("rust-flate2" ,rust-flate2-1.0)
+        ;("rust-insta" ,rust-insta-0.12)
+        ("rust-rayon" ,rust-rayon-1.3)
+        ("rust-ref-cast" ,rust-ref-cast-1.0)
+        ("rust-regex" ,rust-regex-1.3)
+        ;("rust-reqwest" ,rust-reqwest-0.10)
+        ("rust-tar" ,rust-tar-0.4)
+        ("rust-termcolor" ,rust-termcolor-1.0)
+        ("rust-walkdir" ,rust-walkdir-2.3))))
     (home-page "https://github.com/dtolnay/syn")
     (synopsis "Parser for Rust source code")
     (description "Parser for Rust source code")
-    (properties '((hidden? . #t)))
     (license (list license:expat license:asl2.0))))
 
 (define-public rust-syn-0.15
@@ -18088,6 +20944,33 @@ cryptographic implementations.")
         ("rust-tempdir" ,rust-tempdir-0.3)
         ("rust-walkdir" ,rust-walkdir-1.0))))))
 
+(define-public rust-syn-mid-0.5
+  (package
+    (name "rust-syn-mid")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "syn-mid" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "12ikg5jfklixq0wsgfl7sdzjqlxgq50ygklxy4f972hjdjgm7qvv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/taiki-e/syn-mid")
+    (synopsis
+     "Provide the features between \"full\" and \"derive\" of syn.")
+    (description
+     "This package provides the features between \"full\" and \"derive\" of syn.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-synom-0.11
   (package
     (name "rust-synom")
@@ -18121,6 +21004,33 @@ cryptographic implementations.")
      "Stripped-down Nom parser used by Syn.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-synstructure-0.12
+  (package
+    (name "rust-synstructure")
+    (version "0.12.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "synstructure" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0igmc5fzpk6fg7kgff914j05lbpc6ai2wmji312v2h8vvjhnwrb7"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-unicode-xid" ,rust-unicode-xid-0.2)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/mystor/synstructure")
+    (synopsis "Helper methods and macros for custom derives")
+    (description
+     "This package provides helper methods and macros for custom derives.")
+    (license license:expat)))
+
 (define-public rust-synstructure-0.10
   (package
     (name "rust-synstructure")
@@ -18168,6 +21078,44 @@ cryptographic implementations.")
      "This package provides helper test traits for synstructure doctests.")
     (license license:expat)))
 
+(define-public rust-syntect-3.3
+  (package
+    (name "rust-syntect")
+    (version "3.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "syntect" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1f6qn1yy15b0hq9h6q1rikqnm3lh56ic6bq3ywsmdsjy8ni9splm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-plist" ,rust-plist-0.4)
+        ("rust-yaml-rust" ,rust-yaml-rust-0.4)
+        ("rust-regex-syntax" ,rust-regex-syntax-0.6)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-flate2" ,rust-flate2-1.0)
+        ("rust-serde-json" ,rust-serde-json-1.0)
+        ("rust-fnv" ,rust-fnv-1.0)
+        ("rust-bitflags" ,rust-bitflags-1)
+        ("rust-lazycell" ,rust-lazycell-1.2)
+        ("rust-bincode" ,rust-bincode-1.2)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-walkdir" ,rust-walkdir-2.3)
+        ("rust-onig" ,rust-onig-5.0))))
+    (home-page "https://github.com/trishume/syntect")
+    (synopsis "Library for syntax highlighting and code intelligence")
+    (description
+     "This package provides a library for syntax highlighting and code
+intelligence using Sublime Text's grammars.")
+    (license license:expat)))
+
 (define-public rust-syntex-0.58
  (package
    (name "rust-syntex")
@@ -18320,6 +21268,58 @@ syntax extension expansion.")
         ("rust-errno" ,rust-errno-0.2)
         ("rust-libc" ,rust-libc-0.2))))))
 
+(define-public rust-syslog-4.0
+  (package
+    (name "rust-syslog")
+    (version "4.0.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "syslog" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "09ykcbvwx8icvf303mqyz76ji8j6fgyyx97zpr23s788ni112r50"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-time" ,rust-time-0.1)
+        ("rust-error-chain" ,rust-error-chain-0.11)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-log" ,rust-log-0.4))))
+    (home-page "https://github.com/Geal/rust-syslog")
+    (synopsis "Send log messages to syslog")
+    (description "Send log messages to syslog.")
+    (license license:expat)))
+
+(define-public rust-syslog-3.3
+  (package
+    (name "rust-syslog")
+    (version "3.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "syslog" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0hpdnk2zm6xawpz6fv6qbn0ncfm5p0wm5c6gq7yhaz2gvsnb1jdv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-time" ,rust-time-0.1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-log" ,rust-log-0.3)
+        ("rust-unix-socket" ,rust-unix-socket-0.5))))
+    (home-page "https://github.com/Geal/rust-syslog")
+    (synopsis "Send log messages to syslog")
+    (description "Send log messages to syslog.")
+    (license license:expat)))
+
 (define-public rust-takeable-option-0.4
   (package
     (name "rust-takeable-option")
@@ -18399,6 +21399,29 @@ memory all at once.")
 @code{build.rs} scripts.")
     (license (list license:isc license:asl2.0))))
 
+(define-public rust-target-lexicon-0.10
+  (package
+    (name "rust-target-lexicon")
+    (version "0.10.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "target-lexicon" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "17diw9c3d1vb5rmwwk2ghsyhfs0gj5jm78hrwxxhmd67vhw743mb"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/CraneStation/target-lexicon")
+    (synopsis
+      "Targeting utilities for compilers and related tools")
+    (description
+      "Targeting utilities for compilers and related tools")
+    (license license:asl2.0)))
+
 (define-public rust-tempdir-0.3
   (package
     (name "rust-tempdir")
@@ -19083,7 +22106,7 @@ in Rust.")
 (define-public rust-tinytemplate-1.0
   (package
     (name "rust-tinytemplate")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
      (origin
        (method url-fetch)
@@ -19092,7 +22115,7 @@ in Rust.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "084w41m75i95sdid1wwlnav80jsl1ggyryl4nawxvb6amigvfx25"))))
+         "06ipxjwl1w6synvql8b50qxbqv0w04agvmmfqcdynr9ygmkcd8sp"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -19100,7 +22123,7 @@ in Rust.")
        (("rust-serde" ,rust-serde-1.0)
         ("rust-serde-json" ,rust-serde-json-1.0))
        #:cargo-development-inputs
-       (("rust-criterion" ,rust-criterion-0.2)
+       (("rust-criterion" ,rust-criterion-0.3)
         ("rust-serde-derive" ,rust-serde-derive-1.0))))
     (home-page "https://github.com/bheisler/TinyTemplate")
     (synopsis "Simple, lightweight template engine")
@@ -19328,7 +22351,7 @@ the current thread.")
 (define-public rust-tokio-io-0.1
   (package
     (name "rust-tokio-io")
-    (version "0.1.12")
+    (version "0.1.13")
     (source
      (origin
        (method url-fetch)
@@ -19337,7 +22360,7 @@ the current thread.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "09jrz1hh4h1vj45qy09y7m7m8jsy1hl6g32clnky25mdim3dp42h"))))
+         "0x06zyzinans1pn90g6i150lgixijdf1cg8y2gipjd09ms58dz2p"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -19768,6 +22791,34 @@ serializing Rust structures.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-toml-0.2
+  (package
+    (name "rust-toml")
+    (version "0.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "toml" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1d1cz43bxrx4fd6j2p6myckf81f72bp47akg36y3flxjkhj60svk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rustc-serialize" ,rust-rustc-serialize-0.3)
+        ("rust-serde" ,rust-serde-0.8))))
+    (home-page "https://github.com/alexcrichton/toml-rs")
+    (synopsis "Rust encoder and decoder of TOML-formatted files and streams")
+    (description
+     "This package provides a native Rust encoder and decoder of TOML-formatted
+files and streams.  Provides implementations of the standard
+Serialize/Deserialize traits for TOML data to facilitate deserializing and
+serializing Rust str")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-tracing-core-0.1
   (package
     (name "rust-tracing-core")
@@ -20053,6 +23104,30 @@ with the Unicode character database.")
      "Unchecked indexing wrapper using regular index syntax.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-unicase-2.6
+  (package
+    (name "rust-unicase")
+    (version "2.6.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unicase" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1xmlbink4ycgxrkjspp0mf7pghcx4m7vxq7fpfm04ikr2zk7pwsh"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-version-check" ,rust-version-check-0.9))))
+    (home-page "https://github.com/seanmonstar/unicase")
+    (synopsis "Case-insensitive wrapper around strings")
+    (description
+     "This package provides a case-insensitive wrapper around strings.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-unicase-2.4
   (package
     (name "rust-unicase")
@@ -20283,6 +23358,30 @@ whitespace from a string.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-unix-socket-0.5
+  (package
+    (name "rust-unix-socket")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unix_socket" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0r0mxf3mmqvimnx4mpks1f6c4haj6jcxc0k9bs7w61f42w2718ka"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-libc" ,rust-libc-0.2))))
+    (home-page "https://github.com/rust-lang-nursery/unix-socket")
+    (synopsis "Unix domain socket bindings")
+    (description "This package provides unix domain socket bindings.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-unreachable-1.0
   (package
     (name "rust-unreachable")
@@ -20508,7 +23607,7 @@ Unix users and groups.")
 (define-public rust-utf8-ranges-1.0
   (package
     (name "rust-utf8-ranges")
-    (version "1.0.3")
+    (version "1.0.4")
     (source
      (origin
        (method url-fetch)
@@ -20517,7 +23616,7 @@ Unix users and groups.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1ppzjsxmv1p1xfid8wwn07ciikk84k30frl28bwsny6za1vall4x"))))
+         "1fpc32znar5v02nwsw7icl41jzzzzhy0si6ngqjylzrbxxpi3bml"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -20568,6 +23667,35 @@ Unix users and groups.")
     (description "This package provides a table-driven UTF-8 parser.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-uuid-0.8
+  (package
+    (name "rust-uuid")
+    (version "0.8.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "uuid" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "049w16qwk3d3b9cmpgvd7fvcnwgs75l8rlsagh06w7ga9dm2zplz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-winapi" ,rust-winapi-0.3)
+        ("rust-sha1" ,rust-sha1-0.6)
+        ("rust-md5" ,rust-md5-0.6)
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-slog" ,rust-slog-2.5))))
+    (home-page "https://github.com/uuid-rs/uuid")
+    (synopsis "Library to generate and parse UUIDs")
+    (description
+     "This package provides a library to generate and parse UUIDs.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-uuid-0.7
   (package
     (name "rust-uuid")
@@ -20674,6 +23802,57 @@ Unix users and groups.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-vecmath-1.0
+  (package
+    (name "rust-vecmath")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "vecmath" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0shmj76rj7rqv377vy365xwr5rx23kxqgkqxxrymdjjvv3hf2slm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-float" ,rust-piston-float-1.0))))
+    (home-page "https://github.com/pistondevelopers/vecmath")
+    (synopsis "Library for vector math designed for reexporting")
+    (description
+     "This package provides a simple and type agnostic library for vector math
+designed for reexporting.")
+    (license license:expat)))
+
+(define-public rust-vergen-3.1
+  (package
+    (name "rust-vergen")
+    (version "3.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "vergen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1jrr0wihm9si98qz8ghjfnalfvmfv8rqvkgj2npqa7yzjs4hvrac"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-chrono" ,rust-chrono-0.4)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "http://github.com/rustyhorde/vergen")
+    (synopsis "Generate version related functions")
+    (description
+     "Generate version related functions.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-version-check-0.9
   (package
     (name "rust-version-check")
@@ -20860,6 +24039,31 @@ updated when the crate version changes.")
 specified across Unix and Windows platforms.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-walkdir-2.3
+  (package
+    (name "rust-walkdir")
+    (version "2.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "walkdir" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0z9g39f49cycdm9vzjf8hnfh3f1csxgd65kmlphj8r2vffy84wbp"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-winapi-util" ,rust-winapi-util-0.1)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-same-file" ,rust-same-file-1.0))))
+    (home-page "https://github.com/BurntSushi/walkdir")
+    (synopsis "Recursively walk a directory")
+    (description "Recursively walk a directory.")
+    (license (list license:unlicense license:expat))))
+
 (define-public rust-walkdir-2.2
   (package
     (name "rust-walkdir")
@@ -20911,6 +24115,33 @@ specified across Unix and Windows platforms.")
         ("rust-rand" ,rust-rand-0.3)
         ("rust-rustc-serialize" ,rust-rustc-serialize-0.3))))))
 
+(define-public rust-wasi-0.9
+  (package
+    (name "rust-wasi")
+    (version "0.9.0+wasi-snapshot-preview1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "wasi" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "06g5v3vrdapfzvfq662cij7v8a1flwr2my45nnncdv2galrdzkfc"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-compiler-builtins" ,rust-compiler-builtins-0.1)
+        ("rust-rustc-std-workspace-alloc" ,rust-rustc-std-workspace-alloc-1.0)
+        ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0))))
+    (home-page "https://github.com/bytecodealliance/wasi")
+    (synopsis "Experimental WASI API bindings for Rust")
+    (description
+     "This package provides an experimental WASI API bindings for Rust.")
+    (license (list license:asl2.0
+                   license:expat))))
+
 (define-public rust-wasi-0.5
   (package
     (name "rust-wasi")
@@ -20934,7 +24165,7 @@ in Rust.")
 (define-public rust-wasm-bindgen-0.2
   (package
     (name "rust-wasm-bindgen")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
      (origin
        (method url-fetch)
@@ -20943,7 +24174,7 @@ in Rust.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0v31s91andxcj73w63g3fkbw3ld6cfsaa4135qcjna22vypyj1aj"))))
+         "0zx42zryw03w3maz8p65gr5bhhybr2sdzgcck5p3gy47abh7ri9c"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -20969,7 +24200,7 @@ in Rust.")
 (define-public rust-wasm-bindgen-backend-0.2
   (package
     (name "rust-wasm-bindgen-backend")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
      (origin
        (method url-fetch)
@@ -20978,7 +24209,7 @@ in Rust.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0icskn0qlj30np6x6nbyl1i9dndckx0pczaq69dm42r92rcbkk8i"))))
+         "1k9p8a7ng6nqan0m9555wj936lm2s1qz0fnafclwlv61yrxx6ryr"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -21056,7 +24287,7 @@ in Rust.")
 (define-public rust-wasm-bindgen-macro-0.2
   (package
     (name "rust-wasm-bindgen-macro")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
      (origin
        (method url-fetch)
@@ -21065,7 +24296,7 @@ in Rust.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1hwxw0nhi2n4izhjn2fvnrrn59xqjxs3ybkgzdv1b4p65ivr8h2p"))))
+         "1973xr0vr2aj85fkp3smk61z5ki7c4fhxlicfjxq3a0y7sv53lcb"))))
     (build-system cargo-build-system)
     (arguments
      `(#:tests? #f      ; 'Async blocks are unstable'
@@ -21087,7 +24318,7 @@ dependency.")
 (define-public rust-wasm-bindgen-macro-support-0.2
   (package
     (name "rust-wasm-bindgen-macro-support")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
      (origin
        (method url-fetch)
@@ -21096,7 +24327,7 @@ dependency.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0s3n7v741i4wkzib41m126li40qlhqyirnxpigkypsi59wsk2l78"))))
+         "0ca9bb9hnyzcmjww83x8asb76drf55ijhqv8yrl7igpixqv5p2nn"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -21115,7 +24346,7 @@ attribute that is not in the shared backend crate.")
 (define-public rust-wasm-bindgen-shared-0.2
   (package
     (name "rust-wasm-bindgen-shared")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
       (origin
         (method url-fetch)
@@ -21123,9 +24354,8 @@ attribute that is not in the shared backend crate.")
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "00cnbabf4k9bahb217vkilmjwqwzpwp112vlvgfw1x19r4gydrzm"))))
+          "0ffn4152w8n629f29lwjgj3adiyixvdbff3mld49gisssbknzxys"))))
     (build-system cargo-build-system)
-    ;(arguments '(#:skip-build? #t))
     (home-page "https://rustwasm.github.io/wasm-bindgen/")
     (synopsis "Shared support between wasm-bindgen and wasm-bindgen cli")
     (description "This package provides shared support between
@@ -21617,7 +24847,7 @@ protocol extensions.  Look at the crate wayland-client for usable bindings.")
 (define-public rust-web-sys-0.3
   (package
     (name "rust-web-sys")
-    (version "0.3.35")
+    (version "0.3.37")
     (source
      (origin
        (method url-fetch)
@@ -21626,16 +24856,12 @@ protocol extensions.  Look at the crate wayland-client for usable bindings.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0fzmxcyahy3ghl8lkjkchj9krmnr56shvbqgr7db3hm8dappryda"))))
+         "1jy4q5jawzg3dxzhfwa0g3fsz7h4j0ra6y232ikc6mlcimj52vrd"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-js-sys" ,rust-js-sys-0.3)
-        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
-        ("rust-anyhow" ,rust-anyhow-1.0)
-        ("rust-env-logger" ,rust-env-logger-0.7)
-        ("rust-sourcefile" ,rust-sourcefile-0.1)
-        ("rust-wasm-bindgen-webidl" ,rust-wasm-bindgen-webidl-0.2))
+        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2))
        #:cargo-development-inputs
        (("rust-wasm-bindgen-futures" ,rust-wasm-bindgen-futures-0.4)
         ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.3))))
@@ -21668,6 +24894,32 @@ protocol extensions.  Look at the crate wayland-client for usable bindings.")
      "This package provides a WebIDL Parser.")
     (license license:expat)))
 
+(define-public rust-which-3.1
+  (package
+    (name "rust-which")
+    (version "3.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "which" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "094pw9pi48szshn9ln69z2kg7syq1jp80h5ps1qncbsaw4d0f4fh"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:skip-build? #t
+        #:cargo-inputs
+        (("rust-failure" ,rust-failure-0.1)
+         ("rust-libc" ,rust-libc-0.2))))
+    (home-page "https://github.com/harryfei/which-rs.git")
+    (synopsis "Rust equivalent of Unix command \"which\"")
+    (description
+     "This package provides a Rust equivalent of Unix command \"which\".  Locate
+installed executable in cross platforms.")
+    (license license:expat)))
+
 (define-public rust-which-2.0
   (package
     (name "rust-which")
@@ -21826,7 +25078,7 @@ i686-pc-windows-gnu target.  Please don't use this crate directly, depend on
 (define-public rust-winapi-util-0.1
   (package
     (name "rust-winapi-util")
-    (version "0.1.2")
+    (version "0.1.4")
     (source
       (origin
         (method url-fetch)
@@ -21834,7 +25086,7 @@ i686-pc-windows-gnu target.  Please don't use this crate directly, depend on
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1j839dc6y8vszvrsb7yk0qvs0w6asnahxzbyans37vnsw6vbls3i"))))
+          "0vj3984cxwnf1ys3fdz6bpl7p0kdsgykpzbhmcmwi759cd8mqlgs"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs (("rust-winapi" ,rust-winapi-0.3))))
@@ -22246,7 +25498,7 @@ to XDG Base Directory specification")
 (define-public rust-xml-rs-0.8
   (package
     (name "rust-xml-rs")
-    (version "0.8.0")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
@@ -22255,14 +25507,37 @@ to XDG Base Directory specification")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1db4v716rbpgjiasaim2s17rmvsfcq1qzwg6nji6mdf5k34i46sl"))))
+         "0c905wsmk995xypxljpxzq6vv660r1pzgyrpsfiz13kw3hf0dzcs"))))
     (build-system cargo-build-system)
-    (arguments `(#:skip-build? #t))
+    (arguments
+     `(#:cargo-development-inputs
+       (("rust-doc-comment" ,rust-doc-comment-0.3)
+        ("rust-lazy-static" ,rust-lazy-static-1))))
     (home-page "https://github.com/netvl/xml-rs")
     (synopsis "XML library in pure Rust")
     (description "An XML library in pure Rust.")
     (license license:expat)))
 
+(define-public rust-y4m-0.5
+  (package
+    (name "rust-y4m")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "y4m" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "06g8c53qk4cla3xczywx5qlklvzsw54x77vm727mhizlsp5n93ar"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page "https://github.com/image-rs/y4m")
+    (synopsis "YUV4MPEG2 (.y4m) Encoder/Decoder.")
+    (description "YUV4MPEG2 (.y4m) Encoder/Decoder.")
+    (license license:expat)))
+
 (define-public rust-yaml-rust-0.4
   (package
     (name "rust-yaml-rust")
diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm
index af51c0fcfc..5d0521a216 100644
--- a/gnu/packages/rust-apps.scm
+++ b/gnu/packages/rust-apps.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
+;;; Copyright © 2020 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -290,7 +291,7 @@ gitignore rules.")
         ("serde" ,rust-serde-1.0)
         ("serde-json" ,rust-serde-json-1.0)
         ("syn" ,rust-syn-1.0)
-        ("tempfile" ,rust-tempfile-3.0)
+        ("tempfile" ,rust-tempfile-3.1)
         ("toml" ,rust-toml-0.5))))
     (home-page "https://github.com/eqrion/cbindgen/")
     (synopsis "Tool for generating C bindings to Rust code")
@@ -298,6 +299,21 @@ gitignore rules.")
      "This package provides a tool for generating C/C++ bindings to Rust code.")
     (license license:mpl2.0)))
 
+(define-public rust-cbindgen-0.12
+  (package
+    (inherit rust-cbindgen)
+    (name "rust-cbindgen")
+    (version "0.12.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cbindgen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "13jzbmjz1bmmfr0i80hw6ar484mgabx3hbpb2ynhk0ddqi0yr58m"))))))
+
 (define-public tokei
   (package
     (name "tokei")
@@ -358,3 +374,36 @@ gitignore rules.")
 show number of files, total lines within those files and code, comments, and
 blanks grouped by language.")
     (license (list license:expat license:asl2.0))))
+
+(define-public rust-cargo-c
+  (package
+    (name "rust-cargo-c")
+    (version "0.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cargo-c" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1is72jm0r73pqx2g3h1n6lvrcirwd91mmajsmb3jjg4jnayfkp0w"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-cbindgen" ,rust-cbindgen-0.12)
+        ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.3)
+        ("rust-structopt" ,rust-structopt-0.3)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-toml" ,rust-toml-0.5)
+        ("rust-cargo-metadata" ,rust-cargo-metadata-0.9)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-regex" ,rust-regex-1.3))))
+    (home-page "https://github.com/lu-zero/cargo-c")
+    (synopsis "Build and install C-compatible libraries")
+    (description
+     "This package produces and installs a correct pkg-config file, a static
+library and a dynamic library, and a C header to be used by any C (and
+C-compatible) software.")
+    (license license:expat)))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 84b051832a..ce5261c788 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -66,6 +66,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix svn-download)
+  #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
@@ -90,6 +91,7 @@
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
+  #:use-module (gnu packages crates-io)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages dejagnu)
   #:use-module (gnu packages dns)
@@ -140,6 +142,7 @@
   #:use-module (gnu packages qt)
   #:use-module (gnu packages rdesktop)
   #:use-module (gnu packages ruby)
+  #:use-module (gnu packages rust-apps)
   #:use-module (gnu packages samba)
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages serialization)
@@ -3949,3 +3952,87 @@ result in several formats:
 @end itemize\n")
     (home-page "https://www.gen2vdr.de/wirbel/w_scan/index2.html")
     (license license:gpl2+)))
+
+(define-public rav1e
+  (package
+    (name "rav1e")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rav1e" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1bsmj8kqzs5pf8dl98rsl6a67cljj1gkj3b5hmd8hn8wdy4ya173"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-simd-helpers" ,rust-simd-helpers-0.1)
+        ("rust-ivf" ,rust-ivf-0.1)
+        ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-paste" ,rust-paste-0.1)
+        ("rust-signal-hook" ,rust-signal-hook-0.1)
+        ("rust-aom-sys" ,rust-aom-sys-0.1)
+        ("rust-nasm-rs" ,rust-nasm-rs-0.1)
+        ("rust-arbitrary" ,rust-arbitrary-0.2)
+        ("rust-better-panic" ,rust-better-panic-0.2)
+        ("rust-noop-proc-macro"
+         ,rust-noop-proc-macro-0.2)
+        ("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-rand-chacha" ,rust-rand-chacha-0.2)
+        ("rust-err-derive" ,rust-err-derive-0.2)
+        ("rust-interpolate-name"
+         ,rust-interpolate-name-0.2)
+        ("rust-rustc-version" ,rust-rustc-version-0.2)
+        ("rust-scan-fmt" ,rust-scan-fmt-0.2)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-image" ,rust-image-0.22)
+        ("rust-arg-enum-proc-macro"
+         ,rust-arg-enum-proc-macro-0.3)
+        ("rust-num-derive" ,rust-num-derive-0.3)
+        ("rust-dav1d-sys" ,rust-dav1d-sys-0.3)
+        ("rust-backtrace" ,rust-backtrace-0.3)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-y4m" ,rust-y4m-0.5)
+        ("rust-arrayvec" ,rust-arrayvec-0.5)
+        ("rust-toml" ,rust-toml-0.5)
+        ("rust-fern" ,rust-fern-0.5)
+        ("rust-rust-hawktracer"
+         ,rust-rust-hawktracer-0.7)
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-itertools" ,rust-itertools-0.8)
+        ("rust-bitstream-io" ,rust-bitstream-io-0.8)
+        ("rust-console" ,rust-console-0.9)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-cc" ,rust-cc-1.0)
+        ("rust-rayon" ,rust-rayon-1.3)
+        ("rust-byteorder" ,rust-byteorder-1.3)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-vergen" ,rust-vergen-3.1))
+       #:cargo-development-inputs
+       (("rust-rand-chacha" ,rust-rand-chacha-0.2)
+        ("rust-interpolate-name"
+         ,rust-interpolate-name-0.2)
+        ("rust-criterion" ,rust-criterion-0.3)
+        ("rust-pretty-assertions"
+         ,rust-pretty-assertions-0.6)
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-semver" ,rust-semver-0.9))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'build
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (invoke "cargo" "cinstall" "--release"
+                       (string-append "--prefix=" out))))))))
+    (native-inputs
+     `(("cargo-c" ,rust-cargo-c)))
+    (inputs
+     `(("nasm" ,nasm)))
+    (home-page "https://github.com/xiph/rav1e/")
+    (synopsis "The fastest and safest AV1 encoder")
+    (description
+     "The fastest and safest AV1 encoder.")
+    (license license:bsd-2)))

From 910bf1f7a11b669b9c307fb5af8c1fb0be01d537 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <lars@6xq.net>
Date: Sun, 26 Apr 2020 17:54:54 +0200
Subject: [PATCH 003/215] gnu: Add tarsplitter.

* gnu/packages/compression.scm (tarsplitter): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/compression.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 33801d201d..8b93cc93dc 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -27,6 +27,7 @@
 ;;; Copyright © 2019 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2020 Lars-Dominik Braun <lars@6xq.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -52,6 +53,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system go)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
@@ -2131,3 +2133,37 @@ independent.  Supported formats are 7z, ARJ, bzip2, gzip, LHA, lzma, lzop,
 RAR, RPM, DEB, tar, and ZIP.  It cannot perform functions for archives, whose
 archiver is not installed.")
     (license license:gpl2+)))
+
+(define-public tarsplitter
+  (package
+    (name "tarsplitter")
+    (version "2.2.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/AQUAOSOTech/tarsplitter.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "17qkg95r97kcrs17b0mcqswx99280ni47j5yx8xa7nl3bdhm6325"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/AQUAOSOTech/tarsplitter"
+       #:install-source? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-documentation
+           (lambda* (#:key import-path outputs #:allow-other-keys)
+             (let* ((source (string-append "src/" import-path))
+                    (out (assoc-ref outputs "out"))
+                    (doc (string-append out "/share/doc/" ,name "-" ,version)))
+               (with-directory-excursion source
+                 (install-file "README.md" doc))
+               #t))))))
+    (home-page "https://github.com/AQUAOSOTech/tarsplitter")
+    (synopsis "Multithreaded tar utility")
+    (description
+     "Archive huge numbers of files, or spilt massive tar archives into smaller
+chunks.")
+    (license license:expat)))

From 121191f23ae89415dfbbd3052c7342188cded135 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Mon, 2 Mar 2020 20:13:39 +0000
Subject: [PATCH 004/215] substitute: Use the same port for multiple request
 batches.

In http-multiple-get.

* guix/scripts/substitute.scm (http-multiple-get): Switch port to p in one
occurrence.
---
 guix/scripts/substitute.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm
index 95b47a7816..2cb240c2a0 100755
--- a/guix/scripts/substitute.scm
+++ b/guix/scripts/substitute.scm
@@ -538,7 +538,7 @@ initial connection on which HTTP requests are sent."
              (()
               (reverse result))
              (remainder
-              (connect port remainder result))))
+              (connect p remainder result))))
           ((head tail ...)
            (let* ((resp   (read-response p))
                   (body   (response-body-port resp))

From d5abb3049ee4e97865f691eba4c59f5b51de3271 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Mon, 2 Mar 2020 20:17:18 +0000
Subject: [PATCH 005/215] substitute: Make http-multiple-get batch size
 configurable.

* guix/scripts/substitute.scm (http-multiple-get): Add batch-size parameter.
---
 guix/scripts/substitute.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm
index 2cb240c2a0..0777aa3d3e 100755
--- a/guix/scripts/substitute.scm
+++ b/guix/scripts/substitute.scm
@@ -494,7 +494,8 @@ MAX-LENGTH first elements."
            (loop (+ 1 len) tail (cons head result)))))))
 
 (define* (http-multiple-get base-uri proc seed requests
-                            #:key port (verify-certificate? #t))
+                            #:key port (verify-certificate? #t)
+                            (batch-size 1000))
   "Send all of REQUESTS to the server at BASE-URI.  Call PROC for each
 response, passing it the request object, the response, a port from which to
 read the response body, and the previous result, starting with SEED, à la
@@ -504,7 +505,7 @@ initial connection on which HTTP requests are sent."
                 (requests requests)
                 (result   seed))
     (define batch
-      (at-most 1000 requests))
+      (at-most batch-size requests))
 
     ;; (format (current-error-port) "connecting (~a requests left)..."
     ;;         (length requests))

From 928dc1bb1c1e96e6dfbe03dac2185ecf41a7b4f5 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Mon, 2 Mar 2020 20:20:40 +0000
Subject: [PATCH 006/215] substitute: Close port at the end of
 http-multiple-get.

* guix/scripts/substitute.scm (http-multiple-get): Add close-port call.
---
 guix/scripts/substitute.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm
index 0777aa3d3e..ba2b2d2d4e 100755
--- a/guix/scripts/substitute.scm
+++ b/guix/scripts/substitute.scm
@@ -537,6 +537,7 @@ initial connection on which HTTP requests are sent."
           (()
            (match (drop requests processed)
              (()
+              (close-port p)
               (reverse result))
              (remainder
               (connect p remainder result))))

From 53aa66c3dff8a59b5c596691d9126db6a2327983 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 7 Apr 2020 22:10:40 +0100
Subject: [PATCH 007/215] reconfigure: Don't call build-derivations for
 upgrade-services test

This commit adjusts the upgrade-services system test to not build anything
when computing the derivation for the system test.  I came across this when
looking at issues computing the system test derivations to store in the Guix
Data Service.

* gnu/tests/reconfigure.scm (run-upgrade-services-test): Remove the use of,
and definition for ensure-service-file.
---
 gnu/tests/reconfigure.scm | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/gnu/tests/reconfigure.scm b/gnu/tests/reconfigure.scm
index 8b85920979..928a210a94 100644
--- a/gnu/tests/reconfigure.scm
+++ b/gnu/tests/reconfigure.scm
@@ -136,14 +136,6 @@ Shepherd (PID 1) by unloading obsolete services and loading new services."
                       (stop #~(const #t))
                       (respawn? #f)))
 
-  ;; Return the Shepherd service file for SERVICE, after ensuring that it
-  ;; exists in the store.
-  (define (ensure-service-file service)
-    (let ((file (shepherd-service-file service)))
-      (mlet* %store-monad ((store-object (lower-object file))
-                           (_ (built-derivations (list store-object))))
-        (return file))))
-
   (define (test enable-dummy disable-dummy)
     (with-imported-modules '((gnu build marionette))
       #~(begin
@@ -187,10 +179,12 @@ Shepherd (PID 1) by unloading obsolete services and loading new services."
           (test-end)
           (exit (= (test-runner-fail-count (test-runner-current)) 0)))))
 
-  (mlet* %store-monad ((file (ensure-service-file dummy-service)))
-    (let ((enable (upgrade-services-program (list file) '(dummy) '() '()))
+  (gexp->derivation
+   "upgrade-services"
+   (let* ((file (shepherd-service-file dummy-service))
+          (enable (upgrade-services-program (list file) '(dummy) '() '()))
           (disable (upgrade-services-program '() '() '(dummy) '())))
-      (gexp->derivation "upgrade-services" (test enable disable)))))
+     (test enable disable))))
 
 (define* (run-install-bootloader-test)
   "Run a test of an OS running INSTALL-BOOTLOADER-PROGRAM, which installs a

From f47623843116c4a83240bb646edfcd9c0e1d8187 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 7 Apr 2020 22:21:58 +0100
Subject: [PATCH 008/215] gnu: guile3.0-chickadee: Rename to
 guile3.0-chickadee.

This avoids having to packages, both called guile-chickadee.

* gnu/packages/game-development.scm (guile3.0-chickadee)[name]: Change from
guile-chickadee to guile3.0-chickadee.
---
 gnu/packages/game-development.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 2a66f4a40c..d4b2fdcab2 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1777,7 +1777,7 @@ that parenthetically inclined game developers need to make 2D (and eventually
 (define-public guile3.0-chickadee
   (package
     (inherit guile-chickadee)
-    (name "guile-chickadee")
+    (name "guile3.0-chickadee")
     (version "0.4.0")
     (source (origin
               (method url-fetch)

From ec20858a6a9453af1d9bcf3b6efe564f352af2a7 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:02:00 +0200
Subject: [PATCH 009/215] gnu: Add r-pasilla.

* gnu/packages/bioconductor.scm (r-pasilla): New variable.
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 68d8e5b574..2d7663715a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -811,6 +811,32 @@ performing parallel computations on multicore machines.")
 Disease Ontology.")
     (license license:artistic2.0)))
 
+(define-public r-pasilla
+  (package
+    (name "r-pasilla")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://bioconductor.org/packages/release/data/experiment"
+                    "/src/contrib/pasilla_" version ".tar.gz"))
+              (sha256
+               (base32
+                "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocstyle" ,r-biocstyle)
+       ("r-dexseq" ,r-dexseq)
+       ("r-knitr" ,r-knitr)
+       ("r-rmarkdown" ,r-rmarkdown)))
+    (home-page "https://www.bioconductor.org/packages/pasilla/")
+    (synopsis "Data package with per-exon and per-gene read counts")
+    (description "This package provides per-exon and per-gene read counts
+computed for selected genes from RNA-seq data that were presented in the
+article 'Conservation of an RNA regulatory map between Drosophila and mammals'
+by Brooks et al., Genome Research 2011.")
+    (license license:lgpl2.1+)))
+
 (define-public r-pfam-db
   (package
     (name "r-pfam-db")

From 3699bcf54ac51c99c2807afd60d1eeebc00329ec Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:07:45 +0200
Subject: [PATCH 010/215] gnu: Add r-motifdb.

* gnu/packages/bioconductor.scm (r-motifdb): New variable.
---
 gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2d7663715a..9ecf42e783 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3998,6 +3998,30 @@ database (e.g. JASPAR).  It can also be used to visualize motifs, motif
 distributions, modules and filter motifs.")
     (license license:gpl2)))
 
+(define-public r-motifdb
+  (package
+   (name "r-motifdb")
+   (version "1.28.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "MotifDb" version))
+            (sha256
+             (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc"))))
+   (properties `((upstream-name . "MotifDb")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-biocgenerics" ,r-biocgenerics)
+      ("r-biostrings" ,r-biostrings)
+      ("r-iranges" ,r-iranges)
+      ("r-rtracklayer" ,r-rtracklayer)
+      ("r-s4vectors" ,r-s4vectors)
+      ("r-splitstackshape" ,r-splitstackshape)))
+   (home-page "https://www.bioconductor.org/packages/MotifDb/")
+   (synopsis "Annotated collection of protein-DNA binding sequence motifs")
+   (description "This package provides more than 2000 annotated position
+frequency matrices from nine public sources, for multiple organisms.")
+   (license license:artistic2.0)))
+
 (define-public r-motifstack
   (package
     (name "r-motifstack")

From 886125d791bd1e0ca9d28f7adbb74ffb6f662a33 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:24:03 +0200
Subject: [PATCH 011/215] gnu: Add r-motifbreakr.

* gnu/packages/bioconductor.scm (r-motifbreakr): New variable.
---
 gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9ecf42e783..a27845581f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4022,6 +4022,54 @@ distributions, modules and filter motifs.")
 frequency matrices from nine public sources, for multiple organisms.")
    (license license:artistic2.0)))
 
+(define-public r-motifbreakr
+  (package
+   (name "r-motifbreakr")
+   (version "2.0.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "motifbreakR" version))
+            (sha256
+             (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n"))))
+   (properties `((upstream-name . "motifbreakR")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-grimport" ,r-grimport)
+      ("r-stringr" ,r-stringr)
+      ("r-biocgenerics" ,r-biocgenerics)
+      ("r-s4vectors" ,r-s4vectors)
+      ("r-iranges" ,r-iranges)
+      ("r-genomeinfodb" ,r-genomeinfodb)
+      ("r-genomicranges" ,r-genomicranges)
+      ("r-biostrings" ,r-biostrings)
+      ("r-bsgenome" ,r-bsgenome)
+      ("r-rtracklayer" ,r-rtracklayer)
+      ("r-variantannotation" ,r-variantannotation)
+      ("r-biocparallel" ,r-biocparallel)
+      ("r-motifstack" ,r-motifstack)
+      ("r-gviz" ,r-gviz)
+      ("r-matrixstats" ,r-matrixstats)
+      ("r-tfmpvalue" ,r-tfmpvalue)
+      ("r-motifdb" ,r-motifdb)))
+   (home-page "https://www.bioconductor.org/packages/motifbreakR/")
+   (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
+   (description "This package allows biologists to judge in the first place
+whether the sequence surrounding the polymorphism is a good match, and in
+the second place how much information is gained or lost in one allele of
+the polymorphism relative to another.  This package gives a choice of
+algorithms for interrogation of genomes with motifs from public sources:
+@enumerate
+@item a weighted-sum probability matrix;
+@item log-probabilities;
+@item weighted by relative entropy.
+@end enumerate
+
+This package can predict effects for novel or previously described variants in
+public databases, making it suitable for tasks beyond the scope of its original
+design.  Lastly, it can be used to interrogate any genome curated within
+Bioconductor.")
+   (license license:gpl2+)))
+
 (define-public r-motifstack
   (package
     (name "r-motifstack")

From b58a22e5b7468906b1e223309e110109808f40ea Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 26 Apr 2020 03:36:57 -0400
Subject: [PATCH 012/215] gnu: Add hackneyed-x11-cursors.

* gnu/packages/xorg.scm (hackneyed-x11-cursors): New variable.
---
 gnu/packages/xorg.scm | 62 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 80158b1cab..95479f18da 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -22,6 +22,7 @@
 ;;; Copyright © 2019 Yoshinori Arai <kumagusu08@gmail.com>
 ;;; Copyright © 2020 Leo Prikler <leo.prikler@student.tugraz.at>
 ;;; Copyright © 2020 Florian Pelz <pelzflorian@pelzflorian.de>
+;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -63,7 +64,9 @@
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages inkscape)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages libbsd)
   #:use-module (gnu packages libedit)
   #:use-module (gnu packages linux)
@@ -2218,6 +2221,65 @@ X server: @code{handhelds}, @code{redglass} and @code{whiteglass}.")
     (license license:x11)))
 
 
+(define-public hackneyed-x11-cursors
+  ;; The current release 0.8 suffers from non-deterministic build problems.
+  (let ((revision "1")
+        (commit "9423cef2e2e5ff6b1d65d61f7108c97bc7f5fdfb"))
+    (package
+      (name "hackneyed-x11-cursors")
+      (version (git-version "0.8.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.com/Enthymeme/hackneyed-x11-cursors.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0f637i76sdwz3nm1g1iynamq6j0i6k3c70fpl0fmd0dlynm8ga96"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ;no test suite
+         #:make-flags (list (string-append "PREFIX=" %output))
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (add-before 'build 'set-inkscape-environment-variable
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((inkscape (string-append (assoc-ref inputs "inkscape")
+                                              "/bin/inkscape")))
+                 (setenv "INKSCAPE" inkscape)
+                 #t)))
+           (add-before 'build 'placate-inkscape-warnings
+             (lambda _
+               (setenv "HOME" (getcwd))
+               #t))
+           (add-after 'build 'generate-black-cursors
+             (lambda* (#:key make-flags parallel-build #:allow-other-keys)
+               (let ((build (assoc-ref %standard-phases 'build))
+                     (make-flags/extended
+                      `(,@make-flags
+                        "THEME_NAME=Hackneyed-Dark"
+                        "COMMON_SOURCE=theme/common-dark.svg"
+                        "RSVG_SOURCE=theme/right-handed-dark.svg"
+                        "LSVG_SOURCE=theme/left-handed-dark.svg")))
+                 (build #:make-flags make-flags/extended
+                        #:parallel-build parallel-build))))
+           (add-after 'install 'install-black-cursors
+             (lambda* (#:key make-flags #:allow-other-keys)
+               (apply invoke `("make" "install" ,@make-flags
+                               "THEME_NAME=Hackneyed-Dark")))))))
+      (native-inputs `(("imagemagick" ,imagemagick)
+                       ("inkscape" ,inkscape)
+                       ("xcursorgen" ,xcursorgen)))
+      (home-page "https://gitlab.com/Enthymeme/hackneyed-x11-cursors")
+      (synopsis "Classic cursor theme for X11")
+      (description "Hackneyed is a scalable cursor theme mildly resembling old
+Windows 3.x cursors.  The cursors are available in white and black colors.  A
+left-handed version of the cursors is also included.")
+      (license license:x11))))
+
 (define-public xcursorgen
   (package
     (name "xcursorgen")

From 63daca1e927136d184f41ebdd9b01923d1ee3bff Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:33:42 +0200
Subject: [PATCH 013/215] gnu: Add r-snplocs-hsapiens-dbsnp144-grch37.

* gnu/packages/bioconductor.scm (r-snplocs-hsapiens-dbsnp144-grch37): New
  variable.
---
 gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a27845581f..b5fa77655c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6466,6 +6466,44 @@ and parameters of which are trained on a set of aligned reads and a reference
 genome sequence.")
     (license license:lgpl3)))
 
+(define-public r-snplocs-hsapiens-dbsnp144-grch37
+  (package
+    (name "r-snplocs-hsapiens-dbsnp144-grch37")
+    (version "0.99.20")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
+                                     version 'annotation))
+              (sha256
+               (base32
+                "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
+    (build-system r-build-system)
+    ;; As this package provides little more than a very large data file it
+    ;; doesn't make sense to build substitutes.
+    (arguments `(#:substitutable? #f))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-iranges" ,r-iranges)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-biostrings" ,r-biostrings)))
+    (home-page
+     "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
+    (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
+    (description "This package provides SNP locations and alleles for Homo
+sapiens extracted from NCBI dbSNP Build 144.  The source data files used for
+this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
+to reference genome GRCh37.p13.  Note that the GRCh37.p13 genome is a
+patched version of GRCh37.  However the patch doesn't alter chromosomes 1-22,
+X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
+the mitochondrion chromosome.  Therefore, the SNPs in this package can be
+injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
+correct position but this injection will exclude chrM (i.e. nothing will be
+injected in that sequence).")
+    (license license:artistic2.0)))
+
 (define-public r-reqon
   (package
     (name "r-reqon")

From 1408e2abeb6e521c6929fb79b37b7d880dc78975 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:47:19 +0200
Subject: [PATCH 014/215] gnu: r-snplocs-hsapiens-dbsnp144-grch37: Fix
 description.

* gnu/packages/bioconductor.scm: Use two spaces after ending a sentence.
---
 gnu/packages/bioconductor.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b5fa77655c..0fc0d7b839 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6497,7 +6497,7 @@ sapiens extracted from NCBI dbSNP Build 144.  The source data files used for
 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
 to reference genome GRCh37.p13.  Note that the GRCh37.p13 genome is a
 patched version of GRCh37.  However the patch doesn't alter chromosomes 1-22,
-X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
+X, Y, MT.  GRCh37 itself is the same as the hg19 genome from UCSC *except* for
 the mitochondrion chromosome.  Therefore, the SNPs in this package can be
 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
 correct position but this injection will exclude chrM (i.e. nothing will be

From ef674a24c527eaf54801707d34dbf5d12ec139cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 22 Apr 2020 15:43:43 +0200
Subject: [PATCH 015/215] profiles: Add lowerable <profile> record type.

* guix/profiles.scm (<profile>): New record type.
* tests/profiles.scm ("<profile>"): New test.
---
 guix/profiles.scm  | 36 ++++++++++++++++++++++++++++++++++++
 tests/profiles.scm | 13 ++++++++++++-
 2 files changed, 48 insertions(+), 1 deletion(-)

diff --git a/guix/profiles.scm b/guix/profiles.scm
index 88606fa4ce..ab265cce62 100644
--- a/guix/profiles.scm
+++ b/guix/profiles.scm
@@ -125,6 +125,15 @@
             profile-derivation
             profile-search-paths
 
+            profile
+            profile?
+            profile-name
+            profile-content
+            profile-hooks
+            profile-locales?
+            profile-allow-collisions?
+            profile-relative-symlinks?
+
             generation-number
             generation-profile
             generation-numbers
@@ -1656,6 +1665,33 @@ are cross-built for TARGET."
                                        . ,(length
                                            (manifest-entries manifest))))))))
 
+;; Declarative profile.
+(define-record-type* <profile> profile make-profile
+  profile?
+  (name               profile-name (default "profile")) ;string
+  (content            profile-content)                  ;<manifest>
+  (hooks              profile-hooks                     ;list of procedures
+                      (default %default-profile-hooks))
+  (locales?           profile-locales?            ;Boolean
+                      (default #t))
+  (allow-collisions?  profile-allow-collisions?   ;Boolean
+                      (default #f))
+  (relative-symlinks? profile-relative-symlinks?  ;Boolean
+                      (default #f)))
+
+(define-gexp-compiler (profile-compiler (profile <profile>) system target)
+  "Compile PROFILE to a derivation."
+  (match profile
+    (($ <profile> name manifest hooks
+                  locales? allow-collisions? relative-symlinks?)
+     (profile-derivation manifest
+                         #:name name
+                         #:hooks hooks
+                         #:locales? locales?
+                         #:allow-collisions? allow-collisions?
+                         #:relative-symlinks? relative-symlinks?
+                         #:system system #:target target))))
+
 (define* (profile-search-paths profile
                                #:optional (manifest (profile-manifest profile))
                                #:key (getenv (const #f)))
diff --git a/tests/profiles.scm b/tests/profiles.scm
index 21c912a532..055924ba3e 100644
--- a/tests/profiles.scm
+++ b/tests/profiles.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Alex Kost <alezost@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -223,6 +223,17 @@
                  (string=? (dirname (readlink bindir))
                            (derivation->output-path guile))))))
 
+(test-assertm "<profile>"
+  (mlet* %store-monad
+      ((entry ->   (package->manifest-entry %bootstrap-guile))
+       (profile -> (profile (hooks '()) (locales? #f)
+                            (content (manifest (list entry)))))
+       (drv        (lower-object profile))
+       (profile -> (derivation->output-path drv))
+       (bindir ->  (string-append profile "/bin"))
+       (_          (built-derivations (list drv))))
+    (return (file-exists? (string-append bindir "/guile")))))
+
 (test-assertm "profile-derivation relative symlinks, one entry"
   (mlet* %store-monad
       ((entry ->   (package->manifest-entry %bootstrap-guile))

From cda751105e26c28256169ca9c267d9e2aafd6558 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 22 Apr 2020 15:51:26 +0200
Subject: [PATCH 016/215] system: 'operating-system-directory-base-entries'
 uses 'profile'.

* gnu/system.scm (operating-system-directory-base-entries): Use a
declarative profile instead of 'profile-derivation'.
---
 gnu/system.scm | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/gnu/system.scm b/gnu/system.scm
index 29e622872d..3a86564fa2 100644
--- a/gnu/system.scm
+++ b/gnu/system.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2016 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
@@ -491,22 +491,22 @@ possible (that is if there's a LINUX keyword argument in the build system)."
 (define* (operating-system-directory-base-entries os)
   "Return the basic entries of the 'system' directory of OS for use as the
 value of the SYSTEM-SERVICE-TYPE service."
-  (let ((locale (operating-system-locale-directory os)))
-    (mlet* %store-monad ((kernel -> (operating-system-kernel os))
-                         (modules ->
-                          (operating-system-kernel-loadable-modules os))
-                         (kernel
-                          (profile-derivation
-                           (packages->manifest
-                            (cons kernel
-                             (map (lambda (module)
-                                    (if (package? module)
-                                        (package-for-kernel kernel module)
-                                        module))
-                                  modules)))
-                           #:hooks (list linux-module-database)))
-                         (initrd -> (operating-system-initrd-file os))
-                         (params -> (operating-system-boot-parameters-file os)))
+  (let* ((locale  (operating-system-locale-directory os))
+         (kernel  (operating-system-kernel os))
+         (modules (operating-system-kernel-loadable-modules os))
+         (kernel  (profile
+                   (content (packages->manifest
+                             (cons kernel
+                                   (map (lambda (module)
+                                          (if (package? module)
+                                              (package-for-kernel kernel
+                                                                  module)
+                                              module))
+                                        modules))))
+                   (hooks (list linux-module-database))))
+         (initrd  (operating-system-initrd-file os))
+         (params  (operating-system-boot-parameters-file os)))
+    (with-monad %store-monad
       (return `(("kernel" ,kernel)
                 ("parameters" ,params)
                 ("initrd" ,initrd)

From 45bd91334f6a932ed65576febd6e71888563cd8f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 22 Apr 2020 15:55:08 +0200
Subject: [PATCH 017/215] services: profile: Use a declarative profile.

* gnu/services.scm (packages->profile-entry): Use 'profile' instead of
'profile-derivation'.
---
 gnu/services.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/services.scm b/gnu/services.scm
index 126e0814eb..ada6268a0b 100644
--- a/gnu/services.scm
+++ b/gnu/services.scm
@@ -691,10 +691,10 @@ executables, making them setuid-root.")))
 
 (define (packages->profile-entry packages)
   "Return a system entry for the profile containing PACKAGES."
-  (mlet %store-monad ((profile (profile-derivation
-                                (packages->manifest
-                                 (delete-duplicates packages eq?)))))
-    (return `(("profile" ,profile)))))
+  (with-monad %store-monad
+    (return `(("profile" ,(profile
+                           (content (packages->manifest
+                                     (delete-duplicates packages eq?)))))))))
 
 (define profile-service-type
   ;; The service that populates the system's profile---i.e.,

From 45c84c8f6f979c84d08b205ed3fb3d6769c4ae3f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 22 Apr 2020 16:11:25 +0200
Subject: [PATCH 018/215] pack: Use a declarative profile.

* guix/scripts/pack.scm (guix-pack): Use a declarative profile instead
of 'profile-derivation'.
---
 guix/scripts/pack.scm | 33 ++++++++++++++++-----------------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm
index 6d63fb4b90..f3d1b41c6f 100644
--- a/guix/scripts/pack.scm
+++ b/guix/scripts/pack.scm
@@ -1071,7 +1071,21 @@ Create a bundle of PACKAGE.\n"))
                    (localstatedir? (assoc-ref opts 'localstatedir?))
                    (entry-point    (assoc-ref opts 'entry-point))
                    (profile-name   (assoc-ref opts 'profile-name))
-                   (gc-root        (assoc-ref opts 'gc-root)))
+                   (gc-root        (assoc-ref opts 'gc-root))
+                   (profile        (profile
+                                    (content manifest)
+
+                                    ;; Always produce relative symlinks for
+                                    ;; Singularity (see
+                                    ;; <https://bugs.gnu.org/34913>).
+                                    (relative-symlinks?
+                                     (or relocatable?
+                                         (eq? 'squashfs pack-format)))
+
+                                    (hooks (if bootstrap?
+                                               '()
+                                               %default-profile-hooks))
+                                    (locales? (not bootstrap?)))))
               (define (lookup-package package)
                 (manifest-lookup manifest (manifest-pattern (name package))))
 
@@ -1085,22 +1099,7 @@ Create a bundle of PACKAGE.\n"))
 to your package list.")))
 
               (run-with-store store
-                (mlet* %store-monad ((profile (profile-derivation
-                                               manifest
-
-                                               ;; Always produce relative
-                                               ;; symlinks for Singularity (see
-                                               ;; <https://bugs.gnu.org/34913>).
-                                               #:relative-symlinks?
-                                               (or relocatable?
-                                                   (eq? 'squashfs pack-format))
-
-                                               #:hooks (if bootstrap?
-                                                           '()
-                                                           %default-profile-hooks)
-                                               #:locales? (not bootstrap?)
-                                               #:target target))
-                                     (drv (build-image name profile
+                (mlet* %store-monad ((drv (build-image name profile
                                                        #:target
                                                        target
                                                        #:compressor

From 0e5c2d5e145118ec47329d6b3a534344d2e89cd3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 22 Apr 2020 16:22:33 +0200
Subject: [PATCH 019/215] services: system: Initial entries are non-monadic.

* gnu/system.scm (operating-system-directory-base-entries): Return a
regular, non-monadic value.
* gnu/services.scm (system-derivation): Adjust accordingly.
* gnu/system/linux-container.scm (container-essential-services): Likewise.
---
 gnu/services.scm               | 5 ++---
 gnu/system.scm                 | 9 ++++-----
 gnu/system/linux-container.scm | 6 ++----
 3 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/gnu/services.scm b/gnu/services.scm
index ada6268a0b..2e4648bf78 100644
--- a/gnu/services.scm
+++ b/gnu/services.scm
@@ -318,11 +318,10 @@ This is a shorthand for (map (lambda (svc) ...) %base-services)."
 ;;; Core services.
 ;;;
 
-(define (system-derivation mentries mextensions)
+(define (system-derivation entries mextensions)
   "Return as a monadic value the derivation of the 'system' directory
 containing the given entries."
-  (mlet %store-monad ((entries    mentries)
-                      (extensions (mapm/accumulate-builds identity
+  (mlet %store-monad ((extensions (mapm/accumulate-builds identity
                                                           mextensions)))
     (lower-object
      (file-union "system"
diff --git a/gnu/system.scm b/gnu/system.scm
index 3a86564fa2..3c511f4089 100644
--- a/gnu/system.scm
+++ b/gnu/system.scm
@@ -506,11 +506,10 @@ value of the SYSTEM-SERVICE-TYPE service."
                    (hooks (list linux-module-database))))
          (initrd  (operating-system-initrd-file os))
          (params  (operating-system-boot-parameters-file os)))
-    (with-monad %store-monad
-      (return `(("kernel" ,kernel)
-                ("parameters" ,params)
-                ("initrd" ,initrd)
-                ("locale" ,locale))))))   ;used by libc
+    `(("kernel" ,kernel)
+      ("parameters" ,params)
+      ("initrd" ,initrd)
+      ("locale" ,locale))))   ;used by libc
 
 (define (operating-system-default-essential-services os)
   "Return the list of essential services for OS.  These are special services
diff --git a/gnu/system/linux-container.scm b/gnu/system/linux-container.scm
index c8807398b3..c5e2e4bf9c 100644
--- a/gnu/system/linux-container.scm
+++ b/gnu/system/linux-container.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
-;;; Copyright © 2016, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2019 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;;
@@ -53,9 +53,7 @@ from OS that are needed on the bare metal and not in a container."
             (operating-system-default-essential-services os)))
 
   (cons (service system-service-type
-                 (let ((locale (operating-system-locale-directory os)))
-                   (with-monad %store-monad
-                     (return `(("locale" ,locale))))))
+                 `(("locale" ,(operating-system-locale-directory os))))
         ;; If network is to be shared with the host, remove network
         ;; configuration files from etc-service.
         (if shared-network?

From ccbc427f9ac8f63478f1692686b042a22c4df2c3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 26 Apr 2020 22:12:32 +0200
Subject: [PATCH 020/215] channels: Use a declarative profile.

* guix/channels.scm (package-cache-file): Use 'profile' instead of
'profile-derivation'.
---
 guix/channels.scm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/guix/channels.scm b/guix/channels.scm
index 785b97722e..041fae2a9c 100644
--- a/guix/channels.scm
+++ b/guix/channels.scm
@@ -568,9 +568,7 @@ channel instances."
 (define (package-cache-file manifest)
   "Build a package cache file for the instance in MANIFEST.  This is meant to
 be used as a profile hook."
-  (mlet %store-monad ((profile (profile-derivation manifest
-                                                   #:hooks '())))
-
+  (let ((profile (profile (content manifest) (hooks '()))))
     (define build
       #~(begin
           (use-modules (gnu packages))

From 3b177a6c33baa0d78ebd5407119511807d59a590 Mon Sep 17 00:00:00 2001
From: Brice Waegeneire <brice@waegenei.re>
Date: Sun, 26 Apr 2020 22:51:02 +0200
Subject: [PATCH 021/215] gnu: Add loadable module to wireguard-linux-compat.

* gnu/packages/vpn.scm (wireguard-linux-compat)[build-system]: Replace
'gnu-build-system' by 'linux-module-build-system'.
[outputs]: Add 'kernel-patch'.
[arguments]: Adjust the build system. Add phases 'change-directory' and
'reset-cwd'. Rename phases 'build' to 'build-patch' and 'install' to
'install-patch'.
[description]: Mention the loadable module.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/vpn.scm | 31 ++++++++++++++++++++++---------
 1 file changed, 22 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 739522959c..a9e20049c6 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2019, 2020 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -34,6 +35,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system linux-module)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages admin)
@@ -465,19 +467,24 @@ The peer-to-peer VPN implements a Layer 2 (Ethernet) network between the peers
               (sha256
                (base32
                 "0ymprz3h4b92wlcqm5k5vmcgap8pjv202bgkdx0axmp12n1lmyvx"))))
-    (build-system gnu-build-system)
+    (build-system linux-module-build-system)
+    (outputs '("out"
+               "kernel-patch"))
     (arguments
      `(#:tests? #f ; No test suite
-       #:modules ((guix build gnu-build-system)
+       #:modules ((guix build linux-module-build-system)
                   (guix build utils)
                   (ice-9 popen)
                   (ice-9 textual-ports))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure) ; No ./configure script
-         (replace 'build
+         (add-before 'build 'change-directory
+           (lambda _
+             (chdir "./src")
+             #t))
+         (add-after 'build 'build-patch
            (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((patch-builder "./kernel-tree-scripts/create-patch.sh")
+             (let* ((patch-builder "../kernel-tree-scripts/create-patch.sh")
                     (port (open-input-pipe patch-builder))
                     (str (get-string-all port)))
                (close-pipe port)
@@ -485,15 +492,21 @@ The peer-to-peer VPN implements a Layer 2 (Ethernet) network between the peers
                  (lambda (port)
                    (format port "~a" str))))
                #t))
-         (replace 'install
+         (add-after 'install 'install-patch
            (lambda* (#:key outputs #:allow-other-keys)
              (install-file "wireguard.patch"
-                           (assoc-ref %outputs "out"))
+                           (assoc-ref %outputs "kernel-patch"))
+             #t))
+         ;; So that 'install-license-files' works...
+         (add-before 'install-license-files 'reset-cwd
+           (lambda _
+             (chdir "..")
              #t)))))
     (home-page "https://git.zx2c4.com/wireguard-linux-compat/")
     (synopsis "WireGuard kernel module for Linux 3.10 through 5.5")
-    (description "This is an out-of-tree Linux kernel patch adding WireGuard to
-kernel versions 3.10 through 5.5.  WireGuard was added to Linux 5.6.")
+    (description "This package contains an out-of-tree kernel patch and
+a loadable module adding WireGuard to Linux kernel versions 3.10 through 5.5.
+WireGuard was added to Linux 5.6.")
     (license license:gpl2)))
 
 (define-public wireguard-tools

From 8472c26c254c0381018a3903feb55f31b1ea96f1 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 26 Apr 2020 23:01:03 -0400
Subject: [PATCH 022/215] gnu: liblinphone: Remove hicolor-icon-theme and
 murrine inputs.

Icon themes and theme engines are best left for the users to select and
install themselves.

* gnu/packages/linphone.scm (liblinphone)[inputs]: Remove hicolor-icon-theme.
[propagated-inputs]: Remove murrine.
---
 gnu/packages/linphone.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/linphone.scm b/gnu/packages/linphone.scm
index 8962f2001e..e8aeabe419 100644
--- a/gnu/packages/linphone.scm
+++ b/gnu/packages/linphone.scm
@@ -459,7 +459,6 @@ decoding, and rendering.")
        ("belcard" ,belcard)
        ("bellesip" ,belle-sip)
        ("bzrtp", bzrtp)
-       ("hicolor-icon-theme" ,hicolor-icon-theme) ; Hard-coded for GTK UI
        ("glib" ,glib)
        ("gtk2" ,gtk+-2)
        ("mediastreamer2" ,mediastreamer2)
@@ -469,8 +468,6 @@ decoding, and rendering.")
        ("six" ,python-six)
        ("sqlite" ,sqlite)
        ("udev" ,eudev)))
-    (propagated-inputs
-     `(("murrine" ,murrine)))           ; Required for GTK UI
     (synopsis "Belledonne Communications Softphone Library")
     (description "Liblinphone is a high-level SIP library integrating
 all calling and instant messaging features into an unified

From 1ae43257347db6e93c6aac37fa622969f245294c Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 26 Apr 2020 23:10:21 -0400
Subject: [PATCH 023/215] gnu: liblinphone: Fix the input type of some
 dependencies.

Libraries being linked to such as libxml2, libiconv and zlib should appear as
'inputs' rather than 'native-inputs'.

* gnu/packages/linphone.scm (liblinphone)[native-inputs]: Move libiconv,
libxml2 and zlib to...
[inputs]: ...here.  Move eudev, python-pystache and python-six to
native-inputs.
---
 gnu/packages/linphone.scm | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/linphone.scm b/gnu/packages/linphone.scm
index e8aeabe419..09d5a1121e 100644
--- a/gnu/packages/linphone.scm
+++ b/gnu/packages/linphone.scm
@@ -447,27 +447,28 @@ decoding, and rendering.")
                 ""))
              #t)))))
     (native-inputs
-     `(("dot" ,graphviz)
+     `(("gettext" ,gettext-minimal)
+       ("udev" ,eudev)                  ;for libudev.h
+       ;; For generating the C++ wrappers.
+       ("dot" ,graphviz)
        ("doxygen" ,doxygen)
-       ("gettext" ,gettext-minimal)
-       ("iconv" ,libiconv)
        ("python" ,python)
-       ("xml2" ,libxml2)
-       ("zlib" ,zlib)))
+       ("pystache" ,python-pystache)
+       ("six" ,python-six)))
     (inputs
      `(("bctoolbox" ,bctoolbox)
        ("belcard" ,belcard)
        ("bellesip" ,belle-sip)
        ("bzrtp", bzrtp)
+       ("iconv" ,libiconv)
        ("glib" ,glib)
        ("gtk2" ,gtk+-2)
        ("mediastreamer2" ,mediastreamer2)
        ("notify" ,libnotify)
        ("ortp" ,ortp)
-       ("pystache" ,python-pystache)
-       ("six" ,python-six)
        ("sqlite" ,sqlite)
-       ("udev" ,eudev)))
+       ("xml2" ,libxml2)
+       ("zlib" ,zlib)))
     (synopsis "Belledonne Communications Softphone Library")
     (description "Liblinphone is a high-level SIP library integrating
 all calling and instant messaging features into an unified

From 9c63165d9ee33a7a7e9017d7a36f658b5c2c415c Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Mon, 27 Apr 2020 00:50:48 -0400
Subject: [PATCH 024/215] gnu: liblinphone: Move documentation and tester to
 separate outputs.

* gnu/packages/linphone.scm (liblinphone)[outputs]: Add a "doc" and "tester"
outputs.
[phases]: Add a separate-outputs phase.  Move the
glib-or-gtk-compile-schemas and glib-or-gtk-wrap phases after it.
---
 gnu/packages/linphone.scm | 32 +++++++++++++++++++++++++++-----
 1 file changed, 27 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/linphone.scm b/gnu/packages/linphone.scm
index 09d5a1121e..e7d3cf7aaf 100644
--- a/gnu/packages/linphone.scm
+++ b/gnu/packages/linphone.scm
@@ -416,6 +416,7 @@ decoding, and rendering.")
                        "/linphone-" version ".tar.gz"))
        (sha256
         (base32 "0phhkx55xdyg28d4wn8l8q4yvsmdgzmjiw584d4s190sq1azm91x"))))
+    (outputs '("out" "doc" "tester"))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; No test target
@@ -436,16 +437,37 @@ decoding, and rendering.")
                   (guix build utils))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'install 'glib-or-gtk-compile-schemas
-           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
-         (add-after 'install 'glib-or-gtk-wrap
-           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
          (add-after 'unpack 'patch
            (lambda _
              (substitute* "gtk/main.c"
                (("#include \"liblinphone_gitversion.h\"")
                 ""))
-             #t)))))
+             #t))
+         (add-after 'install 'separate-outputs
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (doc (assoc-ref outputs "doc"))
+                    (tester (assoc-ref outputs "tester"))
+                    (tester-name (string-append ,name "_tester")))
+               ;; Copy the tester executable.
+               (mkdir-p (string-append tester "/bin"))
+               (rename-file (string-append out "/bin/" tester-name)
+                            (string-append tester "/bin/" tester-name))
+               ;; Copy the tester data files.
+               (mkdir-p (string-append tester "/share/"))
+               (rename-file (string-append out "/share/" tester-name)
+                            (string-append tester "/share/" tester-name))
+               ;; Copy the HTML and XML documentation.
+               (copy-recursively
+                (string-append out "/share/doc/linphone-" ,version)
+                (string-append doc "/share/doc/" ,name "-" ,version))
+               (delete-file-recursively
+                (string-append out "/share/doc/linphone-" ,version))
+               #t)))
+         (add-after 'separate-outputs 'glib-or-gtk-compile-schemas
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
+         (add-after 'glib-or-gtk-compile-schemas 'glib-or-gtk-wrap
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
     (native-inputs
      `(("gettext" ,gettext-minimal)
        ("udev" ,eudev)                  ;for libudev.h

From 8521d93854db773806824416be0fef6675ed3719 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:11:21 +0200
Subject: [PATCH 025/215] gnu: Add r-reordercluster.

* gnu/packages/cran.scm (r-reordercluster): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b918a4aa49..94ed889609 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -449,6 +449,27 @@ small, reproducible, and runnable examples on code-oriented websites or email.
 such as copy/paste from an R session.")
     (license license:expat)))
 
+(define-public r-reordercluster
+  (package
+   (name "r-reordercluster")
+   (version "1.0")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "ReorderCluster" version))
+            (sha256
+             (base32
+              "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-gplots" ,r-gplots)
+      ("r-rcpp" ,r-rcpp)))
+   (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
+   (synopsis "Reordering the dendrogram according to the class labels")
+   (description "This package provides tools for performing the leaf reordering
+for the dendrogram that preserves the hierarchical clustering result and at the
+same time tries to group instances from the same class together.")
+   (license license:gpl3+)))
+
 (define-public r-callr
   (package
     (name "r-callr")

From df6c7f04878f9881d805517f77a8dc493edd8a8f Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:18:48 +0200
Subject: [PATCH 026/215] gnu: Add r-ecp.

* gnu/packages/cran.scm (r-ecp): New variable.
---
 gnu/packages/cran.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 94ed889609..246a76a6e2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
@@ -177,6 +177,30 @@ legends.")
 control over dimensions and appearance.")
     (license license:gpl2+)))
 
+(define-public r-ecp
+  (package
+    (name "r-ecp")
+    (version "3.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "ecp" version))
+              (sha256
+               (base32
+                "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://cran.r-project.org/web/packages/ecp/")
+    (synopsis "Multiple change-point analysis of multivariate data")
+    (description
+     "This package implements various procedures for finding multiple
+change-points.  Two methods make use of dynamic programming and pruning, with
+no distributional assumptions other than the existence of certain absolute
+moments in one method.  Hierarchical and exact search methods are included.
+All methods return the set of estimated change-points as well as other summary
+information.")
+    (license license:gpl2+)))
+
 (define-public r-ellipsis
   (package
     (name "r-ellipsis")

From e8d435f7a2919e8f05fc3822d1a43f50c6c5cc8a Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:24:20 +0200
Subject: [PATCH 027/215] gnu: Add r-ideoviz.

* gnu/packages/bioconductor.scm (r-ideoviz): New variable.
---
 gnu/packages/bioconductor.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0fc0d7b839..9540de3b72 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
 ;;;
@@ -718,6 +718,30 @@ annotations.")
      "This is a manifest package for Illumina's EPIC methylation arrays.")
     (license license:artistic2.0)))
 
+(define-public r-ideoviz
+  (package
+    (name "r-ideoviz")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "IdeoViz" version))
+              (sha256
+               (base32
+                "0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-iranges" ,r-iranges)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-genomeinfodb" ,r-genomeinfodb)))
+    (home-page "https://bioconductor.org/packages/IdeoViz/")
+    (synopsis "Plots data along a chromosomal ideogram")
+    (description "This package provides functions to plot data associated with
+arbitrary genomic intervals along chromosomal ideogram.")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
 ;; from Bioconductor.
 (define-public r-deconstructsigs

From e658838c62062482f2cdcbc2f94aaae9130c1257 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:28:50 +0200
Subject: [PATCH 028/215] gnu: Add r-bezier.

* gnu/packages/cran.scm (r-bezier): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 246a76a6e2..529424480a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -83,6 +83,25 @@
   #:use-module (gnu packages web)
   #:use-module (gnu packages xorg))
 
+(define-public r-bezier
+  (package
+    (name "r-bezier")
+    (version "1.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "bezier" version))
+              (sha256
+               (base32
+                "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/bezier/")
+    (synopsis "Bezier curve and spline toolkit")
+    (description
+     "This package is a toolkit for working with Bezier curves and splines.
+The package provides functions for point generation, arc length estimation,
+degree elevation and curve fitting.")
+    (license license:gpl2+)))
+
 (define-public r-clipr
   (package
     (name "r-clipr")

From cb1ab0352b1f70dd1a5c56c7bd12de82c0b7fde5 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:37:42 +0200
Subject: [PATCH 029/215] gnu: Add r-karyoploter.

* gnu/packages/bioconductor.scm (r-karyoploter): New variable.
---
 gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9540de3b72..d74d1cf706 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2583,6 +2583,41 @@ and regression inferences from RNA-sequencing data.")
 gene and isoform level using RNA-seq data")
     (license license:artistic2.0)))
 
+(define-public r-karyoploter
+  (package
+    (name "r-karyoploter")
+    (version "1.12.4")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "karyoploteR" version))
+              (sha256
+               (base32
+                "03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-regioner" ,r-regioner)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-memoise" ,r-memoise)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-biovizbase" ,r-biovizbase)
+       ("r-digest" ,r-digest)
+       ("r-bezier" ,r-bezier)
+       ("r-bamsignals" ,r-bamsignals)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://bioconductor.org/packages/karyoploteR/")
+    (synopsis "Plot customizable linear genomes displaying arbitrary data")
+    (description "This package creates karyotype plots of arbitrary genomes and
+offers a complete set of functions to plot arbitrary data on them.  It mimicks
+many R base graphics functions coupling them with a coordinate change function
+automatically mapping the chromosome and data coordinates into the plot
+coordinates.")
+    (license license:artistic2.0)))
+
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")

From 8ce240fdbf05539b0d13f981b0520be5d84e0e61 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:43:51 +0200
Subject: [PATCH 030/215] gnu: Add r-bsgenome-hsapiens-ucsc-hg38.

* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): New variable.
---
 gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d74d1cf706..66ff6114c3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -493,6 +493,30 @@ annotations for the genome of the model mouse Mus musculus.")
 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-hsapiens-ucsc-hg38
+  (package
+    (name "r-bsgenome-hsapiens-ucsc-hg38")
+    (version "1.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
+                                     version 'annotation))
+              (sha256
+               (base32
+                "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
+    (properties
+     `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)))
+    (home-page
+     "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
+    (synopsis "Full genome sequences for Homo sapiens")
+    (description
+     "This package provides full genome sequences for Homo sapiens (Human)
+as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-ensdb-hsapiens-v75
   (package
     (name "r-ensdb-hsapiens-v75")

From 320dd1195e6ff3bc10001e37e97c161650091ebe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 26 Apr 2020 10:26:32 +0200
Subject: [PATCH 031/215] gnu: Add texlive-inconsolata.

* gnu/packages/tex.scm (texlive-inconsolata): New variable.
---
 gnu/packages/tex.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index d5bcff0371..10270271c9 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4902,6 +4902,32 @@ fonts.  Note that direct substitutes for the bitmapped EC fonts are available,
 via the CM-super, Latin Modern and (in a restricted way) CM-LGC font sets.")
     (license license:lppl1.3+)))
 
+(define-public texlive-inconsolata
+  (package
+    (inherit (simple-texlive-package
+              "texlive-inconsolata"
+              (list "/doc/fonts/inconsolata/"
+                    "/fonts/enc/dvips/inconsolata/"
+                    "/fonts/map/dvips/inconsolata/"
+                    "/fonts/opentype/public/inconsolata/"
+                    "/fonts/tfm/public/inconsolata/"
+                    "/fonts/type1/public/inconsolata/"
+                    "/tex/latex/inconsolata/")
+              (base32
+               "1a77w26m4c4j0202s1qkikz7ha6cxlv8zxhzi9s3l0x1l2pl7cr2")
+              #:trivial? #t))
+    (home-page "https://www.ctan.org/pkg/inconsolata")
+    (synopsis "Monospaced font with support files for use with TeX")
+    (description
+     "Inconsolata is a monospaced font designed by Raph Levien.  This package
+contains the font (in both Adobe Type 1 and OpenType formats) in regular and
+bold weights, with additional glyphs and options to control slashed zero,
+upright quotes and a shapelier lower-case L, plus metric files for use with
+TeX, and LaTeX font definition and other relevant files.")
+    (license (list license:lppl1.3+
+                   license:silofl1.1
+                   license:asl2.0))))
+
 (define-public texlive-times
   (package
     (inherit (simple-texlive-package

From c170a15996caeca35d1077452f15eaba1a9db1de Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 26 Apr 2020 21:00:24 +0200
Subject: [PATCH 032/215] gnu: emacs-org-reveal: Fix syntax error in
 description.

* gnu/packages/emacs-xyz.scm (emacs-org-reveal)[description]: Fix Texinfo
syntax error.
---
 gnu/packages/emacs-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 17aea794c4..a0275cbe18 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -14314,7 +14314,7 @@ notes.")
       (build-system emacs-build-system)
       (home-page "https://github.com/yjwen/org-reveal")
       (synopsis "Org and Reveal.js powered HTML presentation tool")
-      (description "Org-Reveal is a command@{org-mode} extension that allows
+      (description "Org-Reveal is a @command{org-mode} extension that allows
 to create beautiful presentations (slides) with 3D effects from simple but
 powerful Org contents.")
       (license license:gpl3+))))

From d4f86c8b6634d0814ceb51cce4d05da1e16bf408 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 10:40:00 +0200
Subject: [PATCH 033/215] gnu: Add peek.

* gnu/packages/video.scm (peek): New variable.
---
 gnu/packages/video.scm | 37 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index ce5261c788..1ae678da85 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Andy Patterson <ajpatter@uwaterloo.ca>
-;;; Copyright © 2015, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2016, 2017 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
@@ -4036,3 +4036,38 @@ result in several formats:
     (description
      "The fastest and safest AV1 encoder.")
     (license license:bsd-2)))
+
+(define-public peek
+  (package
+    (name "peek")
+    (version "1.5.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/phw/peek.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1xwlfizga6hvjqq127py8vabaphsny928ar7mwqj9cyqfl6fx41x"))))
+    (build-system meson-build-system)
+    (arguments '(#:glib-or-gtk? #t))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (native-inputs
+     `(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database
+       ("gettext" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")         ; for glib-compile-resources
+       ("gtk+-bin" ,gtk+ "bin")         ; For gtk-update-icon-cache
+       ("pkg-config" ,pkg-config)
+       ("vala" ,vala)))
+    (home-page "https://github.com/phw/peek")
+    (synopsis "Simple animated GIF screen recorder")
+    (description
+     "Peek makes it easy to create short screencasts of a screen area.  It was
+built for the specific use case of recording screen areas, e.g. for easily
+showing UI features of your own apps or for showing a bug in bug reports.
+With Peek, you simply place the Peek window over the area you want to record
+and press \"Record\".  Peek is optimized for generating animated GIFs, but you
+can also directly record to WebM or MP4 if you prefer.")
+    (license license:gpl3+)))

From 0c0ef9c5a6e54206eb9ca51f242cd95e07406f26 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:56:07 +0200
Subject: [PATCH 034/215] gnu: Add r-coverageview.

* gnu/packages/bioconductor.scm (r-coverageview): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 66ff6114c3..83ac5dcf7c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1069,6 +1069,33 @@ examples' of Affymetrix data, unlike the artificial examples included in the
 package @code{affy}.")
     (license license:gpl2+)))
 
+(define-public r-coverageview
+  (package
+    (name "r-coverageview")
+    (version "1.24.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "CoverageView" version))
+              (sha256
+               (base32
+                "0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-s4vectors" ,r-s4vectors)
+       ("r-iranges" ,r-iranges)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rsamtools" ,r-rsamtools)))
+    (home-page "https://bioconductor.org/packages/CoverageView/")
+    (synopsis "Coverage visualization package for R")
+    (description "This package provides a framework for the visualization of
+genome coverage profiles.  It can be used for ChIP-seq experiments, but it can
+be also used for genome-wide nucleosome positioning experiments or other
+experiment types where it is important to have a framework in order to inspect
+how the coverage distributed across the genome.")
+    (license license:artistic2.0)))
+
 (define-public r-curatedtcgadata
   (package
     (name "r-curatedtcgadata")

From 415176e89df200c0e8d4cee348bc67b739112bbb Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 11:05:49 +0200
Subject: [PATCH 035/215] gnu: Add r-ggpmisc.

* gnu/packages/cran.scm (r-ggpmisc): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 529424480a..86f33100f1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -121,6 +121,36 @@ degree elevation and curve fitting.")
 the system clipboards.")
     (license license:gpl3)))
 
+(define-public r-ggpmisc
+  (package
+    (name "r-ggpmisc")
+    (version "0.3.4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "ggpmisc" version))
+              (sha256
+               (base32
+                "0xc1yp0kphipq23ri4ij93garx1x2nrf4i0lhs6m10pp9yz7fbmj"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-broom" ,r-broom)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-lubridate" ,r-lubridate)
+       ("r-mass" ,r-mass)
+       ("r-plyr" ,r-plyr)
+       ("r-polynom" ,r-polynom)
+       ("r-splus2r" ,r-splus2r)
+       ("r-tibble" ,r-tibble)
+       ("r-xts" ,r-xts)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://www.r4photobiology.info/")
+    (synopsis "Miscellaneous Extensions to @code{ggplot2}")
+    (description "This package provides extensions to @code{ggplot2},
+respecting the grammar of its graphics paradigm.")
+    (license license:gpl2+)))
+
 (define-public r-oenb
   (package
     (name "r-oenb")

From 91370829f4b7d043673e283466d1795143e91684 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 11:15:38 +0200
Subject: [PATCH 036/215] gnu: Add r-inum.

* gnu/packages/cran.scm (r-inum): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 86f33100f1..74e5fa2b1e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2494,6 +2494,27 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
     ;; Any version of the LGPL.
     (license license:lgpl3+)))
 
+(define-public r-inum
+  (package
+    (name "r-inum")
+    (version "1.0-1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "inum" version))
+              (sha256
+               (base32
+                "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-libcoin" ,r-libcoin)))
+    (home-page "https://cran.r-project.org/web/packages/inum/")
+    (synopsis "Interval and enum-type representation of vectors")
+    (description
+     "This package provides an enum-type representation of vectors and
+representation of intervals, including a method of coercing variables
+in data frames.")
+    (license license:gpl2)))
+
 (define-public r-bdsmatrix
   (package
     (name "r-bdsmatrix")

From 06fc1a51427f5af0e337e16602cb4920865d54fb Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 11:46:08 +0200
Subject: [PATCH 037/215] gnu: Add r-cummerbund.

* gnu/packages/bioconductor.scm (r-cummerbund): New variable.
---
 gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 83ac5dcf7c..b4be8aee15 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1096,6 +1096,36 @@ experiment types where it is important to have a framework in order to inspect
 how the coverage distributed across the genome.")
     (license license:artistic2.0)))
 
+(define-public r-cummerbund
+  (package
+   (name "r-cummerbund")
+   (version "2.28.0")
+   (source (origin
+             (method url-fetch)
+             (uri (bioconductor-uri "cummeRbund" version))
+             (sha256
+              (base32
+               "1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-biobase" ,r-biobase)
+      ("r-biocgenerics" ,r-biocgenerics)
+      ("r-fastcluster", r-fastcluster)
+      ("r-ggplot2" ,r-ggplot2)
+      ("r-gviz" ,r-gviz)
+      ("r-plyr" ,r-plyr)
+      ("r-reshape2" ,r-reshape2)
+      ("r-rsqlite" ,r-rsqlite)
+      ("r-rtracklayer" ,r-rtracklayer)
+      ("r-s4vectors" ,r-s4vectors)))
+   (home-page "https://bioconductor.org/packages/cummeRbund/")
+   (synopsis "Analyze Cufflinks high-throughput sequencing data")
+   (description "This package allows for persistent storage, access,
+exploration, and manipulation of Cufflinks high-throughput sequencing
+data.  In addition, provides numerous plotting functions for commonly
+used visualizations.")
+   (license license:artistic2.0)))
+
 (define-public r-curatedtcgadata
   (package
     (name "r-curatedtcgadata")

From 4c24186ae0798cd3263c1647d5f9aab0719b3d15 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 13:09:02 +0200
Subject: [PATCH 038/215] gnu: Add python-bitarray.

* gnu/packages/python-xyz.scm (python-bitarray): New variable.
---
 gnu/packages/python-xyz.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9460a59e31..31cafd47d1 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -39,7 +39,7 @@
 ;;; Copyright © 2017 Ben Sturmfels <ben@sturm.com.au>
 ;;; Copyright © 2017, 2018, 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 José Miguel Sánchez García <jmi2k@openmailbox.org>
-;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2017, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com>
@@ -640,6 +640,30 @@ certificate returned by the server to which a connection has been established,
 and verifies that it matches the intended target hostname.")
     (license license:psfl)))
 
+(define-public python-bitarray
+  (package
+    (name "python-bitarray")
+    (version "1.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "bitarray" version))
+              (sha256
+               (base32
+                "1kxrlxfj9nrx512sfwifwl9z4v6ky3qschl0zmk3s3dvc3s7bmif"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/ilanschnell/bitarray")
+    (synopsis "Efficient arrays of booleans")
+    (description "This package provides an object type which efficiently
+represents an array of booleans.  Bitarrays are sequence types and behave very
+much like usual lists.  Eight bits are represented by one byte in a contiguous
+block of memory.  The user can select between two representations:
+little-endian and big-endian.  All of the functionality is implemented in C.
+Methods for accessing the machine representation are provided.  This can be
+useful when bit level access to binary files is required, such as portable
+bitmap image files.  Also, when dealing with compressed data which uses
+variable bit length encoding, you may find this module useful.")
+    (license license:psfl)))
+
 (define-public python-boolean.py
   (package
     (name "python-boolean.py")

From c43edf6f3012436aef8196a406bb407beda3e533 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 13:39:25 +0200
Subject: [PATCH 039/215] gnu: Add python-deeptoolsintervals.

* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
---
 gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6c5b49e37e..cd401d97f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2334,6 +2334,27 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
 files.  The code was previously part of the cutadapt tool.")
     (license license:expat)))
 
+(define-public python-deeptoolsintervals
+  (package
+    (name "python-deeptoolsintervals")
+    (version "0.1.9")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "deeptoolsintervals" version))
+              (sha256
+               (base32
+                "1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x"))))
+    (build-system python-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/deeptools/deeptools_intervals")
+    (synopsis "Create GTF-based interval trees with associated meta-data")
+    (description
+     "This package provides a Python module creating/accessing GTF-based
+interval trees with associated meta-data.  It is primarily used by the
+@code{deeptools} package.")
+    (license license:expat)))
+
 (define-public cutadapt
   (package
     (name "cutadapt")

From ccf70a80a12be86ed609ce7d37d3ae32f75edc39 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 13:40:00 +0200
Subject: [PATCH 040/215] gnu: Add python-deeptools.

* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
---
 gnu/packages/bioinformatics.scm | 37 ++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cd401d97f3..8ef2880472 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
@@ -2355,6 +2355,41 @@ interval trees with associated meta-data.  It is primarily used by the
 @code{deeptools} package.")
     (license license:expat)))
 
+(define-public python-deeptools
+  (package
+    (name "python-deeptools")
+    (version "3.4.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "deepTools" version))
+              (sha256
+               (base32
+                "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-matplotlib" ,python-matplotlib)
+       ("python-numpy" ,python-numpy)
+       ("python-numpydoc" ,python-numpydoc)
+       ("python-py2bit" ,python-py2bit)
+       ("python-pybigwig" ,python-pybigwig)
+       ("python-pysam" ,python-pysam)
+       ("python-scipy" ,python-scipy)
+       ("python-deeptoolsintervals" ,python-deeptoolsintervals)
+       ("python-plotly" ,python-plotly)))
+    (home-page "https://pypi.org/project/deepTools/")
+    (synopsis "Useful tools for exploring deep sequencing data")
+    (description "This package addresses the challenge of handling large amounts
+of data that are now routinely generated from DNA sequencing centers.
+@code{deepTools} contains useful modules to process the mapped reads data for
+multiple quality checks, creating normalized coverage files in standard bedGraph
+and bigWig file formats, that allow comparison between different files.  Finally,
+using such normalized and standardized files, deepTools can create many
+publication-ready visualizations to identify enrichments and for functional
+annotations of the genome.")
+    ;; The file deeptools/cm.py is licensed under the BSD license.  The
+    ;; remainder of the code is licensed under the MIT license.
+    (license (list license:bsd-3 license:expat))))
+
 (define-public cutadapt
   (package
     (name "cutadapt")

From 639ae3f20bea5ccd7f4a4df7a828569639220e79 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 13:54:43 +0200
Subject: [PATCH 041/215] gnu: Add python-scikit-rebate.

* gnu/packages/machine-learning.scm (python-scikit-rebate): New variable.
---
 gnu/packages/machine-learning.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 9a88b53415..223d03e979 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -867,6 +867,35 @@ data analysis.")
                  (base32
                   "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj")))))))
 
+(define-public python-scikit-rebate
+  (package
+    (name "python-scikit-rebate")
+    (version "0.6")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "skrebate" version))
+              (sha256
+               (base32
+                "1h7qs9gjxpzqabzhb8rmpv3jpmi5iq41kqdibg48299h94iikiw7"))))
+    (build-system python-build-system)
+    ;; Pandas is only needed to run the tests.
+    (native-inputs
+     `(("python-pandas" ,python-pandas)))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-joblib" ,python-joblib)))
+    (home-page "https://epistasislab.github.io/scikit-rebate/")
+    (synopsis "Relief-based feature selection algorithms for Python")
+    (description "Scikit-rebate is a scikit-learn-compatible Python
+implementation of ReBATE, a suite of Relief-based feature selection algorithms
+for Machine Learning.  These algorithms excel at identifying features that are
+predictive of the outcome in supervised learning problems, and are especially
+good at identifying feature interactions that are normally overlooked by
+standard feature selection algorithms.")
+    (license license:expat)))
+
 (define-public python-autograd
   (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
          (revision "0")

From 2ef4d273d13faccbc9e11a74cfdbd0a9f4f1c898 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jakub=20K=C4=85dzio=C5=82ka?= <kuba@kadziolka.net>
Date: Sun, 26 Apr 2020 17:58:58 +0200
Subject: [PATCH 042/215] file-systems: mount the PID cgroup filesystem.

* gnu/system/file-systems.scm (%control-groups): Add "pids".
* gnu/services/docker.scm (docker-shepherd-service): Resolve a TODO.

This has allowed me to make a specific configuration of nsjail work.
---
 gnu/services/docker.scm     | 3 ++-
 gnu/system/file-systems.scm | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/services/docker.scm b/gnu/services/docker.scm
index 04f9127346..d6dc792821 100644
--- a/gnu/services/docker.scm
+++ b/gnu/services/docker.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -94,7 +95,7 @@ loop-back communications.")
                           file-system-/sys/fs/cgroup/cpuset
                           file-system-/sys/fs/cgroup/devices
                           file-system-/sys/fs/cgroup/memory
-                          ; TODO: file-system-/sys/fs/cgroup/pids
+                          file-system-/sys/fs/cgroup/pids
                           networking
                           udev))
            (start #~(make-forkexec-constructor
diff --git a/gnu/system/file-systems.scm b/gnu/system/file-systems.scm
index 3b599efa8e..b41f66e943 100644
--- a/gnu/system/file-systems.scm
+++ b/gnu/system/file-systems.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -389,7 +390,7 @@ TARGET in the other system."
                    ;; parent directory.
                    (dependencies (list parent))))
                '("cpuset" "cpu" "cpuacct" "memory" "devices" "freezer"
-                 "blkio" "perf_event")))))
+                 "blkio" "perf_event" "pids")))))
 
 (define %elogind-file-systems
   ;; We don't use systemd, but these file systems are needed for elogind,

From f38ba7b65dca8a4116ba8983357588f8a73a543f Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Mon, 27 Apr 2020 16:54:34 +0200
Subject: [PATCH 043/215] gnu: fldigi: Update to 4.1.12.

* gnu/packages/radio.scm (fldigi): Update to 4.1.12.
---
 gnu/packages/radio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index fff68cf657..b748aa4183 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -537,14 +537,14 @@ using GNU Radio and the Qt GUI toolkit.")
 (define-public fldigi
   (package
     (name "fldigi")
-    (version "4.1.11")
+    (version "4.1.12")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "http://www.w1hkj.com/files/fldigi/fldigi-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1y62xn1pim38ibaf2mbl8b7aq20jdaac6lgggb9r402w9bj5b196"))))
+        (base32 "1yjjv2ss84xfiaidypp476mhrbpnw4zf7mb5cdqwhdh604x0svr1"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

From 138896e1ea4d0ba420d04bff067692fecf93a613 Mon Sep 17 00:00:00 2001
From: "Boris A. Dekshteyn" <boris.dekshteyn@gmail.com>
Date: Tue, 28 Apr 2020 02:36:38 +1200
Subject: [PATCH 044/215] gnu: herbstluftwm: Update to 0.8.1
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

 * gnu/packages/wm.scm: herbstluftwm: Update to 0.8.1

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
---
 gnu/packages/wm.scm | 34 ++++++++++++++++------------------
 1 file changed, 16 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index a2c992d2c6..e173e5443a 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -33,6 +33,7 @@
 ;;; Copyright © 2019, 2020 Alexandru-Sergiu Marton <brown121407@member.fsf.org>
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
+;;; Copyright © 2020 Boris A. Dekshteyn <harlequin78@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -149,7 +150,7 @@ the leaves of a full binary tree.")
 (define-public herbstluftwm
   (package
     (name "herbstluftwm")
-    (version "0.7.2")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
@@ -157,9 +158,9 @@ the leaves of a full binary tree.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1kc18aj9j3nfz6fj4qxg9s3gg4jvn6kzi3ii24hfm0vqdpy17xnz"))
+         "0c1lf82z6a56g8asin91cmqhzk3anw0xwc44b31bpjixadmns57y"))
        (file-name (string-append "herbstluftwm-" version ".tar.gz"))))
-    (build-system gnu-build-system)
+    (build-system cmake-build-system)
     (inputs
      `(("dzen"        ,dzen)
        ("dmenu"       ,dmenu)
@@ -169,13 +170,20 @@ the leaves of a full binary tree.")
        ("xsetroot"    ,xsetroot)
        ("libx11"      ,libx11)
        ("libxext"     ,libxext)
-       ("libxinerama" ,libxinerama)))
+       ("libxinerama" ,libxinerama)
+       ("libxrandr"   ,libxrandr)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("asciidoc"   ,asciidoc)
+       ("pkg-config" ,pkg-config)))
     (arguments
-     '(#:phases
+     '(#:tests? #f
+       #:configure-flags
+       (let ((out (assoc-ref %outputs "out")))
+         (list "-DCC=gcc"
+               (string-append "-DCMAKE_INSTALL_SYSCONF_PREFIX=" out "/etc")
+               (string-append "-DBASHCOMPLETIONDIR=" out "/etc/bash_completion.d")))
+       #:phases
        (modify-phases %standard-phases
-         (delete 'configure)            ; no configure script
          (add-after 'install 'install-xsession
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -190,17 +198,7 @@ the leaves of a full binary tree.")
                      Comment=Manual tiling window manager~@
                      Exec=~a/bin/herbstluftwm~@
                      Type=XSession~%" out)))
-               #t))))
-       #:tests? #f
-       #:make-flags
-       (let ((out (assoc-ref %outputs "out")))
-         (list "CC=gcc"
-               (string-append "PREFIX=''")
-               (string-append "DESTDIR=" out)
-               (string-append "FISHCOMPLETIONDIR="
-                              "/share/fish/vendor_completions.d")
-               (string-append "BASHCOMPLETIONDIR=" out
-                              "/etc/bash_completion.d")))))
+               #t))))))
     (synopsis "Tiling window manager for X11")
     (description "herbstluftwm is a manual tiling window manager for X11 using
 Xlib and GLib.  Its main features are:

From c53886a55a40e106740209cf587fef4e52226aae Mon Sep 17 00:00:00 2001
From: Raghav Gururajan <raghavgururajan@disroot.org>
Date: Mon, 27 Apr 2020 09:32:43 -0400
Subject: [PATCH 045/215] gnu: ktsuss: Use setuid "su" and "sudo" commands.

This has ktsudo actually gain root access.

* gnu/packages/admin.scm (ktsuss)[arguments]: Instead of <sudo>/bin/{su,sudo}
file names, use the setuid' verrsions.
---
 gnu/packages/admin.scm | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 236eebe53c..cb3de79713 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -150,24 +150,22 @@
        (list "--enable-sudo=yes")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-sudo-path
-           (lambda* (#:key inputs #:allow-other-keys)
+         (add-after 'unpack 'patch-file-names
+           (lambda _
              (substitute* "configure.ac"
+               (("supath=`which su 2>/dev/null`")
+                "supath=/run/setuid-programs/su")
                (("sudopath=`which sudo 2>/dev/null`")
-                (string-append "sudopath="
-                               (string-append (assoc-ref inputs "sudo")
-                                              "/bin/sudo"))))
+                "sudopath=/run/setuid-programs/sudo"))
              #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
-       ("autogen" ,autogen)
        ("automake" ,automake)
        ("libtool" ,libtool)
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("glib" ,glib)
-       ("gtk+" ,gtk+-2)
-       ("sudo" ,sudo)))
+       ("gtk+" ,gtk+-2)))
     (synopsis "Graphical front end for @command{su}")
     (description
      "Ktsuss stands for ``Keep the @command{su} simple, stupid''.

From 58a361fef40f86d28938c7a964ca38032ff7f5a0 Mon Sep 17 00:00:00 2001
From: Alex McGrath <amk@amk.ie>
Date: Thu, 16 Apr 2020 21:55:28 +0100
Subject: [PATCH 046/215] gnu: Add wf-recorder.

* gnu/packages/video.scm (wf-recorder): New variable.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
---
 gnu/packages/video.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 1ae678da85..e3d145a840 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -40,6 +40,7 @@
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2020 Alex McGrath <amk@amk.ie>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -4071,3 +4072,33 @@ With Peek, you simply place the Peek window over the area you want to record
 and press \"Record\".  Peek is optimized for generating animated GIFs, but you
 can also directly record to WebM or MP4 if you prefer.")
     (license license:gpl3+)))
+
+(define-public wf-recorder
+  (package
+    (name "wf-recorder")
+    (version "0.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ammen99/wf-recorder.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1cw6kpcbl33wh95pvy32xrsrm6kkk1awccr3phyh885xjs3b3iim"))))
+    (build-system meson-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("ffmpeg" ,ffmpeg)
+       ("pulseaudio" ,pulseaudio)
+       ("wayland" ,wayland)
+       ("wayland-protocols" ,wayland-protocols)
+       ("libx264" ,libx264)))
+    (home-page "https://github.com/ammen99/wf-recorder")
+    (synopsis "Screen recorder for wlroots-based compositors")
+    (description
+     "@code{wf-recorder} is a utility program for screen recording of
+wlroots-based compositors.  More specifically, those that support
+@code{wlr-screencopy-v1} and @code{xdg-output}.")
+    (license license:expat)))

From f4f4aa628a171aa5bc40b8e5cd04ed30d36fc2b7 Mon Sep 17 00:00:00 2001
From: TomZ <tomz@freedommail.ch>
Date: Fri, 24 Apr 2020 22:39:49 +0200
Subject: [PATCH 047/215] doc: guix: Fix grammar in "Debugging Build Failures"
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* doc/guix.texi (Debugging Build Failures): Fix grammar.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
---
 doc/guix.texi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 6613a4af13..b4efc458b5 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -8830,7 +8830,7 @@ $ guix environment --no-grafts -C foo --ad-hoc strace gdb
 Here, @command{guix environment -C} creates a container and spawns a new
 shell in it (@pxref{Invoking guix environment}).  The @command{--ad-hoc
 strace gdb} part adds the @command{strace} and @command{gdb} commands to
-the container, which would may find handy while debugging.  The
+the container, which you may find handy while debugging.  The
 @option{--no-grafts} option makes sure we get the exact same
 environment, with ungrafted packages (@pxref{Security Updates}, for more
 info on grafts).

From bb6d9e26334c93b84553eb273d1540d08fd15852 Mon Sep 17 00:00:00 2001
From: Vincent Legoll <vincent.legoll@gmail.com>
Date: Sun, 26 Apr 2020 23:10:10 +0200
Subject: [PATCH 048/215] gnu: tarsplitter: Fix typo in description
 (spilt/split).

* gnu/packages/compression.scm (tarsplitter)[description]: Fix typo.
---
 gnu/packages/compression.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 8b93cc93dc..18512ee1bc 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -2164,6 +2164,6 @@ archiver is not installed.")
     (home-page "https://github.com/AQUAOSOTech/tarsplitter")
     (synopsis "Multithreaded tar utility")
     (description
-     "Archive huge numbers of files, or spilt massive tar archives into smaller
+     "Archive huge numbers of files, or split massive tar archives into smaller
 chunks.")
     (license license:expat)))

From 693d0fffc81ab7ebcc05622f88cc41a25c2d3c7a Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Mon, 27 Apr 2020 22:21:11 +0300
Subject: [PATCH 049/215] gnu: Add sbcl-stumpwm-swm-gaps.

* gnu/packages/wm.scm (sbcl-stumpwm-swm-gaps): New variable.
---
 gnu/packages/wm.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index e173e5443a..4d1b6b3fd4 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -1760,6 +1760,36 @@ rendering.")
 windows in the current X session.")
       (license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
 
+(define-public sbcl-stumpwm-swm-gaps
+  (let ((commit "dd5b037923ec7d3cc27c55806bcec5a1b8cf4e91")
+        (revision "1"))
+    (package
+      (name "sbcl-swm-gaps")
+      (version (git-version "0.0.1" revision commit)) ;no upstream release
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/stumpwm/stumpwm-contrib.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0ahxdj9f884afpzxczx6mx7l4nwg4kw6afqaq7lwhf7lxcwylldn"))))
+      (inputs
+       `(("stumpwm" ,stumpwm "lib")))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       '(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'chdir
+             (lambda _
+               (chdir "util/swm-gaps"))))))
+      (home-page "https://github.com/stumpwm/stumpwm-contrib")
+      (synopsis "Gaps between windows for StumpWM")
+      (description "This package provides a StumpWM module which adds gaps
+between windows.")
+      (license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
+
 (define-public lemonbar
   (let ((commit "35183ab81d2128dbb7b6d8e119cc57846bcefdb4")
         (revision "1"))

From 78799a6fdc5a00b3a0e62c0e99c3340298d36eff Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 21:34:10 +0200
Subject: [PATCH 050/215] gnu: Update minimap2 to 2.17.

* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8ef2880472..7b24d8bb64 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13207,7 +13207,7 @@ version does count multisplits.")
 (define-public minimap2
   (package
     (name "minimap2")
-    (version "2.10")
+    (version "2.17")
     (source
      (origin
        (method url-fetch)
@@ -13216,7 +13216,7 @@ version does count multisplits.")
                            "minimap2-" version ".tar.bz2"))
        (sha256
         (base32
-         "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj"))))
+         "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are none

From 5dfe02c60767a633c67f7f6fc9557b54b3c99b63 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 27 Apr 2020 22:12:59 +0200
Subject: [PATCH 051/215] tests: Remove trailing commas in JSON tests.

These commas are rejected by Guile-JSON 3.5.0.

* tests/crate.scm (test-foo-dependencies)
(test-root-dependencies, test-intermediate-1-dependencies)
(test-intermediate-2-dependencies): Remove trailing commas.
* tests/gem.scm (test-bar-json): Likewise.
* tests/pypi.scm (test-json): Likewise.
---
 tests/crate.scm | 23 ++++++++++++-----------
 tests/gem.scm   |  2 +-
 tests/pypi.scm  |  7 ++++---
 3 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/tests/crate.scm b/tests/crate.scm
index aa51faebf9..61a04f986b 100644
--- a/tests/crate.scm
+++ b/tests/crate.scm
@@ -55,7 +55,7 @@
   \"dependencies\": [
      {
        \"crate_id\": \"bar\",
-       \"kind\": \"normal\",
+       \"kind\": \"normal\"
      }
   ]
 }")
@@ -87,20 +87,20 @@
   \"dependencies\": [
      {
        \"crate_id\": \"intermediate-1\",
-       \"kind\": \"normal\",
+       \"kind\": \"normal\"
      },
      {
        \"crate_id\": \"intermediate-2\",
-       \"kind\": \"normal\",
+       \"kind\": \"normal\"
      }
      {
        \"crate_id\": \"leaf-alice\",
-       \"kind\": \"normal\",
+       \"kind\": \"normal\"
      },
      {
        \"crate_id\": \"leaf-bob\",
-       \"kind\": \"normal\",
-     },
+       \"kind\": \"normal\"
+     }
   ]
 }")
 
@@ -131,15 +131,15 @@
   \"dependencies\": [
      {
        \"crate_id\": \"intermediate-2\",
-       \"kind\": \"normal\",
+       \"kind\": \"normal\"
      },
      {
        \"crate_id\": \"leaf-alice\",
-       \"kind\": \"normal\",
+       \"kind\": \"normal\"
      },
      {
        \"crate_id\": \"leaf-bob\",
-       \"kind\": \"normal\",
+       \"kind\": \"normal\"
      }
   ]
 }")
@@ -171,8 +171,8 @@
   \"dependencies\": [
      {
        \"crate_id\": \"leaf-bob\",
-       \"kind\": \"normal\",
-     },
+       \"kind\": \"normal\"
+     }
   ]
 }")
 
@@ -233,6 +233,7 @@
 (define test-source-hash
   "")
 
+
 (test-begin "crate")
 
 (test-equal "guix-package->crate-name"
diff --git a/tests/gem.scm b/tests/gem.scm
index 455fc15189..751bba656f 100644
--- a/tests/gem.scm
+++ b/tests/gem.scm
@@ -52,7 +52,7 @@
   \"homepage_uri\": \"https://example.com\",
   \"dependencies\": {
     \"runtime\": [
-      { \"name\": \"bundler\" },
+      { \"name\": \"bundler\" }
     ]
   },
   \"licenses\": null
diff --git a/tests/pypi.scm b/tests/pypi.scm
index 19af6e61fb..6788c8db3e 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -46,13 +46,13 @@
     \"1.0.0\": [
       {
         \"url\": \"https://example.com/foo-1.0.0.egg\",
-        \"packagetype\": \"bdist_egg\",
+        \"packagetype\": \"bdist_egg\"
       }, {
         \"url\": \"https://example.com/foo-1.0.0.tar.gz\",
-        \"packagetype\": \"sdist\",
+        \"packagetype\": \"sdist\"
       }, {
         \"url\": \"https://example.com/foo-1.0.0-py2.py3-none-any.whl\",
-        \"packagetype\": \"bdist_wheel\",
+        \"packagetype\": \"bdist_wheel\"
       }
     ]
   }
@@ -120,6 +120,7 @@ Provides-Extra: testing
 Requires-Dist: pytest (>=3.1.0); extra == 'testing'
 ")
 
+
 (test-begin "pypi")
 
 (test-equal "guix-package->pypi-name, old URL style"

From 5fbc753ab524809cd81e3e5c54b3d0acbe33792d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 27 Apr 2020 22:17:53 +0200
Subject: [PATCH 052/215] import: crate: Gracefully handle non-existent crates.

Fixes <https://bugs.gnu.org/40891>.
Reported by Hartmut Goebel <h.goebel@crazy-compilers.com>.

* guix/import/crate.scm (crate->guix-package): Wrap value of
'version-number' and 'version*' in (and crate ...).
---
 guix/import/crate.scm | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/guix/import/crate.scm b/guix/import/crate.scm
index 0b4482e876..e3ec11d7f8 100644
--- a/guix/import/crate.scm
+++ b/guix/import/crate.scm
@@ -201,14 +201,16 @@ latest version of CRATE-NAME."
     (lookup-crate crate-name))
 
   (define version-number
-    (or version
-        (crate-latest-version crate)))
+    (and crate
+         (or version
+             (crate-latest-version crate))))
 
   (define version*
-    (find (lambda (version)
-            (string=? (crate-version-number version)
-                      version-number))
-          (crate-versions crate)))
+    (and crate
+         (find (lambda (version)
+                 (string=? (crate-version-number version)
+                           version-number))
+               (crate-versions crate))))
 
   (and crate version*
        (let* ((dependencies   (crate-version-dependencies version*))

From 47f82b310e320ed6c0282c89748485d1f9212d2c Mon Sep 17 00:00:00 2001
From: Raghav Gururajan <raghavgururajan@disroot.org>
Date: Wed, 22 Apr 2020 20:55:40 -0400
Subject: [PATCH 053/215] guix: edit: Make nano the default editor.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* guix/scripts/edit.scm: Make nano the default editor.

Nano is sensible default, as it is installed by base system.
For development, user can set custom value for $EDITOR.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 guix/scripts/edit.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/guix/scripts/edit.scm b/guix/scripts/edit.scm
index a6fd1d2751..43f3011869 100644
--- a/guix/scripts/edit.scm
+++ b/guix/scripts/edit.scm
@@ -56,10 +56,9 @@ Start $VISUAL or $EDITOR to edit the definitions of PACKAGE...\n"))
   (show-bug-report-information))
 
 (define %editor
-  ;; XXX: It would be better to default to something more likely to be
-  ;; pre-installed on an average GNU system.  Since Nano is not suited for
-  ;; editing Scheme, Emacs is used instead.
-  (make-parameter (or (getenv "VISUAL") (getenv "EDITOR") "emacs")))
+  ;; Nano is sensible default, as it is installed by base system.
+  ;; For development, user can set custom value for $EDITOR.
+  (make-parameter (or (getenv "VISUAL") (getenv "EDITOR") "nano")))
 
 (define (search-path* path file)
   "Like 'search-path' but exit if FILE is not found."

From 619f9181a363576894a433206008b139255062dd Mon Sep 17 00:00:00 2001
From: "operator.name" <operator.name@protonmail.com>
Date: Wed, 22 Apr 2020 19:57:07 +0100
Subject: [PATCH 054/215] doc: Update url to singularity before link rot
 occurs.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* doc/guix.texi: Update url to singularity before link rot occurs.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 doc/guix.texi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index b4efc458b5..f779281e05 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -5118,7 +5118,7 @@ guix pack -f squashfs bash guile emacs geiser
 @noindent
 The result is a SquashFS file system image that can either be mounted or
 directly be used as a file system container image with the
-@uref{https://singularity.lbl.gov, Singularity container execution
+@uref{https://www.sylabs.io/docs/, Singularity container execution
 environment}, using commands like @command{singularity shell} or
 @command{singularity exec}.
 

From 89909327d017198969436237acc7c93823ff8147 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?=
 <bjoern.hoefling@bjoernhoefling.de>
Date: Tue, 28 Apr 2020 00:15:34 +0200
Subject: [PATCH 055/215] gnu: stellarium: Update to 0.20.1.

* gnu/packages/astronomy.scm (stellarium): Update to 0.20.1.
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2c976354f1..28c010ad6a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -157,7 +157,7 @@ programs for the manipulation and analysis of astronomical data.")
 (define-public stellarium
   (package
     (name "stellarium")
-    (version "0.19.3")
+    (version "0.20.1")
     (source
      (origin
        (method url-fetch)
@@ -165,7 +165,7 @@ programs for the manipulation and analysis of astronomical data.")
                            "/releases/download/v" version
                            "/stellarium-" version ".tar.gz"))
        (sha256
-        (base32 "0p92rgclag0nkic9gk3p9vclb8xx9hv4zlgyij6cyh43s7c1avhp"))))
+        (base32 "034jkrdaaamvbrkfwi3qcl6h8hwfnw2nvf7a82faj55rskcpnkhm"))))
     (build-system cmake-build-system)
     (inputs
      `(("qtbase" ,qtbase)

From c1dc7858d7e460b17f13354cb75d3c9599b775f3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:37:07 +0200
Subject: [PATCH 056/215] gnu: r-with-tests, r-minimal: Update to 4.0.0.

* gnu/packages/statistics.scm (r-with-tests, r-minimal): Update to 4.0.0.
(r-with-tests)[arguments]: Add phase "set-locales".
[native-inputs]: Add texlive-ae, texlive-inconsolata, and
texlive-latex-xkeyval to texlive-union.
[inputs]: Replace pcre with pcre2.
---
 gnu/packages/statistics.scm | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b8e516f49c..f1cd024274 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -183,7 +183,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "3.6.3")
+    (version "4.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -191,7 +191,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "13xaxwfbzj0bd6rn2n27z0n04lb93mcyq991w4vdbbg8v282jc49"))))
+                "0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -269,6 +269,11 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
                  (("my \\$date = strftime \"%B %Y\", localtime" line)
                   (string-append line " 1"))))
              #t))
+         (add-before 'build 'set-locales
+           (lambda _
+             (setlocale LC_ALL "C")
+             (setenv "LC_ALL" "C")
+             #t))
          (add-before 'configure 'set-default-pager
           ;; Set default pager to "cat", because otherwise it is "false",
           ;; making "help()" print nothing at all.
@@ -322,7 +327,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("texinfo" ,texinfo) ; for building HTML manuals
-       ("texlive" ,(texlive-union (list texlive-fonts-ec
+       ("texlive" ,(texlive-union (list texlive-ae
+                                        texlive-inconsolata
+                                        texlive-fonts-ec
                                         texlive-amsfonts
                                         texlive-latex-base
                                         texlive-latex-fancyvrb
@@ -331,7 +338,8 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
                                         texlive-latex-oberdiek
                                         texlive-latex-tools
                                         texlive-latex-upquote
-                                        texlive-latex-url)))
+                                        texlive-latex-url
+                                        texlive-latex-xkeyval)))
        ("tzdata" ,tzdata-for-tests)
        ("xz" ,xz)))
     (inputs
@@ -347,7 +355,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("libpng" ,libpng)
        ("libtiff" ,libtiff)
        ("libxt" ,libxt)
-       ("pcre" ,pcre)
+       ("pcre2" ,pcre2)
        ("readline" ,readline)
        ;; This avoids a reference to the ungraftable static bash.  R uses the
        ;; detected shell for the "system" procedure.

From 288ab9039be11d167f0bc7c502c244a4d6982735 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:38:56 +0200
Subject: [PATCH 057/215] gnu: r-foreign: Update to 0.8-78.

* gnu/packages/statistics.scm (r-foreign): Update to 0.8-78.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f1cd024274..9c2f717195 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -512,14 +512,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-76")
+    (version "0.8-78")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "1z6x2x1z12wnv0z4p74d91r5wfaq30sdz4ynwx0lncz1q45mhbh5"))))
+         "01anirfbfa3ip5pyqv72cg4x7p0jsppmbvxrllw7bm28fl1hgiyq"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")

From 666d97964ae3c96f416845a83155cadd35bdedb4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:39:02 +0200
Subject: [PATCH 058/215] gnu: r-tibble: Update to 3.0.1.

* gnu/packages/statistics.scm (r-tibble): Update to 3.0.1.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9c2f717195..083fbca7a7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1632,14 +1632,14 @@ like tidy evaluation.")
 (define-public r-tibble
   (package
     (name "r-tibble")
-    (version "3.0.0")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tibble" version))
        (sha256
         (base32
-         "0s84h8ls5qwixbs1n5safr3xqmg3p0llzdrd9sp4vs2572mwzqzi"))))
+         "17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)

From 568d1d7bfc4d47764bc6c63c036a6ba4f412d81f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:39:14 +0200
Subject: [PATCH 059/215] gnu: r-dbplyr: Update to 1.4.3.

* gnu/packages/statistics.scm (r-dbplyr): Update to 1.4.3.
[propagated-inputs]: Add r-lifecycle.
[native-inputs]: Add r-knitr.
---
 gnu/packages/statistics.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 083fbca7a7..bba86279ad 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1702,25 +1702,28 @@ database.")
 (define-public r-dbplyr
   (package
     (name "r-dbplyr")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbplyr" version))
        (sha256
         (base32
-         "1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp"))))
+         "1si8sahr1kwq1xgjzi9klkahad07pyrsngy75y1f74f64907pb39"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
        ("r-dbi" ,r-dbi)
        ("r-dplyr" ,r-dplyr)
        ("r-glue" ,r-glue)
+       ("r-lifecycle" ,r-lifecycle)
        ("r-purrr" ,r-purrr)
        ("r-r6" ,r-r6)
        ("r-rlang" ,r-rlang)
        ("r-tibble" ,r-tibble)
        ("r-tidyselect" ,r-tidyselect)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/tidyverse/dbplyr")
     (synopsis "Dplyr back end for databases")
     (description

From 7ef5f77b910fe44a36cb8057f8800d33d8672f32 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:39:41 +0200
Subject: [PATCH 060/215] gnu: r-xml2: Update to 1.3.2.

* gnu/packages/statistics.scm (r-xml2): Update to 1.3.2.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index bba86279ad..8d17bbe74a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2000,14 +2000,14 @@ and environmental data in the framework of Euclidean exploratory methods.")
 (define-public r-xml2
   (package
     (name "r-xml2")
-    (version "1.3.1")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xml2" version))
        (sha256
         (base32
-         "0r7rxp922785dcryghbb3wxqgdav7mafwnmxjqfx8zaj3v1q2j3z"))))
+         "1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz"))))
     (build-system r-build-system)
     (inputs
      `(("libxml2" ,libxml2)

From 67aced632384e608cf6edbd29eea216d17cf8bfc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:40:41 +0200
Subject: [PATCH 061/215] gnu: r-withr: Update to 2.2.0.

* gnu/packages/statistics.scm (r-withr): Update to 2.2.0.
[native-inputs]: Add r-knitr.
---
 gnu/packages/statistics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8d17bbe74a..e27c8a6110 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2457,14 +2457,16 @@ tools to simplify the devolpment of R packages.")
 (define-public r-withr
   (package
     (name "r-withr")
-    (version "2.1.2")
+    (version "2.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "withr" version))
               (sha256
                (base32
-                "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
+                "10mmfffjbnb2zq5x0kqhhb4z6va4micc6pjzvlfji34gyhffa8ac"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/jimhester/withr")
     (synopsis "Run code with temporarily modified global state")
     (description

From 0e3003930e0e302e641db7060893c06ad36f30c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:40:58 +0200
Subject: [PATCH 062/215] gnu: r-plotrix: Update to 3.7-8.

* gnu/packages/statistics.scm (r-plotrix): Update to 3.7-8.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e27c8a6110..2c2179bff5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2527,13 +2527,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.7-7")
+    (version "3.7-8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "1x92mmyfry127zzr6cmcj6kjsc4zhxrrdlr0jcxn3bb0hpdfps54"))))
+                "104llmr6dvlcnfpmd8zbdlv63k79djc4qqgadjavj4v4cmz1zkcc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")

From d29cd83bd8f4bc76ab92cfe5503a5ab3276778cd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:41:04 +0200
Subject: [PATCH 063/215] gnu: r-purrr: Update to 0.3.4.

* gnu/packages/statistics.scm (r-purrr): Update to 0.3.4.
[native-inputs]: Add r-knitr.
---
 gnu/packages/statistics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 2c2179bff5..6bf952734c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3756,18 +3756,20 @@ It uses and relies on grid graphics and formal (S4) classes and methods.")
 (define-public r-purrr
   (package
     (name "r-purrr")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "purrr" version))
        (sha256
         (base32
-         "17lyys7dxjrwsfkq7a7hw65iy3qn3pp1sn70srdy64jf8adahc8g"))))
+         "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magrittr" ,r-magrittr)
        ("r-rlang" ,r-rlang)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/hadley/purrr")
     (synopsis "Functional programming tools")
     (description

From befa394f454901c51a735acf495d701464823a38 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 16:22:21 +0200
Subject: [PATCH 064/215] gnu: Add r-ingredients.

* gnu/packages/cran.scm (r-ingredients): New variable.
---
 gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 74e5fa2b1e..b8549ec3e3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15357,6 +15357,46 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
     ;; whole is distributed under the terms of the AGPL 3.
     (license license:agpl3)))
 
+(define-public r-ingredients
+  (package
+    (name "r-ingredients")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ingredients" version))
+       (sha256
+        (base32
+         "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967"))))
+    (properties `((upstream-name . "ingredients")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-scales" ,r-scales)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://ModelOriented.github.io/ingredients/")
+    (synopsis "Effects and importances of model ingredients")
+    (description
+     "This is a collection of tools for assessment of feature importance and
+feature effects.  Key functions are:
+
+@itemize
+@item @code{feature_importance()} for assessment of global level feature
+  importance,
+@item @code{ceteris_paribus()} for calculation of the what-if plots,
+@item @code{partial_dependence()} for partial dependence plots,
+@item @code{conditional_dependence()} for conditional dependence plots,
+@item @code{accumulated_dependence()} for accumulated local effects plots,
+@item @code{aggregate_profiles()} and @code{cluster_profiles()} for
+  aggregation of ceteris paribus profiles,
+@item generic @code{print()} and @code{plot()} for better usability of
+  selected explainers,
+@item generic @code{plotD3()} for interactive, D3 based explanations, and
+@item generic @code{describe()} for explanations in natural language.
+@end itemize\n")
+    (license license:gpl3)))
+
 (define-public r-dalex
   (package
     (name "r-dalex")

From 50f298a54f4db6a34406ca475909b800c24fee69 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 16:22:32 +0200
Subject: [PATCH 065/215] gnu: Add r-ibreakdown.

* gnu/packages/cran.scm (r-ibreakdown): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b8549ec3e3..f5e69fb1bc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15397,6 +15397,32 @@ feature effects.  Key functions are:
 @end itemize\n")
     (license license:gpl3)))
 
+(define-public r-ibreakdown
+  (package
+    (name "r-ibreakdown")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "iBreakDown" version))
+       (sha256
+        (base32
+         "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
+    (properties `((upstream-name . "iBreakDown")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://ModelOriented.github.io/iBreakDown/")
+    (synopsis "Model agnostic instance level variable attributions")
+    (description
+     "This package provides a model agnostic tool for decomposition of
+predictions from black boxes.  It supports additive attributions and
+attributions with interactions.  The Break Down Table shows contributions of
+every variable to a final prediction.  The Break Down Plot presents variable
+contributions in a concise graphical way.  This package works for
+classification and regression models.")
+    (license license:gpl3)))
+
 (define-public r-dalex
   (package
     (name "r-dalex")

From 92f5ed2fd79b2ff7147e91d0581b8cae8af2ed67 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:26:21 +0200
Subject: [PATCH 066/215] gnu: r-shinyfiles: Update to 0.8.0.

* gnu/packages/cran.scm (r-shinyfiles): Update to 0.8.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f5e69fb1bc..819e55509d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1121,13 +1121,13 @@ application framework for R, making it easy to create attractive dashboards.")
 (define-public r-shinyfiles
   (package
     (name "r-shinyfiles")
-    (version "0.7.5")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyFiles" version))
        (sha256
-        (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
+        (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
     (properties `((upstream-name . "shinyFiles")))
     (build-system r-build-system)
     (propagated-inputs

From d911e22af3f14ab1abc241c51687f6a1f102605a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:26:32 +0200
Subject: [PATCH 067/215] gnu: r-powerlaw: Update to 0.70.6.

* gnu/packages/cran.scm (r-powerlaw): Update to 0.70.6.
[propagated-inputs]: Remove r-vgam; add r-pracma.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 819e55509d..a23af8eb3e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2004,17 +2004,19 @@ multi-dimensional data.")
 (define-public r-powerlaw
   (package
     (name "r-powerlaw")
-    (version "0.70.4")
+    (version "0.70.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "poweRlaw" version))
        (sha256
-        (base32 "19zah9mx93az5lh9vicn3c8q1xb12g0w46dh5p901fbyimc32vwk"))))
+        (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
     (properties `((upstream-name . "poweRlaw")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-vgam" ,r-vgam)))
+     `(("r-pracma" ,r-pracma)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/csgillespie/poweRlaw")
     (synopsis "Tools for the analysis of heavy tailed distributions")
     (description

From 4c0cf66cfcca77001bc98109a13819d9f425b415 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:01 +0200
Subject: [PATCH 068/215] gnu: r-ff: Update to 2.2-14.2.

* gnu/packages/cran.scm (r-ff): Update to 2.2-14.2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a23af8eb3e..f242f1cff7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2125,14 +2125,14 @@ any subsequent lookup as it keeps the hash table in memory.")
 (define-public r-ff
   (package
     (name "r-ff")
-    (version "2.2-14")
+    (version "2.2-14.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ff" version))
        (sha256
         (base32
-         "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
+         "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-bit" ,r-bit)))
     (home-page "http://ff.r-forge.r-project.org/")

From 92d81a5e5b80a8c8522571804dc05c661b5eec63 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:07 +0200
Subject: [PATCH 069/215] gnu: r-distillery: Update to 1.0-7.

* gnu/packages/cran.scm (r-distillery): Update to 1.0-7.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f242f1cff7..98512ef65d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2389,14 +2389,14 @@ quantile mixture from L-moments and trimmed L-moments.")
 (define-public r-distillery
   (package
     (name "r-distillery")
-    (version "1.0-6")
+    (version "1.0-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "distillery" version))
        (sha256
         (base32
-         "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
+         "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
     (build-system r-build-system)
     (home-page "https://ral.ucar.edu/staff/ericg/")
     (synopsis "Functions for confidence intervals and object information")

From 839c39b178d84e1d2d75d3a5a051edde5003063d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:15 +0200
Subject: [PATCH 070/215] gnu: r-broom: Update to 0.5.6.

* gnu/packages/cran.scm (r-broom): Update to 0.5.6.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 98512ef65d..ba4460c865 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3222,14 +3222,14 @@ by base R methods related to model fitting.")
 (define-public r-broom
   (package
     (name "r-broom")
-    (version "0.5.5")
+    (version "0.5.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "broom" version))
        (sha256
         (base32
-         "0n7zd64263kfavdi28rl2bxrsa00c3m4vjhhjdrfwvvmrcxj39fx"))))
+         "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)
@@ -3241,6 +3241,8 @@ by base R methods related to model fitting.")
        ("r-stringr" ,r-stringr)
        ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/tidyverse/broom")
     (synopsis "Convert statistical analysis objects into tidy data frames")
     (description

From e965442b381ff3408d5085c44c308be008945098 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:31 +0200
Subject: [PATCH 071/215] gnu: r-tsp: Update to 1.1-10.

* gnu/packages/cran.scm (r-tsp): Update to 1.1-10.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ba4460c865..cda16a7c3a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4045,14 +4045,14 @@ timeout.  It can also poll several processes at once.")
 (define-public r-tsp
   (package
     (name "r-tsp")
-    (version "1.1-9")
+    (version "1.1-10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TSP" version))
        (sha256
         (base32
-         "183m6crb0dv17llj86059n3hbgsahbhfcqlx0ijdzkssg11i1cy7"))))
+         "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
     (properties `((upstream-name . "TSP")))
     (build-system r-build-system)
     (propagated-inputs `(("r-foreach" ,r-foreach)))

From f1f77bb64e5b1b11c3e17434e7d37b1b0061a134 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:42 +0200
Subject: [PATCH 072/215] gnu: r-tinytex: Update to 0.22.

* gnu/packages/cran.scm (r-tinytex): Update to 0.22.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cda16a7c3a..e31a222035 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4314,14 +4314,14 @@ terminals.")
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.21")
+    (version "0.22")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "088zzc2v0izbcs45p19v547pi78vkr08ibpvvi1g9bkbya4x3mq9"))))
+         "0s9f62v3ps5f8903ar6kxlf1z3b4v78vlw1nb05bq55dgj8brg3b"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-xfun" ,r-xfun)))

From 35f84a7f2761dd4547c9fe6f12908963c7bf9579 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:50 +0200
Subject: [PATCH 073/215] gnu: r-insight: Update to 0.8.3.

* gnu/packages/cran.scm (r-insight): Update to 0.8.3.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e31a222035..acf9e71cf5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6575,14 +6575,14 @@ other add-on packages.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.8.2")
+    (version "0.8.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "0fjf7dwpv1a7qfbzixppg348z1ksq19kdjm08vcb2am7w0k3plcj"))))
+         "0lm5a4r368mq1pwmxjk2xnz25lb9j4v7mdkl1bahk2alklxgb8yj"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))

From 09bb872aff9351ad3953fb5345bb9df5912bd54d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:54 +0200
Subject: [PATCH 074/215] gnu: r-raster: Update to 3.1-5.

* gnu/packages/cran.scm (r-raster): Update to 3.1-5.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index acf9e71cf5..84ec8727a3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7432,14 +7432,14 @@ used to teach mathematics, statistics, computation and modeling.")
 (define-public r-raster
   (package
     (name "r-raster")
-    (version "3.0-12")
+    (version "3.1-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "raster" version))
        (sha256
         (base32
-         "0rrbsigkqxsdic8fly6nrsc79zsliwvr1x2b4xqpl9d34vr50dvg"))))
+         "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)

From 27588b365f05635d1e57f8193211eeb0715d2e14 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:03 +0200
Subject: [PATCH 075/215] gnu: r-emmeans: Update to 1.4.6.

* gnu/packages/cran.scm (r-emmeans): Update to 1.4.6.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 84ec8727a3..1520f72ffa 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8443,14 +8443,14 @@ Hothorn, Westfall, 2010, CRC Press).")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.4.5")
+    (version "1.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "10fmvmd6q4zjr6b18hhc85mwrzv778qzj6lwl9kbs2fsfvsgw7mm"))))
+         "0mxk7ghlv4r6sna4897q1la2xgyn1dw3r9srhm9x4h5l4701avfa"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-estimability" ,r-estimability)
@@ -8458,6 +8458,8 @@ Hothorn, Westfall, 2010, CRC Press).")
        ("r-numderiv" ,r-numderiv)
        ("r-plyr" ,r-plyr)
        ("r-xtable" ,r-xtable)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/rvlenth/emmeans")
     (synopsis "Estimated marginal means, aka least-squares means")
     (description

From 09410f17d2eb0a5a151e0417b4206ad9c844f0eb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:18 +0200
Subject: [PATCH 076/215] gnu: r-bayestestr: Update to 0.6.0.

* gnu/packages/cran.scm (r-bayestestr): Update to 0.6.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1520f72ffa..9a2d455e4c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8678,14 +8678,14 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.5.3")
+    (version "0.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "1q24qh5p6bz4nbf4546kckh7d518x5pm1yhhbc8fwcnbca4kgqjz"))))
+         "0s7wdmk8avgaqk2b7fcf4bsh13isrkl1q4y7z2y8jhdagxxxnzd1"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs

From e2a50e5ec4859824557c6e63606541af8b4cf0d8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:26 +0200
Subject: [PATCH 077/215] gnu: r-ggeffects: Update to 0.14.3.

* gnu/packages/cran.scm (r-ggeffects): Update to 0.14.3.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9a2d455e4c..0b417e9c01 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8732,14 +8732,14 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "0.14.2")
+    (version "0.14.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "1y3yfb07jrr6vkc8hk6rp52l70dj7042jvqgjzllslzy7hx2jhyw"))))
+         "06p80bgjhjknzlb4vs4n41i9n9vv5agncakl9f92zkaahgyzd6sd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-insight" ,r-insight)

From 71c0a61cac534992e27f87af610c1bdc1f264b67 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:33 +0200
Subject: [PATCH 078/215] gnu: r-rgl: Update to 0.100.54.

* gnu/packages/cran.scm (r-rgl): Update to 0.100.54.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0b417e9c01..02a57850f9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9516,14 +9516,14 @@ Bioconductor packages.")
 (define-public r-rgl
   (package
     (name "r-rgl")
-    (version "0.100.50")
+    (version "0.100.54")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgl" version))
        (sha256
         (base32
-         "165p932ml7dpjkm41zc47p5cdxar69il0m5yvg0avi8q01vr17ay"))))
+         "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
     (build-system r-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

From d62d838bf9e0bcd4850c6e2f2513e5cd74c87c5e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:40 +0200
Subject: [PATCH 079/215] gnu: r-protviz: Update to 0.6.4.

* gnu/packages/cran.scm (r-protviz): Update to 0.6.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 02a57850f9..4a7cc14fae 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11599,14 +11599,14 @@ library.")
 (define-public r-protviz
   (package
     (name "r-protviz")
-    (version "0.6.3")
+    (version "0.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "protViz" version))
        (sha256
         (base32
-         "1ldciqh3f43xr9663yyhd9r6qwrg4c4vmkprlcancbnd460wakg7"))))
+         "1qq9bf4485x8cviry9fmhnv4hw9aw657w134003myzcv42c4pml6"))))
     (properties `((upstream-name . "protViz")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))

From fbcbf8d5862ad003376bf039b35f023e04adbe21 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:50 +0200
Subject: [PATCH 080/215] gnu: r-future: Update to 1.17.0.

* gnu/packages/cran.scm (r-future): Update to 1.17.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4a7cc14fae..6dac025b90 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11857,14 +11857,14 @@ them in distributed compute environments.")
 (define-public r-future
   (package
     (name "r-future")
-    (version "1.16.0")
+    (version "1.17.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future" version))
        (sha256
         (base32
-         "1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm"))))
+         "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)

From c6eb1fe616a4eb8c487b994d3d1aec2f930e78ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:55 +0200
Subject: [PATCH 081/215] gnu: r-etm: Update to 1.1.

* gnu/packages/cran.scm (r-etm): Update to 1.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6dac025b90..5f1089e36f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11649,14 +11649,14 @@ JASA, 94:496-509.")
 (define-public r-etm
   (package
     (name "r-etm")
-    (version "1.0.5.1")
+    (version "1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "etm" version))
        (sha256
         (base32
-         "0m41pm277sd50pharigcqzr1a2g92wnmdf6fcab6fx16ia2fzrm7"))))
+         "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-data-table" ,r-data-table)

From 5123ec7858528c323898c99895e891af244a4f67 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:00 +0200
Subject: [PATCH 082/215] gnu: r-future-apply: Update to 1.5.0.

* gnu/packages/cran.scm (r-future-apply): Update to 1.5.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5f1089e36f..8ff6bcbe2d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11889,14 +11889,14 @@ the local machine to, say, distributed processing on a remote compute cluster.")
 (define-public r-future-apply
   (package
     (name "r-future-apply")
-    (version "1.4.0")
+    (version "1.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future.apply" version))
        (sha256
         (base32
-         "1kgq6dv96hdy35kysqkn606nj7s9dp4ibgpm6n46gqhc5n75lzkk"))))
+         "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll"))))
     (properties `((upstream-name . "future.apply")))
     (build-system r-build-system)
     (propagated-inputs

From bf4e440c194ddff9ea8dcc0a9a9713bd65d4ad6c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:05 +0200
Subject: [PATCH 083/215] gnu: r-sf: Update to 0.9-2.

* gnu/packages/cran.scm (r-sf): Update to 0.9-2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8ff6bcbe2d..ac979a3a4a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -13355,14 +13355,14 @@ tessellation.")
 (define-public r-sf
   (package
     (name "r-sf")
-    (version "0.9-1")
+    (version "0.9-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sf" version))
        (sha256
         (base32
-         "1qghrskqwwlwxmmvkv7knhlr1a32ngyimycasy5gfazgviljsfn4"))))
+         "01xplgy5nlwy3ajfch4h1ssa1xhm7q0jzscpz04dmvgqfzwhhdfh"))))
     (build-system r-build-system)
     (inputs
      `(("gdal" ,gdal)

From 838ec254a0aada2c95906d8ea29ab9ee5390032f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:09 +0200
Subject: [PATCH 084/215] gnu: r-optparse: Update to 1.6.6.

* gnu/packages/cran.scm (r-optparse): Update to 1.6.6.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ac979a3a4a..75adaa24ff 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -13851,17 +13851,19 @@ authoring books and technical documents with R Markdown.")
 (define-public r-optparse
   (package
     (name "r-optparse")
-    (version "1.6.4")
+    (version "1.6.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "optparse" version))
        (sha256
         (base32
-         "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
+         "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-getopt" ,r-getopt)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/trevorld/optparse")
     (synopsis "Command line option parser")
     (description

From 1816cb262c6cdb7c3b443b90311b0695594d38a2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:23 +0200
Subject: [PATCH 085/215] gnu: r-rex: Update to 1.2.0.

* gnu/packages/cran.scm (r-rex): Update to 1.2.0.
[propagated-inputs]: Remove r-magrittr.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 75adaa24ff..13a7cb56b5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15023,18 +15023,19 @@ external dependencies.  This package has is implemented purely in R.")
 (define-public r-rex
   (package
     (name "r-rex")
-    (version "1.1.2")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rex" version))
        (sha256
         (base32
-         "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
+         "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-lazyeval" ,r-lazyeval)
-       ("r-magrittr" ,r-magrittr)))
+     `(("r-lazyeval" ,r-lazyeval)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/kevinushey/rex")
     (synopsis "Friendly regular expressions")
     (description

From 8165bf6d902c2e4b0a89f96f2f3f29ab3d24f6bb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:48 +0200
Subject: [PATCH 086/215] gnu: r-dalex: Update to 1.2.0.

* gnu/packages/cran.scm (r-dalex): Update to 1.2.0.
[propagated-inputs]: Add r-ibreakdown and r-ingredients.
---
 gnu/packages/cran.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 13a7cb56b5..87a4cc0517 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15435,17 +15435,20 @@ classification and regression models.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "1.0.1")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "1jbyn57vn6d281a5y15h5d8ljin8cdb9lr7lbgggc950blyfv4g0"))))
+         "0mfcci54622gnk8al9fl2jhs9i2vfly7lam04y5rdacbyiam49j6"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-ibreakdown" ,r-ibreakdown)
+       ("r-ingredients" ,r-ingredients)))
     (home-page "https://pbiecek.github.io/DALEX/")
     (synopsis "Descriptive machine learning explanations")
     (description

From 5ffe706b84c2bb870410a3841a29e68a2b5d4683 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:30:10 +0200
Subject: [PATCH 087/215] gnu: r-systemfonts: Update to 0.2.0.

* gnu/packages/cran.scm (r-systemfonts): Update to 0.2.0.
[inputs]: Remove freetype.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 87a4cc0517..5058079249 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16026,22 +16026,22 @@ both R code and compiled C/C++/FORTRAN code.")
 (define-public r-systemfonts
   (package
     (name "r-systemfonts")
-    (version "0.1.1")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "systemfonts" version))
        (sha256
         (base32
-         "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
+         "1aba07djvxqdmnsdbwvzcsbm2fddnhrssa54xyrlviiwsv2c1qsd"))))
     (properties `((upstream-name . "systemfonts")))
     (build-system r-build-system)
     (inputs
      `(("fontconfig" ,fontconfig)
-       ("freetype" ,freetype)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("pkg-config" ,pkg-config)
+       ("r-knitr" ,r-knitr)))
     (home-page "https://github.com/r-lib/systemfonts")
     (synopsis "System native font finding")
     (description

From 169f9fe13a4afd7ea4d51d26ce676e6eeb51f160 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:30:40 +0200
Subject: [PATCH 088/215] gnu: Add r-qgam.

* gnu/packages/cran.scm (r-qgam): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5058079249..3b20ced31a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16949,6 +16949,39 @@ for original research.  A variety of user defined options and formatting are
 included.")
     (license license:gpl3)))
 
+(define-public r-qgam
+  (package
+    (name "r-qgam")
+    (version "1.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "qgam" version))
+       (sha256
+        (base32
+         "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
+    (properties `((upstream-name . "qgam")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-doparallel" ,r-doparallel)
+       ("r-mgcv" ,r-mgcv)
+       ("r-plyr" ,r-plyr)
+       ("r-shiny" ,r-shiny)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://cran.r-project.org/web/packages/qgam/")
+    (synopsis "Smooth additive quantile regression models")
+    (description
+     "This package provides smooth additive quantile regression models, fitted
+using the methods of Fasiolo et al. (2017).  Differently from @code{quantreg},
+the smoothing parameters are estimated automatically by marginal loss
+minimization, while the regression coefficients are estimated using either
+PIRLS or Newton algorithm.  The learning rate is determined so that the
+Bayesian credible intervals of the estimated effects have approximately the
+correct coverage.  The main function is @code{qgam()} which is similar to
+@code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
+regression models.")
+    (license license:gpl2+)))
+
 (define-public r-abtest
   (package
     (name "r-abtest")

From e1fe5e9bed78de5a64af326b562940092c2a49ea Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:30:46 +0200
Subject: [PATCH 089/215] gnu: r-abtest: Update to 0.2.1.

* gnu/packages/cran.scm (r-abtest): Update to 0.2.1.
[propagated-inputs]: Add r-qgam; remove r-vgam.
---
 gnu/packages/cran.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3b20ced31a..51825645a4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16985,25 +16985,25 @@ regression models.")
 (define-public r-abtest
   (package
     (name "r-abtest")
-    (version "0.2.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abtest" version))
        (sha256
         (base32
-         "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
+         "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
     (properties `((upstream-name . "abtest")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)
        ("r-mvtnorm" ,r-mvtnorm)
        ("r-plotrix" ,r-plotrix)
+       ("r-qgam" ,r-qgam)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
        ("r-sn" ,r-sn)
-       ("r-truncnorm" ,r-truncnorm)
-       ("r-vgam" ,r-vgam)))
+       ("r-truncnorm" ,r-truncnorm)))
     (home-page "https://cran.r-project.org/web/packages/abtest/")
     (synopsis "Bayesian A/B testing")
     (description

From 2c439cae92dc21192f8a33ca632d26d84af3844e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:09 +0200
Subject: [PATCH 090/215] gnu: r-fda: Update to 5.1.4.

* gnu/packages/cran.scm (r-fda): Update to 5.1.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 51825645a4..7ba591c607 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18333,14 +18333,14 @@ actigraphy-measured activity counts data.")
 (define-public r-fda
   (package
     (name "r-fda")
-    (version "2.4.8.1")
+    (version "5.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fda" version))
        (sha256
         (base32
-         "0g50kj1dx7zarjv0lgwyzd2c7bv6di7nkndmywday5vjywgl8m7a"))))
+         "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
     (properties `((upstream-name . "fda")))
     (build-system r-build-system)
     (propagated-inputs

From 1d9e71ed299ef048bbf4fe4ead43c8dae8e92885 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:17 +0200
Subject: [PATCH 091/215] gnu: r-stopwords: Update to 2.0.

* gnu/packages/cran.scm (r-stopwords): Update to 2.0.
[propagated-inputs]: Add r-desc and r-usethis.
---
 gnu/packages/cran.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7ba591c607..aaf3cd6618 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19739,17 +19739,20 @@ character codes as well as the UN M.49 area codes.")
 (define-public r-stopwords
   (package
     (name "r-stopwords")
-    (version "1.0")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stopwords" version))
        (sha256
         (base32
-         "1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv"))))
+         "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
     (properties `((upstream-name . "stopwords")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-isocodes" ,r-isocodes)))
+    (propagated-inputs
+     `(("r-desc" ,r-desc)
+       ("r-isocodes" ,r-isocodes)
+       ("r-usethis" ,r-usethis)))
     (home-page "https://github.com/quanteda/stopwords")
     (synopsis "Multilingual stopword lists")
     (description

From ed720abc2605248590222f9a6e07501af3895cd0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:35 +0200
Subject: [PATCH 092/215] gnu: r-topicmodels: Update to 0.2-11.

* gnu/packages/cran.scm (r-topicmodels): Update to 0.2-11.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index aaf3cd6618..baf1e0c18a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19856,14 +19856,14 @@ machine learning, visually representing text and text analyses, and more.")
 (define-public r-topicmodels
   (package
     (name "r-topicmodels")
-    (version "0.2-9")
+    (version "0.2-11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "topicmodels" version))
        (sha256
         (base32
-         "1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0"))))
+         "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
     (properties `((upstream-name . "topicmodels")))
     (build-system r-build-system)
     (native-inputs

From cda0683295210544e095aaa3828b679b74bb80ae Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:42 +0200
Subject: [PATCH 093/215] gnu: r-seurat: Update to 3.1.5.

* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5.
[propagated-inputs]: Remove r-metap.
---
 gnu/packages/bioinformatics.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7b24d8bb64..bceea38087 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9716,13 +9716,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.1.4")
+    (version "3.1.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0lhjbjhv1hnx5i3gkx41k68i8ykay3f24708h30wx9xywww9lsvi"))))
+                "1lbq2pqhb6ih6iqawlnzdh05zff71pwbw1cpfv2sld3pd7kz0zkm"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9744,7 +9744,6 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-lmtest" ,r-lmtest)
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
-       ("r-metap" ,r-metap)
        ("r-patchwork" ,r-patchwork)
        ("r-pbapply" ,r-pbapply)
        ("r-plotly" ,r-plotly)

From 9c726c485a576d89ace6f789cfb778ecc6d76b49 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:56 +0200
Subject: [PATCH 094/215] gnu: r-hdf5array: Update to 1.14.4.

* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bceea38087..48b4ade7d8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10689,14 +10689,14 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.14.3")
+    (version "1.14.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1z153a7nxmlml72pl1saasj2il9g5ahpynkpv3mkhhsvl5kbwbh6"))))
+         "0ib0grhd9zbrn0dkrm4aa7qj7h0y6z1dvyx1ab3w6vczw7xghsfb"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs

From 0877b74f6e5ee30ce36caea57e3f165e1cd4a731 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 00:24:38 +0200
Subject: [PATCH 095/215] gnu: kaldi: Update to 0-2.d4791c0.

* gnu/packages/machine-learning.scm (kaldi): Update to 0-2.d4791c0.
---
 gnu/packages/machine-learning.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 223d03e979..1072930bfa 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -1056,8 +1056,8 @@ association studies (GWAS) on extremely large data sets.")
 
 ;; There have been no proper releases yet.
 (define-public kaldi
-  (let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
-        (revision "1"))
+  (let ((commit "d4791c0f3fc1a09c042dac365e120899ee2ad21e")
+        (revision "2"))
     (package
       (name "kaldi")
       (version (git-version "0" revision commit))
@@ -1069,7 +1069,7 @@ association studies (GWAS) on extremely large data sets.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
+                  "07k80my6f19mhrkwbzhjsnpf9871wmrwkl0ym468i830w67qyjrz"))))
       (build-system gnu-build-system)
       (arguments
        `(#:test-target "test"

From b3cf5f8601dd3e35295f0bc2f5193a12fb51ede6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 08:42:39 +0200
Subject: [PATCH 096/215] gnu: gst-kaldi-nnet2-online: Update to 0-2.cb227ef.

* gnu/packages/machine-learning.scm (gst-kaldi-nnet2-online): Update to
0-2.cb227ef.
---
 gnu/packages/machine-learning.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 1072930bfa..0f960ada95 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1167,8 +1167,8 @@ written in C++.")
       (license license:asl2.0))))
 
 (define-public gst-kaldi-nnet2-online
-  (let ((commit "617e43e73c7cc45eb9119028c02bd4178f738c4a")
-        (revision "1"))
+  (let ((commit "cb227ef43b66a9835c14eb0ad39e08ee03c210ad")
+        (revision "2"))
     (package
       (name "gst-kaldi-nnet2-online")
       (version (git-version "0" revision commit))
@@ -1180,7 +1180,7 @@ written in C++.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0xh3w67b69818s6ib02ara4lw7wamjdmh4jznvkpzrs4skbs9jx9"))))
+                  "1i6ffwiavxx07ri0lxix6s8q0r31x7i4xxvhys5jxkixf5q34w8g"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f                    ; there are none

From d9e9a2617664ae830c77e8a64aa733400a57c566 Mon Sep 17 00:00:00 2001
From: Konrad Hinsen <konrad.hinsen@fastmail.net>
Date: Fri, 24 Apr 2020 14:36:20 +0200
Subject: [PATCH 097/215] gnu: python-scikit-learn: Make python-joblib a
 propagated input.

* gnu/packages/machine-learning.scm (python-scikit-learn)
[native-inputs]: Move 'python-joblib' to ...
[propagated-inputs]: ... here.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
---
 gnu/packages/machine-learning.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 0f960ada95..f979a64d55 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -13,6 +13,7 @@
 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
+;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -835,13 +836,13 @@ computing environments.")
     (inputs
      `(("openblas" ,openblas)))
     (native-inputs
-     `(("python-joblib" ,python-joblib)
-       ("python-pytest" ,python-pytest)
+     `(("python-pytest" ,python-pytest)
        ("python-pandas" ,python-pandas) ;for tests
        ("python-cython" ,python-cython)))
     (propagated-inputs
      `(("python-numpy" ,python-numpy)
-       ("python-scipy" ,python-scipy)))
+       ("python-scipy" ,python-scipy)
+       ("python-joblib" ,python-joblib)))
     (home-page "https://scikit-learn.org/")
     (synopsis "Machine Learning in Python")
     (description

From 0ae85052889d47c4ede88bb34c4b00b3e557e1d9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 28 Apr 2020 10:11:22 +0200
Subject: [PATCH 098/215] gnu: hpcguix-web: Use guile3.0-guix.

* gnu/packages/web.scm (hpcguix-web): Update to latest revision and use
  guile3.0 inputs.
---
 gnu/packages/web.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 16e2832a62..f5189dc7f9 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -7153,8 +7153,8 @@ compressed JSON header blocks.
                "0wwhwv7cvi1vxpdjwvg0kpa4jzhszclpnwrwfcw728zz53a47z09"))))))
 
 (define-public hpcguix-web
-  (let ((commit "f39c90b35e99e4122b0866ec4337020d61c81508")
-        (revision "4"))
+  (let ((commit "9de63562b06b4aef3a3afe5ecb18d3c91e57ee74")
+        (revision "5"))
     (package
       (name "hpcguix-web")
       (version (git-version "0.0.1" revision commit))
@@ -7166,7 +7166,7 @@ compressed JSON header blocks.
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0idzzlwnaymk6hm5q9nh146h5m6vd8acp32vlmzp6qq08mimfkq7"))))
+                  "0wjgj2s7v2cyz6dx24c111rxs99i84sfvxl4ch8brnh02j2606jz"))))
       (build-system gnu-build-system)
       (arguments
        `(#:modules ((guix build gnu-build-system)
@@ -7222,11 +7222,11 @@ compressed JSON header blocks.
          ("uglify-js" ,uglify-js)
          ("pkg-config" ,pkg-config)))
       (inputs
-       `(("guix" ,guix)))
+       `(("guix" ,guile3.0-guix)))
       (propagated-inputs
-       `(("guile" ,guile-2.2)
-         ("guile-commonmark" ,guile-commonmark)
-         ("guile-json" ,guile-json-3)))
+       `(("guile" ,guile-next)
+         ("guile-commonmark" ,guile3.0-commonmark)
+         ("guile-json" ,guile3.0-json)))
       (home-page "https://github.com/UMCUGenetics/hpcguix-web")
       (synopsis "Web interface for cluster deployments of Guix")
       (description "Hpcguix-web provides a web interface to the list of packages

From 79c4fb4f366cff3ad75982b4a09c6bd82e604674 Mon Sep 17 00:00:00 2001
From: Christopher Howard <christopher@librehacker.com>
Date: Tue, 28 Apr 2020 10:06:34 +0200
Subject: [PATCH 099/215] gnu: Add hackrf.

* gnu/packages/radio.scm (hackrf): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
---
 gnu/packages/radio.scm | 69 +++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 68 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index b748aa4183..24ee67017a 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
-;;; Copyright © 2019 Christopher Howard <christopher@librehacker.com>
+;;; Copyright © 2019, 2020 Christopher Howard <christopher@librehacker.com>
 ;;; Copyright © 2019, 2020 Evan Straw <evan.straw99@gmail.com>
 ;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2020 Danny Milosavljevic <dannym@scratchpost.org>
@@ -654,6 +654,73 @@ for correctness.")
     (home-page "http://www.w1hkj.com/")
     (license license:gpl3+)))
 
+(define-public hackrf
+  ;; Using a git commit because there have been many many commits
+  ;; since the relase two years ago, but no sign of a promised
+  ;; release for many months now.
+  (let ((commit "43e6f99fe8543094d18ff3a6550ed2066c398862")
+        (revision "0"))
+    (package
+     (name "hackrf")
+     (version (git-version "2018.01.1" revision commit))
+     (source
+      (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/mossmann/hackrf.git")
+             (commit commit)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0avnv693xi0zsnrvkbfn0ln1r3s1iyj0bz7sc3gxay909av0pvbc"))))
+     (build-system cmake-build-system)
+     (arguments
+      '(#:configure-flags
+        (list "-DUDEV_RULES_GROUP=dialout"
+              (string-append "-DUDEV_RULES_PATH="
+                             (assoc-ref %outputs "out")
+                             "/lib/udev/rules.d"))
+        #:phases
+        (modify-phases %standard-phases
+          (add-before 'configure 'enter-source-directory
+            (lambda _
+              (chdir "host")
+              #t))
+          (add-after 'install 'delete-static-library
+            (lambda* (#:key outputs #:allow-other-keys)
+              (delete-file (string-append (assoc-ref outputs "out")
+                                          "/lib/libhackrf.a"))
+              #t))
+          (add-before 'install-license-files 'leave-source-directory
+            (lambda _
+              (chdir "..")
+              #t)))
+        #:tests? #f)) ; no test suite
+     (native-inputs
+      `(("pkg-config" ,pkg-config)))
+     (inputs
+      `(("fftw" ,fftw)
+        ("fftwf" ,fftwf)
+        ("libusb" ,libusb)))
+     (home-page "https://greatscottgadgets.com/hackrf/")
+     (synopsis "User-space library and utilities for HackRF SDR")
+     (description
+      "Command line utilities and a C library for controlling the HackRF
+Software Defined Radio (SDR) over USB.  Installing this package installs
+the userspace hackrf utilities and C library.  To install the hackrf
+udev rules, you must add this package as a system service via
+modify-services.  E.g.:
+
+@lisp
+(services
+ (modify-services
+  %desktop-services
+  (udev-service-type config =>
+   (udev-configuration (inherit config)
+    (rules (cons hackrf
+            (udev-configuration-rules config)))))))
+@end lisp")
+     (license license:gpl2))))
+
 (define-public hamlib
   (package
     (name "hamlib")

From 62d45e463c3b1ecad90004c47356cba342dd23d8 Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Tue, 28 Apr 2020 10:10:16 +0200
Subject: [PATCH 100/215] gnu: gnuradio-osmosdr: Add hackrf support.

* gnu/packages/radio.scm (gnuradio-osmosdr)[inputs]: Add hackrf.
---
 gnu/packages/radio.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 24ee67017a..4e11dda40a 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -399,8 +399,8 @@ environment.")
        ("fftwf" ,fftwf)
        ("gmp" ,gmp)
        ("gnuradio" ,gnuradio)
+       ("hackrf" ,hackrf)
        ("log4cpp" ,log4cpp)
-       ;; TODO: Add more drivers.
        ("rtl-sdr" ,rtl-sdr)
        ("volk" ,volk)))
     (synopsis "GNU Radio block for interfacing with various radio hardware")

From ef3cc2d8833b0ec46b26c32413245ef8a8086e66 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:37:10 +0200
Subject: [PATCH 101/215] gnu: Add emacs-trashed.

* gnu/packages/emacs-xyz.scm (emacs-trashed): New variable.
---
 gnu/packages/emacs-xyz.scm | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index a0275cbe18..0ae3f72fb7 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -34,7 +34,7 @@
 ;;; Copyright © 2017, 2018, 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Sohom Bhattacharjee <soham.bhattacharjee15@gmail.com>
 ;;; Copyright © 2018, 2019 Mathieu Lirzin <mthl@gnu.org>
-;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2018, 2019, 2020 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2018, 2019 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2018, 2019 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
@@ -22585,3 +22585,26 @@ ASCII UML sequence diagrams in Emacs, which can be embedded in source code,
 comments or emails.")
       (license license:gpl3+))))
 
+(define-public emacs-trashed
+  (package
+    (name "emacs-trashed")
+    (version "1.9.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/shingo256/trashed/")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "13grdi12iwlw4fiphdfmvclfpbr6ajlgfbfyi7v41z8k3rxz4ypz"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/shingo256/trashed/")
+    (synopsis "View and edit system trash can in Emacs")
+    (description "Open, view, browse, restore or permanently delete trashed
+files or directories in trash can with Dired-like look and feel.  The trash
+can has to be compliant with freedesktop.org. In Emacs, you can trash files by
+deleting them with @code{(setq delete-by-moving-to-trash t)}.  This package
+provides a simple but convenient user interface to manage those trashed
+files.")
+    (license license:gpl3+)))

From eac71f54fe561aadc02067d114c8f32ff3f359cb Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:42:44 +0200
Subject: [PATCH 102/215] gnu: sbcl-cl-cffi-gtk-gobject: Link source to parent
 to reduce closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-gobject)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index cc9bda8ac6..b8efaf985f 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -2916,7 +2916,20 @@ is a library for creating graphical user interfaces.")
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "gobject/gobject.init.lisp"
                (("libgobject" all) (string-append
-                                    (assoc-ref inputs "glib") "/lib/" all))))))))))
+                                    (assoc-ref inputs "glib") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-gobject")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-gio
   (package

From 6a7f36686499086086b23cb7238c91c899de7f67 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:44:47 +0200
Subject: [PATCH 103/215] gnu: sbcl-cl-cffi-gtk-gio: Link source to parent to
 reduce closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-gio)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index b8efaf985f..fbb502cc73 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -2949,7 +2949,20 @@ is a library for creating graphical user interfaces.")
              (substitute* "gio/gio.init.lisp"
                (("libgio" all)
                 (string-append
-                 (assoc-ref inputs "glib") "/lib/" all))))))))))
+                 (assoc-ref inputs "glib") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-gio")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-cairo
   (package

From 8f46a9d67f54ffbe04d4201bdfcc8b460f640805 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:45:05 +0200
Subject: [PATCH 104/215] gnu: sbcl-cl-cffi-gtk-cairo: Link source to parent to
 reduce closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-cairo)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index fbb502cc73..e938bd6aa2 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -2981,7 +2981,20 @@ is a library for creating graphical user interfaces.")
              (substitute* "cairo/cairo.init.lisp"
                (("libcairo" all)
                 (string-append
-                 (assoc-ref inputs "cairo") "/lib/" all))))))))))
+                 (assoc-ref inputs "cairo") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-cairo")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-pango
   (package

From d27f033f97ab7a71e0a3af004d3e11bea9374676 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:45:18 +0200
Subject: [PATCH 105/215] gnu: sbcl-cl-cffi-gtk-pango: Link source to parent to
 reduce closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-pango)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index e938bd6aa2..b2b5e006a6 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3015,7 +3015,20 @@ is a library for creating graphical user interfaces.")
              (substitute* "pango/pango.init.lisp"
                (("libpango" all)
                 (string-append
-                 (assoc-ref inputs "pango") "/lib/" all))))))))))
+                 (assoc-ref inputs "pango") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-pango")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-gdk-pixbuf
   (package

From 2666a3361ec76fefe10257da3c6eb0f854ed24db Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:45:32 +0200
Subject: [PATCH 106/215] gnu: sbcl-cl-cffi-gtk-gdk-pixbuf: Link source to
 parent to reduce closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-gdk-pixbuf)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index b2b5e006a6..fa86769872 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3037,6 +3037,7 @@ is a library for creating graphical user interfaces.")
     (inputs
      `(("gdk-pixbuf" ,gdk-pixbuf)
        ("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
+       ("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
        ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
     (arguments
      `(#:asd-file "gdk-pixbuf/cl-cffi-gtk-gdk-pixbuf.asd"
@@ -3047,7 +3048,20 @@ is a library for creating graphical user interfaces.")
              (substitute* "gdk-pixbuf/gdk-pixbuf.init.lisp"
                (("libgdk_pixbuf" all)
                 (string-append
-                 (assoc-ref inputs "gdk-pixbuf") "/lib/" all))))))))))
+                 (assoc-ref inputs "gdk-pixbuf") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-gdk-pixbuf")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-gdk
   (package

From 80d8c00c84191206e3c1edfb7d6a9d47a15ec1bf Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:45:47 +0200
Subject: [PATCH 107/215] gnu: sbcl-cl-cffi-gtk-gdk: Link source to parent to
 reduce closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-gdk)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index fa86769872..7f78a09ece 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3069,6 +3069,7 @@ is a library for creating graphical user interfaces.")
     (name "sbcl-cl-cffi-gtk-gdk")
     (inputs
      `(("gtk" ,gtk+)
+       ("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
        ("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
        ("cl-cffi-gtk-gio" ,sbcl-cl-cffi-gtk-gio)
        ("cl-cffi-gtk-gdk-pixbuf" ,sbcl-cl-cffi-gtk-gdk-pixbuf)
@@ -3088,7 +3089,20 @@ is a library for creating graphical user interfaces.")
              (substitute* "gdk/gdk.package.lisp"
                (("libgtk" all)
                 (string-append
-                 (assoc-ref inputs "gtk") "/lib/" all))))))))))
+                 (assoc-ref inputs "gtk") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-gdk")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk
   (package

From 143eaa82d6d7048705b42597465473bcf309204b Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:46:05 +0200
Subject: [PATCH 108/215] gnu: sbcl-cl-cffi-gtk: Link source to parent to
 reduce closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 7f78a09ece..5cf8a86940 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3121,7 +3121,22 @@ is a library for creating graphical user interfaces.")
        #:test-asd-file "test/cl-cffi-gtk-test.asd"
        ;; TODO: Tests fail with memory fault.
        ;; See https://github.com/Ferada/cl-cffi-gtk/issues/24.
-       #:tests? #f))))
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public cl-cffi-gtk
   (sbcl-package->cl-source-package sbcl-cl-cffi-gtk))

From 8ac4be51defa0e6d578307645cf9e35e0b321848 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 11:46:45 +0200
Subject: [PATCH 109/215] gnu: ecl: Update to 20.4.24.

* gnu/packages/lisp.scm (ecl): Update to 20.4.24.
[native-inputs]: Add texinfo to make the manual.
[license]: Set to lgpl2.1+.
---
 gnu/packages/lisp.scm | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 27d38cd471..e57ce31dc7 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -222,7 +222,7 @@ interface to the Tk widget system.")
 (define-public ecl
   (package
     (name "ecl")
-    (version "16.1.3")
+    (version "20.4.24")
     (source
      (origin
        (method url-fetch)
@@ -230,17 +230,22 @@ interface to the Tk widget system.")
              "https://common-lisp.net/project/ecl/static/files/release/"
              name "-" version ".tgz"))
        (sha256
-        (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))))
+        (base32 "01qgdmr54wkj854f69qdm9sybrvd6gd21dpx4askdaaqybnkh237"))))
     (build-system gnu-build-system)
     ;; src/configure uses 'which' to confirm the existence of 'gzip'.
-    (native-inputs `(("cl-asdf" ,cl-asdf)
-                     ("which" ,which)))
-    (inputs `(("gmp" ,gmp)
-              ("libatomic-ops" ,libatomic-ops)
-              ("libgc" ,libgc)
-              ("libffi" ,libffi)))
+    (native-inputs
+     `(("cl-asdf" ,cl-asdf)
+       ("which" ,which)
+       ("texinfo" ,texinfo)))
+    (inputs
+     `(("gmp" ,gmp)
+       ("libatomic-ops" ,libatomic-ops)
+       ("libgc" ,libgc)
+       ("libffi" ,libffi)))
     (arguments
      `(#:configure-flags '("--without-rt")
+       ;; FIXME: As of version 20.4.24, we pass 17995 tests and fail 7.
+       ;; 2-3 tests may be due to FHS assumptions.
        #:tests? #t
        #:parallel-tests? #f
        #:phases
@@ -301,9 +306,10 @@ bytecode compiler and interpreter, being able to compile Common Lisp with any
 C/C++ compiler, being able to build standalone executables and libraries, and
 supporting ASDF, Sockets, Gray streams, MOP, and other useful components.")
     ;; Note that the file "Copyright" points to some files and directories
-    ;; which aren't under the lgpl2.0+ and instead contain many different,
+    ;; which aren't under the lgpl2.1+ and instead contain many different,
     ;; non-copyleft licenses.
-    (license license:lgpl2.0+)))
+    ;; See https://common-lisp.net/project/ecl/posts/ECL-license.html.
+    (license license:lgpl2.1+)))
 
 (define-public clisp
   (package

From 83812f34d7a01bb404d8dda17bd4c72bf30b8371 Mon Sep 17 00:00:00 2001
From: "Boris A. Dekshteyn" <boris.dekshteyn@gmail.com>
Date: Tue, 28 Apr 2020 14:09:19 +1200
Subject: [PATCH 110/215] gnu: Add kbdd-0.7.1
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/xdisorg.scm (kbdd): New variable.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
---
 gnu/packages/xdisorg.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index bc2c9c4622..df61a95cbb 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -35,6 +35,7 @@
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020 Damien Cassou <damien@cassou.me>
 ;;; Copyright © 2020 John Soo <jsoo1@asu.edu>
+;;; Copyright © 2020 Boris A. Dekshteyn <boris.dekshteyn@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2286,3 +2287,40 @@ to find all available clips and launches @command{dmenu} (or @command{rofi},
 depending on the value of @code{CM_LAUNCHER}) to let the user select a clip.
 After selection, the clip is put onto the PRIMARY and CLIPBOARD X selections.")
       (license license:public-domain))))
+
+(define-public kbdd
+  (package
+    (name "kbdd")
+    (version "0.7.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/qnikst/kbdd.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0qkq75grbd4wkx4nlvswgavpijk9ad0pzqyj89a0ayjsbsn36pqy"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("glib" ,glib "bin")
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("dbus-glib", dbus-glib)
+       ("glib" ,glib)
+       ("libx11" ,libx11)))
+    (home-page "https://github.com/qnikst/kbdd")
+    (synopsis "Per-window keyboard layout switching daemon for X")
+    (description "@command{kbdd} is a simple keyboard layout switching
+program, which is designed to run in an X11 session and remember
+keyboard layouts on a per-window basis.  That can be very handy for a
+user of a non-US keyboard who does not want to jump through layouts back
+and forth while typing in terminals (mostly in a latin alphabet) and
+some kind of chat (in native language).
+
+@command{kbdd} also supports D-Bus signals, which makes it possible to
+create layout indicator widgets.")
+    (license license:bsd-2)))

From 9a2fcb6325eb652971de4936911267d1fc5bb549 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 11:22:47 +0200
Subject: [PATCH 111/215] gnu: Add c-blosc.

* gnu/packages/compression.scm (c-blosc): New variable.
---
 gnu/packages/compression.scm | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 18512ee1bc..85f802a069 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
@@ -2167,3 +2167,30 @@ archiver is not installed.")
      "Archive huge numbers of files, or split massive tar archives into smaller
 chunks.")
     (license license:expat)))
+
+(define-public c-blosc
+  (package
+    (name "c-blosc")
+    (version "1.18.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Blosc/c-blosc.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ywq8j70149859vvs19wgjq89d6xsvvmvm2n1dmkzpchxgrvnw70"))))
+    (build-system cmake-build-system)
+    (home-page "https://blosc.org")
+    (synopsis "Blocking, shuffling and lossless compression library")
+    (description
+     "Blosc is a high performance compressor optimized for binary data. It has
+been designed to transmit data to the processor cache faster than the
+traditional, non-compressed, direct memory fetch approach via a
+@code{memcpy()} system call.  Blosc is meant not only to reduce the size of
+large datasets on-disk or in-memory, but also to accelerate memory-bound
+computations.")
+    ;; Blosc itself is released under BSD-3 but it incorporates code under
+    ;; other non-copyleft licenses.
+    (license license:bsd-3)))

From 0b2c88382830e281912cc04867f45e15c2f9657f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 12:20:18 +0200
Subject: [PATCH 112/215] gnu: Add hdf5-blosc.

* gnu/packages/maths.scm (hdf5-blosc): New variable.
---
 gnu/packages/maths.scm | 41 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 40 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 73ee161e81..d7ce900682 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier <bavier@posteo.net>
 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
@@ -1298,6 +1298,45 @@ Swath).")
                #t))))))
     (synopsis "Management suite for data with parallel IO support")))
 
+(define-public hdf5-blosc
+  (package
+    (name "hdf5-blosc")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Blosc/hdf5-blosc.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "-DBLOSC_INSTALL_DIR="
+                            (assoc-ref %build-inputs "c-blosc"))
+             (string-append "-DPLUGIN_INSTALL_PATH="
+                            (assoc-ref %outputs "out")
+                            "/hdf5/lib/plugin"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-build-blosc
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("set\\(BLOSC_INSTALL_DIR.*") "")
+               (("ExternalProject_Add\\(project_blosc") "message("))
+             #t)))))
+    (inputs
+     `(("c-blosc" ,c-blosc)
+       ("hdf5" ,hdf5-1.10)))
+    (home-page "https://github.com/Blosc/hdf5-blosc")
+    (synopsis "Filter for HDF5 using the Blosc compressor")
+    (description "This is a filter for HDF5 that uses the Blosc compressor; by
+installing this filter, you can read and write HDF5 files with
+Blosc-compressed datasets.")
+    (license license:expat)))
+
 (define-public h5check
   (package
     (name "h5check")

From 545e12f40dcd8cfc779e8802dadead7a7cdc8364 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 12:23:13 +0200
Subject: [PATCH 113/215] gnu: Add variant-tools.

* gnu/packages/bioinformatics.scm (variant-tools): New variable.
---
 gnu/packages/bioinformatics.scm | 40 +++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 48b4ade7d8..f90a0bf90c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9158,6 +9158,46 @@ samples into a single report.  It contains modules for a large number of
 common bioinformatics tools.")
     (license license:gpl3+)))
 
+(define-public variant-tools
+  (package
+    (name "variant-tools")
+    (version "3.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/vatlab/varianttools.git")
+             ;; There is no tag corresponding to version 3.1.2
+             (commit "813ae4a90d25b69abc8a40f4f70441fe09015249")))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g"))))
+    (build-system python-build-system)
+    (inputs
+     `(("boost" ,boost)
+       ("c-blosc" ,c-blosc)
+       ("gsl" ,gsl)
+       ("hdf5" ,hdf5)
+       ("hdf5-blosc" ,hdf5-blosc)
+       ("python-cython" ,python-cython)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-pycurl" ,python-pycurl)
+       ("python-pyzmq" ,python-pyzmq)
+       ("python-scipy" ,python-scipy)
+       ("python-tables" ,python-tables)))
+    (home-page "https://vatlab.github.io/vat-docs/")
+    (synopsis "Analyze genetic variants from Next-Gen sequencing studies")
+    (description
+     "Variant tools is a tool for the manipulation, annotation,
+selection, simulation, and analysis of variants in the context of next-gen
+sequencing analysis.  Unlike some other tools used for next-gen sequencing
+analysis, variant tools is project based and provides a whole set of tools to
+manipulate and analyze genetic variants.")
+    (license license:gpl3+)))
+
 (define-public r-chipseq
   (package
     (name "r-chipseq")

From 085948fbfc8aef4370d8df8784bbd239c333fa99 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 28 Apr 2020 14:38:38 +0200
Subject: [PATCH 114/215] gnu: ungoogled-chromium: Update to
 81.0.4044.129-0.c2a89fb [security fixes].

This fixes CVE-2020-6462 and CVE-2020-6461.

* gnu/packages/chromium.scm (%chromium-version): Set to 81.0.4044.129.
(%ungoogled-revision): Set to c2a89fb6b5b559c826796c811741fa8ed3e11de8.
(%chromium-origin, %ungoogled-origin): Update hashes.
---
 gnu/packages/chromium.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm
index 45d68d2526..131943710a 100644
--- a/gnu/packages/chromium.scm
+++ b/gnu/packages/chromium.scm
@@ -248,8 +248,8 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %chromium-version "81.0.4044.122")
-(define %ungoogled-revision "31d6e60c96481599b42072b4489e4468280198e3")
+(define %chromium-version "81.0.4044.129")
+(define %ungoogled-revision "c2a89fb6b5b559c826796c811741fa8ed3e11de8")
 (define %debian-revision "debian/81.0.4044.92-1")
 (define package-revision "0")
 (define %package-version (string-append %chromium-version "-"
@@ -264,7 +264,7 @@ from forcing GEXP-PROMISE."
                         %chromium-version ".tar.xz"))
     (sha256
      (base32
-      "0ahqh3vmzbpai4xwn7qybgw9phc8ssjdvfc7384mxqk9swqgv7qg"))))
+      "1ls663s1f74p912x42qp3zcvm17kmjiv1ij6yy1c14gdhcpmjx7z"))))
 
 (define %ungoogled-origin
   (origin
@@ -275,7 +275,7 @@ from forcing GEXP-PROMISE."
                               (string-take %ungoogled-revision 7)))
     (sha256
      (base32
-      "1pj2vmzb2fagvypjsjn2kqf5n5k8vnhbisyb0snr6wqvpv09x0vv"))))
+      "0bbr4a2gkgm3ykdgpj8x58sd3dwam6qkifhzfs2997681g7b2v2q"))))
 
 (define %debian-origin
   (origin

From b3d04190f4ebbba9a7879ad72443ea6bf216ba76 Mon Sep 17 00:00:00 2001
From: Joseph LaFreniere <joseph@lafreniere.xyz>
Date: Sun, 26 Apr 2020 11:24:32 -0500
Subject: [PATCH 115/215] gnu: Add emacs-toml-mode.

* gnu/packages/emacs-xyz.scm (emacs-toml-mode): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 0ae3f72fb7..b2da56f34d 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2584,6 +2584,30 @@ strings.")
 Stack Overflow, Super User, and other StackExchange sites.")
       (license license:gpl3+))))
 
+(define-public emacs-toml-mode
+  (let ((version "0.1.3")
+        (revision "0")
+        (commit "f6c61817b00f9c4a3cab1bae9c309e0fc45cdd06"))
+    (package
+      (name "emacs-toml-mode")
+      (version (git-version version revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/dryman/toml-mode.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "05b4ksay85c8y5ncax0qsvnmplwsfiw24z16a58gkarjz938hb57"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/dryman/toml-mode.el")
+      (synopsis "Emacs major mode for editing TOML files")
+      (description
+       "This package provides a major mode for editing files in @acronym{TOML,
+Tom's Obvious, Minimal Language} data format.")
+      (license license:gpl3+))))
+
 (define-public emacs-f
   (package
     (name "emacs-f")

From f15d324afa3b6525f606cc0b82eef6609e8fab9e Mon Sep 17 00:00:00 2001
From: Joseph LaFreniere <joseph@lafreniere.xyz>
Date: Sun, 26 Apr 2020 16:10:20 -0500
Subject: [PATCH 116/215] gnu: emacs-sx: Update to 20191229.

* gnu/packages/emacs-xyz.scm (emacs-sx): Update to 20191229.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index b2da56f34d..1cd7dbca04 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2558,9 +2558,9 @@ strings.")
     (license license:gpl2+)))
 
 (define-public emacs-sx
-  (let ((version "20180212")
-        (revision "1")
-        (commit "833435fbf90d1c9e927d165b155f3b1ef39271de"))
+  (let ((version "20191229")
+        (revision "0")
+        (commit "e9d1093c97507a6d7b4f4710ef65200dae725e5f"))
     (package
       (name "emacs-sx")
       (version (git-version version revision commit))
@@ -2572,8 +2572,7 @@ strings.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32
-           "1369xaxq1vy3d9yh862ddnhddikdpg2d0wv1ly00pnvdp9v4cqgd"))))
+          (base32 "0m90ddwm8j0y6d1ppqhd2gil1107k202blw6mzm5bdambn4nfqkf"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-markdown-mode" ,emacs-markdown-mode)))

From 9615c8511fe4ec4dbd98c80bc1f4549924f85099 Mon Sep 17 00:00:00 2001
From: John Soo <jsoo1@asu.edu>
Date: Mon, 27 Apr 2020 16:27:04 -0700
Subject: [PATCH 117/215] gnu: emacs-evil-org: Update to 1.0.2.

* gnu/packages/emacs-xyz.scm (emacs-evil-org): Update to 1.0.2.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 1cd7dbca04..96be0aa195 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -15881,10 +15881,10 @@ provide an incremental search that moves all fake cursors in sync.")
       (license license:expat))))
 
 (define-public emacs-evil-org
-  (let ((commit "b6d652a9163d3430a9e0933a554bdbee5244bbf6"))
+  (let ((commit "9d4be14118bf27094a30dbff349b815f098aacbf"))
     (package
       (name "emacs-evil-org")
-      (version (git-version "0.1.1" "1" commit))
+      (version (git-version "1.0.2" "1" commit))
       (source
        (origin
          (method git-fetch)
@@ -15894,7 +15894,7 @@ provide an incremental search that moves all fake cursors in sync.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "176hrw7y7nczffbyhsa167b8rvfacsmcafm2gpkrdjqlrikbmrhl"))))
+           "1fxxfkinb0gq4p5b686r7z4jrkv98zfgh5z889zkjacncv8ibswn"))))
       (build-system emacs-build-system)
       (propagated-inputs `(("emacs-evil" ,emacs-evil)))
       (home-page

From 3b33e0e4baba4d121cad88fd116a1048789e5f64 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Tue, 28 Apr 2020 18:18:44 +0200
Subject: [PATCH 118/215] gnu: kakoune: Update to 2020.01.16.

* gnu/packages/text-editors.scm (kakoune): Update to 2020.01.16.
---
 gnu/packages/text-editors.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm
index 36571e7846..f2f675d148 100644
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@ -123,7 +123,7 @@ based command language.")
 (define-public kakoune
   (package
     (name "kakoune")
-    (version "2019.12.10")
+    (version "2020.01.16")
     (source
      (origin
        (method url-fetch)
@@ -131,7 +131,7 @@ based command language.")
                            "releases/download/v" version "/"
                            "kakoune-" version ".tar.bz2"))
        (sha256
-        (base32 "1y1gzax2dl7flh676k0rl1vacv10j7p5krkmb67b0afbrql8vbb6"))))
+        (base32 "1bhd990gywdwdhxc5dn83wwj418c5cw1ndqycf7k0a02kxlg3550"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags

From ae0f26b8f4e0221f1e6f1a5ebf6d5054da506761 Mon Sep 17 00:00:00 2001
From: Alexandros Theodotou <alex@zrythm.org>
Date: Tue, 28 Apr 2020 15:30:04 +0100
Subject: [PATCH 119/215] gnu: lv2: Update to 1.18.0.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/audio.scm (lv2): Update to 1.18.0.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index bf16e09f61..e2e276723b 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1979,14 +1979,14 @@ significantly faster and have minimal dependencies.")
 (define-public lv2
   (package
     (name "lv2")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://lv2plug.in/spec/lv2-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "1ppippbpdpv13ibs06b0bixnazwfhiw0d0ja6hx42jnkgdyp5hyy"))))
+               "0gs7401xz23q9vajqr31aa2db8dvssgyh5zrvr4ipa6wig7yb8wh"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f  ; no check target

From b2c1d4a27301b71d1273786b7aa869e5112d1e3a Mon Sep 17 00:00:00 2001
From: Christopher Lemmer Webber <cwebber@dustycloud.org>
Date: Thu, 2 Apr 2020 15:03:27 -0400
Subject: [PATCH 120/215] gnu: Add emacs-magit-annex.

* gnu/packages/emacs-xyz.scm (emacs-magit-annex): New variable.
---
 gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 96be0aa195..3bf9ffa655 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -475,6 +475,31 @@ these arguments.  The prototypical use is for the command to call an external
 process, passing on the arguments as command line arguments.")
     (license license:gpl3+)))
 
+(define-public emacs-magit-annex
+  (let ((commit "ef5dce6267e9118a5eca82a22bcad0b67826c23a")
+        (revision "1"))
+    (package
+      (name "emacs-magit-annex")
+      (version (git-version "1.7.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/magit/magit-annex.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0vzkydgl889cq173zjl89g2vrddb9abc4a8gljiz3b4a7n5b1nrd"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("magit" ,emacs-magit)
+         ("transient" ,emacs-transient)))
+      (home-page "https://github.com/magit/magit-annex/")
+      (synopsis "Git-annex support for Magit")
+      (description
+       "Magit-annex adds a few git-annex operations to the Magit interface.")
+      (license license:gpl3+))))
+
 (define-public emacs-minions
   (package
     (name "emacs-minions")

From abbca232ca92678a46ab1fbf5f2f376bf6a4a7e2 Mon Sep 17 00:00:00 2001
From: Diego Nicola Barbato <dnbarbato@posteo.de>
Date: Sun, 29 Dec 2019 00:41:48 +0100
Subject: [PATCH 121/215] gnu: Add emacs-wide-int.

* gnu/packages/emacs.scm (emacs-wide-int): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/emacs.scm | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 3d0368be4e..ab7cc20d10 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -401,6 +401,17 @@ editor (without an X toolkit)" )
            ((#:configure-flags cf)
             `(cons "--with-x-toolkit=no" ,cf)))))))
 
+(define-public emacs-wide-int
+  (package
+    (inherit emacs)
+    (name "emacs-wide-int")
+    (synopsis "The extensible, customizable, self-documenting text
+editor (with wide ints)" )
+    (arguments
+     (substitute-keyword-arguments (package-arguments emacs)
+       ((#:configure-flags flags)
+        `(cons "--with-wide-int" ,flags))))))
+
 (define-public guile-emacs
   (let ((commit "41120e0f595b16387eebfbf731fff70481de1b4b")
         (revision "0"))

From a663b7040c3c7ed12d4f673c4ac090ad8d9b8e20 Mon Sep 17 00:00:00 2001
From: Diego Nicola Barbato <dnbarbato@posteo.de>
Date: Sun, 29 Dec 2019 01:03:38 +0100
Subject: [PATCH 122/215] gnu: emacs-telega: Build with emacs-wide-int on
 32-bit systems.

Fixes <https://bugs.gnu.org/39406>.
Reported by <lmedeiros@riseup.net>.

* gnu/packages/emacs-xyz.scm (emacs-telega)[native-inputs]: Replace emacs with
emacs-wide-int on 32-bit systems.  This is needed because Telega requires
64-bit wide ints.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/emacs-xyz.scm | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 3bf9ffa655..5d2aaa4061 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -21467,7 +21467,12 @@ fish-completion.  It can be used in both Eshell and M-x shell.")
       (native-inputs
        `(("tdlib" ,tdlib)
          ("libtgvoip" ,libtgvoip) ; VoIP support.
-         ("emacs" ,emacs)
+         ;; Use Emacs with wide ints on 32-bit architectures.
+         ("emacs" ,(match (%current-system)
+                     ((or "i686-linux" "armhf-linux")
+                      emacs-wide-int)
+                     (_
+                      emacs)))
          ("python" ,python)))
       (synopsis "GNU Emacs client for the Telegram messenger")
       (description

From 19e1f12ce420104451c16ab5412cb65cd8fe68cd Mon Sep 17 00:00:00 2001
From: Diego Nicola Barbato <dnbarbato@posteo.de>
Date: Fri, 7 Feb 2020 17:59:31 +0100
Subject: [PATCH 123/215] gnu: emacs-telega: Test Emacs environment on startup.

Print a more helpful error message when someone attempts to run Telega on an
incompatible Emacs (e.g a 32-bit Emacs without wide ints).

* gnu/packages/patches/emacs-telega-test-env.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/emacs-xyz.scm (emacs-telega)[source]: Use it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/local.mk                                     |  1 +
 gnu/packages/emacs-xyz.scm                       |  1 +
 gnu/packages/patches/emacs-telega-test-env.patch | 14 ++++++++++++++
 3 files changed, 16 insertions(+)
 create mode 100644 gnu/packages/patches/emacs-telega-test-env.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 9f212434a9..9b082a6f2a 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -864,6 +864,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/emacs-magit-log-format-author-margin.patch	\
   %D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch	\
   %D%/packages/patches/emacs-source-date-epoch.patch		\
+  %D%/packages/patches/emacs-telega-test-env.patch		\
   %D%/packages/patches/emacs-undohist-ignored.patch	\
   %D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch	\
   %D%/packages/patches/emacs-zones-called-interactively.patch	\
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 5d2aaa4061..2c61c4189d 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -21376,6 +21376,7 @@ fish-completion.  It can be used in both Eshell and M-x shell.")
          (sha256
           (base32
            "0mv6i80958d9crzspzik5xh5g8326115bvg2frgv0dp9p6rm86m3"))
+         (patches (search-patches "emacs-telega-test-env.patch"))
          (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (arguments
diff --git a/gnu/packages/patches/emacs-telega-test-env.patch b/gnu/packages/patches/emacs-telega-test-env.patch
new file mode 100644
index 0000000000..75fe2e12fc
--- /dev/null
+++ b/gnu/packages/patches/emacs-telega-test-env.patch
@@ -0,0 +1,14 @@
+Test Emacs environment on startup.
+
+Patch by Diego N. Barbato
+
+--- a/telega.el	2020-02-07 17:07:18.549970090 +0100
++++ b/telega.el	2020-02-07 17:10:08.383499765 +0100
+@@ -82,6 +82,7 @@
+   "Start telegramming.
+ If prefix ARG is given, then will not pop to telega root buffer."
+   (interactive "P")
++  (telega-test-env t)
+   (telega--create-hier)
+ 
+   (unless (telega-server-live-p)

From a84b7a4af53553c5816c9534e33ea52802e89b1d Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 14:48:58 +0200
Subject: [PATCH 124/215] gnu: sbcl-parenscript: Update to 2.7.1.

* gnu/packages/lisp-xyz.scm (sbcl-parenscript): Update to 2.7.1.
---
 gnu/packages/lisp-xyz.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 5cf8a86940..c2029d940e 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -2670,10 +2670,11 @@ relational database engine.")
   (sbcl-package->cl-source-package sbcl-cl-sqlite))
 
 (define-public sbcl-parenscript
-  (let ((commit "061d8e286c81c3f45c84fb2b11ee7d83f590a8f8"))
+  ;; Source archives are overwritten on every release, we use the Git repo instead.
+  (let ((commit "7a1ac46353cecd144fc91915ba9f122aafcf4766"))
     (package
       (name "sbcl-parenscript")
-      (version (git-version "2.6" "1" commit))
+      (version (git-version "2.7.1" "1" commit))
       (source
        (origin
          (method git-fetch)
@@ -2683,7 +2684,7 @@ relational database engine.")
          (file-name (git-file-name "parenscript" version))
          (sha256
           (base32
-           "1kbhgsjbikc73m5cwdp4d4fdafyqcr1b7b630qjrziql0nh6mi3k"))))
+           "0c22lqarrpbq82dg1sb3y6mp6w2faczp34ymzhnmff88yfq1xzsf"))))
       (build-system asdf-build-system/sbcl)
       (inputs
        `(("cl-ppcre" ,sbcl-cl-ppcre)

From 27112236ce411cefdd5b5a66bdf73b688adf24f4 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 21:07:23 +0200
Subject: [PATCH 125/215] gnu: sbcl: Update to 2.0.4.

* gnu/packages/lisp.scm (sbcl): Update to 2.0.4.
---
 gnu/packages/lisp.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index e57ce31dc7..219bc4dcf9 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -371,14 +371,14 @@ an interpreter, a compiler, a debugger, and much more.")
 (define-public sbcl
   (package
     (name "sbcl")
-    (version "2.0.3")
+    (version "2.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/sbcl/sbcl/" version "/sbcl-"
                            version "-source.tar.bz2"))
        (sha256
-        (base32 "001gckyw8hl842nk7nwf5kcspzkc1g8dycpwylzh5chl6893ym5m"))))
+        (base32 "1lc2i4qq1kfdybmxnj2zq2hn3hfx0vvlqim4gvlgvs3bfr0lcaqj"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (native-inputs
@@ -397,7 +397,7 @@ an interpreter, a compiler, a debugger, and much more.")
      ;;
      ;; CCL is not bootstrappable so it won't do.  CLISP 2.49 seems to work.
      ;; ECL too.  ECL builds SBCL about 20% slower than CLISP.  As of
-     ;; 2019-09-05, ECL was last updated in 2016 while CLISP was last updated
+     ;; 2019-09-05, ECL was last updated in 2020 while CLISP was last updated
      ;; in 2010.
      ;;
      ;; For now we stick to CLISP for all systems.  We keep the `match' here to

From cd8c419722780765b075a7217b861e7608c0bac2 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Apr 2020 21:07:14 +0300
Subject: [PATCH 126/215] gnu: valgrind: Update source uri.

* gnu/packages/valgrind.scm (valgrind)[source]: Remove valgrind host,
add sourceware host.
[home-page]: Use https.
---
 gnu/packages/valgrind.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/valgrind.scm b/gnu/packages/valgrind.scm
index da912dc465..dd080bb327 100644
--- a/gnu/packages/valgrind.scm
+++ b/gnu/packages/valgrind.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2013, 2014 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -35,7 +35,7 @@
     (version "3.15.0")
     (source (origin
               (method url-fetch)
-              (uri (list (string-append "http://www.valgrind.org/downloads"
+              (uri (list (string-append "https://sourceware.org/pub/valgrind"
                                         "/valgrind-" version ".tar.bz2")
                          (string-append "ftp://sourceware.org/pub/valgrind"
                                         "/valgrind-" version ".tar.bz2")))
@@ -71,7 +71,7 @@
      `(("gdb" ,gdb)))
     (native-inputs
      `(("perl" ,perl)))
-    (home-page "http://www.valgrind.org/")
+    (home-page "https://www.valgrind.org/")
     (synopsis "Debugging and profiling tool suite")
     (description
      "Valgrind is an instrumentation framework for building dynamic analysis

From 0b25812872904d61024791778dae36636c52ded6 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Apr 2020 22:52:20 +0300
Subject: [PATCH 127/215] gnu: openldap: Fix CVE-2020-12243.

* gnu/packages/openldap.scm (openldap)[replacement]: New field.
(openldap/fixed): New variable.
* gnu/packages/patches/openldap-CVE-2020-12243.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
 gnu/local.mk                                  |   3 +-
 gnu/packages/openldap.scm                     |   9 ++
 .../patches/openldap-CVE-2020-12243.patch     | 125 ++++++++++++++++++
 3 files changed, 136 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/openldap-CVE-2020-12243.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 9b082a6f2a..67bf04547c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -10,7 +10,7 @@
 # Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 # Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 # Copyright © 2016, 2017, 2018, 2019 Alex Vong <alexvong1995@gmail.com>
-# Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
+# Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 # Copyright © 2016, 2017, 2018, 2019 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 # Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 # Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
@@ -1276,6 +1276,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/opencv-rgbd-aarch64-test-fix.patch	\
   %D%/packages/patches/openfoam-4.1-cleanup.patch			\
   %D%/packages/patches/openjdk-10-idlj-reproducibility.patch	\
+  %D%/packages/patches/openldap-CVE-2020-12243.patch		\
   %D%/packages/patches/openmpi-mtl-priorities.patch		\
   %D%/packages/patches/openocd-nrf52.patch			\
   %D%/packages/patches/openssl-runpath.patch			\
diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm
index de8239b7fe..aa51520654 100644
--- a/gnu/packages/openldap.scm
+++ b/gnu/packages/openldap.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -57,6 +58,7 @@
 
 (define-public openldap
   (package
+   (replacement openldap/fixed)
    (name "openldap")
    (version "2.4.47")
    (source (origin
@@ -110,6 +112,13 @@
    (license openldap2.8)
    (home-page "https://www.openldap.org/")))
 
+(define openldap/fixed
+  (package
+    (inherit openldap)
+    (source
+      (origin (inherit (package-source openldap))
+              (patches (search-patches "openldap-CVE-2020-12243.patch"))))))
+
 (define-public nss-pam-ldapd
   (package
     (name "nss-pam-ldapd")
diff --git a/gnu/packages/patches/openldap-CVE-2020-12243.patch b/gnu/packages/patches/openldap-CVE-2020-12243.patch
new file mode 100644
index 0000000000..6321998198
--- /dev/null
+++ b/gnu/packages/patches/openldap-CVE-2020-12243.patch
@@ -0,0 +1,125 @@
+From 98464c11df8247d6a11b52e294ba5dd4f0380440 Mon Sep 17 00:00:00 2001
+From: Howard Chu <hyc@openldap.org>
+Date: Thu, 16 Apr 2020 01:08:19 +0100
+Subject: [PATCH] ITS#9202 limit depth of nested filters
+
+Using a hardcoded limit for now; no reasonable apps
+should ever run into it.
+---
+ servers/slapd/filter.c | 41 ++++++++++++++++++++++++++++++++---------
+ 1 file changed, 32 insertions(+), 9 deletions(-)
+
+diff --git a/servers/slapd/filter.c b/servers/slapd/filter.c
+index 3252cf2a7..ed57bbd7b 100644
+--- a/servers/slapd/filter.c
++++ b/servers/slapd/filter.c
+@@ -37,11 +37,16 @@
+ const Filter *slap_filter_objectClass_pres;
+ const struct berval *slap_filterstr_objectClass_pres;
+ 
++#ifndef SLAPD_MAX_FILTER_DEPTH
++#define SLAPD_MAX_FILTER_DEPTH	5000
++#endif
++
+ static int	get_filter_list(
+ 	Operation *op,
+ 	BerElement *ber,
+ 	Filter **f,
+-	const char **text );
++	const char **text,
++	int depth );
+ 
+ static int	get_ssa(
+ 	Operation *op,
+@@ -80,12 +85,13 @@ filter_destroy( void )
+ 	return;
+ }
+ 
+-int
+-get_filter(
++static int
++get_filter0(
+ 	Operation *op,
+ 	BerElement *ber,
+ 	Filter **filt,
+-	const char **text )
++	const char **text,
++	int depth )
+ {
+ 	ber_tag_t	tag;
+ 	ber_len_t	len;
+@@ -126,6 +132,11 @@ get_filter(
+ 	 *
+ 	 */
+ 
++	if( depth > SLAPD_MAX_FILTER_DEPTH ) {
++		*text = "filter nested too deeply";
++		return SLAPD_DISCONNECT;
++	}
++
+ 	tag = ber_peek_tag( ber, &len );
+ 
+ 	if( tag == LBER_ERROR ) {
+@@ -221,7 +232,7 @@ get_filter(
+ 
+ 	case LDAP_FILTER_AND:
+ 		Debug( LDAP_DEBUG_FILTER, "AND\n", 0, 0, 0 );
+-		err = get_filter_list( op, ber, &f.f_and, text );
++		err = get_filter_list( op, ber, &f.f_and, text, depth+1 );
+ 		if ( err != LDAP_SUCCESS ) {
+ 			break;
+ 		}
+@@ -234,7 +245,7 @@ get_filter(
+ 
+ 	case LDAP_FILTER_OR:
+ 		Debug( LDAP_DEBUG_FILTER, "OR\n", 0, 0, 0 );
+-		err = get_filter_list( op, ber, &f.f_or, text );
++		err = get_filter_list( op, ber, &f.f_or, text, depth+1 );
+ 		if ( err != LDAP_SUCCESS ) {
+ 			break;
+ 		}
+@@ -248,7 +259,7 @@ get_filter(
+ 	case LDAP_FILTER_NOT:
+ 		Debug( LDAP_DEBUG_FILTER, "NOT\n", 0, 0, 0 );
+ 		(void) ber_skip_tag( ber, &len );
+-		err = get_filter( op, ber, &f.f_not, text );
++		err = get_filter0( op, ber, &f.f_not, text, depth+1 );
+ 		if ( err != LDAP_SUCCESS ) {
+ 			break;
+ 		}
+@@ -311,10 +322,22 @@ get_filter(
+ 	return( err );
+ }
+ 
++int
++get_filter(
++	Operation *op,
++	BerElement *ber,
++	Filter **filt,
++	const char **text )
++{
++	return get_filter0( op, ber, filt, text, 0 );
++}
++
++
+ static int
+ get_filter_list( Operation *op, BerElement *ber,
+ 	Filter **f,
+-	const char **text )
++	const char **text,
++	int depth )
+ {
+ 	Filter		**new;
+ 	int		err;
+@@ -328,7 +351,7 @@ get_filter_list( Operation *op, BerElement *ber,
+ 		tag != LBER_DEFAULT;
+ 		tag = ber_next_element( ber, &len, last ) )
+ 	{
+-		err = get_filter( op, ber, new, text );
++		err = get_filter0( op, ber, new, text, depth );
+ 		if ( err != LDAP_SUCCESS )
+ 			return( err );
+ 		new = &(*new)->f_next;
+-- 
+2.26.2
+

From ce0f1b1eefbb6d7d6339c0919cc051f9f5cf9b8d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 28 Apr 2020 22:31:32 +0200
Subject: [PATCH 128/215] gnu: guix: Update to 619f918.

* gnu/packages/package-management.scm (guix): Update to 619f918.
---
 gnu/packages/package-management.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 011e442066..44fcb514b7 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -110,8 +110,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "1.1.0")
-        (commit "7dd05396ef4539165f955d9ab57225091f801ce9")
-        (revision 1))
+        (commit "619f9181a363576894a433206008b139255062dd")
+        (revision 2))
     (package
       (name "guix")
 
@@ -127,7 +127,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "110fz4qay4iywpynw1cbv6if8ac0pxp21zhzwvnp2jn1f6vbwf64"))
+                  "1lk0h9zgry7m78nv70gxwb57pw1d5yzay477gxsc43v1aa7zg8sp"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments

From 1797fe132177f8c6738e51130492868f4107f472 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 28 Apr 2020 22:32:06 +0200
Subject: [PATCH 129/215] gnu: guile-json: Update to 3.5.0.

* gnu/packages/guile.scm (guile-json-3): Update to 3.5.0.
---
 gnu/packages/guile.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index c643f9d286..56dda89899 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -488,14 +488,14 @@ specification.  These are the main features:
   (package
     (inherit guile-json-1)
     (name "guile-json")
-    (version "3.2.0")
+    (version "3.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://savannah/guile-json/guile-json-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "14m6b6g2maw0mkvfm4x63rqb54vgbpn1gcqs715ijw4bikfzlqfz"))))))
+                "0nj0684qgh6ppkbdyxqfyjwsv2qbyairxpi8fzrhsi3xnc7jn4im"))))))
 
 (define-public guile3.0-json
   (package-for-guile-3.0 guile-json-3))

From e4aa9ab6378f4422ab31fd977102d7ceb7b3bd43 Mon Sep 17 00:00:00 2001
From: Diego Nicola Barbato <dnbarbato@posteo.de>
Date: Sat, 25 Apr 2020 11:32:07 +0200
Subject: [PATCH 130/215] doc: Mention that PulseAudio service overrides user
 configuration.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* doc/guix.texi (Sound Services): Add a warning that 'pulseaudio-service-type'
  overrides per-user configuration files in '~/.config/pulse'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 doc/guix.texi | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index f779281e05..d0592220a7 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -63,7 +63,7 @@ Copyright @copyright{} 2018, 2019 Florian Pelz@*
 Copyright @copyright{} 2018 Laura Lazzati@*
 Copyright @copyright{} 2018 Alex Vong@*
 Copyright @copyright{} 2019 Josh Holland@*
-Copyright @copyright{} 2019 Diego Nicola Barbato@*
+Copyright @copyright{} 2019, 2020 Diego Nicola Barbato@*
 Copyright @copyright{} 2019 Ivan Petkov@*
 Copyright @copyright{} 2019 Jakob L. Kreuze@*
 Copyright @copyright{} 2019 Kyle Andrews@*
@@ -16289,6 +16289,13 @@ This is the type for the  @uref{https://www.pulseaudio.org/, PulseAudio}
 sound server.  It exists to allow system overrides of the default settings
 via @code{pulseaudio-configuration}, see below.
 
+@quotation Warning
+This service overrides per-user configuration files.  If you want
+PulseAudio to honor configuraton files in @file{~/.config/pulse} you
+have to unset the environment variables @code{PULSE_CONFIG} and
+@code{PULSE_CLIENTCONFIG} in your @file{~/.bash_profile}.
+@end quotation
+
 @quotation Warning
 This service on its own does not ensure, that the @code{pulseaudio} package
 exists on your machine.  It merely adds configuration files for it, as

From f93eebbf9ca8477404827f44daf3121b11120e99 Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Wed, 29 Apr 2020 01:11:53 +0200
Subject: [PATCH 131/215] gnu: Add xnec2c.

* gnu/packages/radio.scm (xnec2c): New variable.
---
 gnu/packages/radio.scm | 49 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 4e11dda40a..b439e5feff 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -829,3 +829,52 @@ modes were all designed for making reliable, confirmed QSOs under extreme
 weak-signal conditions.")
     (home-page "https://www.physics.princeton.edu/pulsar/k1jt/wsjtx.html")
     (license license:gpl3)))
+
+(define-public xnec2c
+  (package
+    (name "xnec2c")
+    (version "4.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.5b4az.org/pkg/nec2/xnec2c/xnec2c-"
+                           version ".tar.bz2"))
+       (sha256
+        (base32 "1myvlkfybb2ha8l0h96ca3iz206zzy9z5iizm0sbab2zzp78n1r9"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-makefile
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* '("Makefile.am" "Makefile.in")
+               ;; The DESTDIR variable does not get replaced the prefix
+               ;; in the final Makefile, so let's do here.
+               (("\\$\\(DESTDIR\\)/usr")
+                (assoc-ref outputs "out")))
+             #t))
+         (add-after 'fix-makefile 'fix-paths
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Increase the max length of the path to the glade file,
+             ;; so that the '/gnu/store/...' path can fit in.
+             (substitute* '("src/shared.c" "src/shared.h")
+               (("char xnec2c_glade\\[64\\];")
+                "char xnec2c_glade[256];"))
+             ;; Fix hard coded references to '/usr/...'.
+             (substitute* '("src/geom_edit.c" "src/main.c")
+               (("\"/usr")
+                (string-append "\"" (assoc-ref outputs "out"))))
+             #t)))))
+    (synopsis "Antenna modeling software")
+    (description
+     "Xnec2c is a GTK3-based graphical version of nec2c, a translation to the
+C language of NEC2, the FORTRAN Numerical Electromagnetics Code commonly used
+for antenna simulation and analysis.  It can be used to define the geometry of
+an antenna, and then plot the radiation pattern or frequency-related data like
+gain and standing wave ratio.")
+    (home-page "http://www.5b4az.org/")
+    (license license:gpl3+)))

From ae1a0f75831cfcc81d4875031407d2934317300b Mon Sep 17 00:00:00 2001
From: Mathieu Othacehe <m.othacehe@gmail.com>
Date: Wed, 29 Apr 2020 09:11:24 +0200
Subject: [PATCH 132/215] tests: install: Increase virtual machine RAM.

It seems that 'guix system init' is consuming more than the 800M of RAM
currently allocated. Until this is understood, bump the limit to 1.2G.

Reported here:
https://lists.gnu.org/archive/html/bug-guix/2020-04/msg00519.html

* gnu/tests/install.scm (run-install): Bump RAM to 1.2G.
---
 gnu/tests/install.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm
index 713e03194b..3c6f6937ca 100644
--- a/gnu/tests/install.scm
+++ b/gnu/tests/install.scm
@@ -252,7 +252,7 @@ packages defined in installation-os."
               (make-marionette
                `(,(which #$(qemu-command system))
                  "-no-reboot"
-                 "-m" "800"
+                 "-m" "1200"
                  #$@(cond
                      ((string=? "ext4" installation-disk-image-file-system-type)
                       #~("-drive"

From be3abf28af02829cfd99c20ad8f0a86023554394 Mon Sep 17 00:00:00 2001
From: Mathieu Othacehe <m.othacehe@gmail.com>
Date: Wed, 29 Apr 2020 09:24:31 +0200
Subject: [PATCH 133/215] tests: install: Fix gui-installed-os test.

This is a follow-up of a860eddbbddeae5d3b6fe084e29ac9fafd2d6f02. If using an
ISO, the main disk is vda and not vdb anymore.

* gnu/tests/install.scm (installation-target-os-for-gui-tests): Use vda2 as
swap partition.
---
 gnu/tests/install.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm
index 3c6f6937ca..8650474fbc 100644
--- a/gnu/tests/install.scm
+++ b/gnu/tests/install.scm
@@ -1074,7 +1074,7 @@ build (current-guix) and then store a couple of full system images.")
                    %base-user-accounts))
     ;; The installer does not create a swap device in guided mode with
     ;; encryption support.
-    (swap-devices (if encrypted? '() '("/dev/vdb2")))
+    (swap-devices (if encrypted? '() '("/dev/vda2")))
     (services (cons (service dhcp-client-service-type)
                     (operating-system-user-services %minimal-os)))))
 

From cf480830e22e7725b8607b5b895e49f74d4e1525 Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Wed, 29 Apr 2020 10:15:57 +0200
Subject: [PATCH 134/215] gnu: gnuradio: Fix search paths for third-party
 blocks.

* gnu/packages/radio.scm (gnuradio)[native-search-paths]: Add definition of
  the GRC_BLOCKS_PATH variable.
---
 gnu/packages/radio.scm | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index b439e5feff..935880780f 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -363,6 +363,10 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).")
                (wrap-program (string-append out "/bin/gnuradio-companion")
                  `("GI_TYPELIB_PATH" ":" prefix ,(filter identity paths))))
              #t)))))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "GRC_BLOCKS_PATH")
+            (files '("/share/gnuradio/grc/blocks")))))
     (synopsis "Toolkit for software-defined radios")
     (description
      "GNU Radio is a development toolkit that provides signal processing blocks

From add3e168bb25e0af8a6225f5c93a311aae0268b2 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Fri, 24 Apr 2020 13:07:07 +0100
Subject: [PATCH 135/215] gnu: ikiwiki: Fetch sources from git repository.

* gnu/packages/web.scm (ikiwiki)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
[source](snippet): New field.
[arguments]<#:phases>[set-modification-times]: New phase.
---
 gnu/packages/web.scm | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index f5189dc7f9..bfd8486dff 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4813,13 +4813,20 @@ NetSurf project.")
     (version "3.20190228")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "http://snapshot.debian.org/archive/debian/"
-                           "20190301T035241Z/pool/main/i/ikiwiki/ikiwiki_"
-                           version ".orig.tar.xz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "git://git.ikiwiki.info/")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "17pyblaqhkb61lxl63bzndiffism8k859p54k3k4sghclq6lsynh"))))
+         "1c0i48jp2vpiwn2pacr6jbjdj26v7s9vzzs7j7gc16bx37dfgbbi"))
+       (snippet
+        '(begin
+           ;; The POT file requires write permission during the build
+           ;; phase.
+           (chmod "po/ikiwiki.pot" #o644)
+           #t))))
     (build-system perl-build-system)
     (arguments
      `(#:phases
@@ -4838,6 +4845,14 @@ NetSurf project.")
              (substitute* "Makefile.PL"
                (("SYSCONFDIR\\?=") "SYSCONFDIR?=$(PREFIX)"))
              #t))
+         (add-before 'build 'set-modification-times
+           ;; The wiki '--refresh' steps, which are executed during
+           ;; the check phase, require recent timestamps on files in
+           ;; the 'doc' and 'underlays' directories.
+           (lambda _
+             (invoke "find"  "doc" "underlays" "-type" "f" "-exec"
+                     "touch" "{}" "+")
+             #t))
          (add-after 'install 'wrap-programs
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out  (assoc-ref outputs "out"))

From 732ffac3bc8131ce0b3baceccafac6b1fa63fee8 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Fri, 24 Apr 2020 20:46:15 +0100
Subject: [PATCH 136/215] gnu: ikiwiki: Build perl inputs for target
 architecture.

* gnu/packages/web.scm (ikiwiki)[native-inputs]: Move perl dependencies ...
[inputs]: ...to here.
---
 gnu/packages/web.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index bfd8486dff..37f2076bd1 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4865,10 +4865,6 @@ NetSurf project.")
                #t))))))
     (native-inputs
      `(("which" ,which)
-       ("perl-html-tagset" ,perl-html-tagset)
-       ("perl-timedate" ,perl-timedate)
-       ("perl-xml-sax" ,perl-xml-sax)
-       ("perl-xml-simple" ,perl-xml-simple)
        ("gettext" ,gettext-minimal)
        ("subversion" ,subversion)
        ("git" ,git)
@@ -4883,11 +4879,15 @@ NetSurf project.")
        ("perl-db-file" ,perl-db-file)
        ("perl-html-parser" ,perl-html-parser)
        ("perl-html-scrubber" ,perl-html-scrubber)
+       ("perl-html-tagset" ,perl-html-tagset)
        ("perl-html-template" ,perl-html-template)
        ("perl-image-magick" ,perl-image-magick)
        ("perl-json" ,perl-json)
        ("perl-text-markdown-discount" ,perl-text-markdown-discount)
+       ("perl-timedate" ,perl-timedate)
        ("perl-uri" ,perl-uri)
+       ("perl-xml-sax" ,perl-xml-sax)
+       ("perl-xml-simple" ,perl-xml-simple)
        ("perl-yaml-libyaml" ,perl-yaml-libyaml)))
     (home-page "https://ikiwiki.info/")
     (synopsis "Wiki compiler, capable of generating HTML")

From b7392ecbbaa52eb54d9cefdccaa2af38d6b6fa62 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Mon, 27 Apr 2020 11:07:23 +0100
Subject: [PATCH 137/215] gnu: ikiwiki: Propagate some inputs.

* gnu/packages/web.scm (ikiwiki)[inputs]: Move perl-html-parser,
perl-html-scrubber, perl-html-template, perl-json,
perl-text-markdown-discount, perl-uri and perl-yaml-libyaml to...
[propagated-inputs]: ...here.  New field.
---
 gnu/packages/web.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 37f2076bd1..21acfcea24 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4877,17 +4877,18 @@ NetSurf project.")
        ("perl-cgi-session" ,perl-cgi-session)
        ("perl-cgi-simple" ,perl-cgi-simple)
        ("perl-db-file" ,perl-db-file)
-       ("perl-html-parser" ,perl-html-parser)
-       ("perl-html-scrubber" ,perl-html-scrubber)
        ("perl-html-tagset" ,perl-html-tagset)
-       ("perl-html-template" ,perl-html-template)
        ("perl-image-magick" ,perl-image-magick)
+       ("perl-timedate" ,perl-timedate)
+       ("perl-xml-sax" ,perl-xml-sax)
+       ("perl-xml-simple" ,perl-xml-simple)))
+    (propagated-inputs
+     `(("perl-html-parser" ,perl-html-parser)
+       ("perl-html-scrubber" ,perl-html-scrubber)
+       ("perl-html-template" ,perl-html-template)
        ("perl-json" ,perl-json)
        ("perl-text-markdown-discount" ,perl-text-markdown-discount)
-       ("perl-timedate" ,perl-timedate)
        ("perl-uri" ,perl-uri)
-       ("perl-xml-sax" ,perl-xml-sax)
-       ("perl-xml-simple" ,perl-xml-simple)
        ("perl-yaml-libyaml" ,perl-yaml-libyaml)))
     (home-page "https://ikiwiki.info/")
     (synopsis "Wiki compiler, capable of generating HTML")

From cf47084a884c8cc76f81a0a396b84d56f8d01904 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Tue, 28 Apr 2020 16:13:55 +0100
Subject: [PATCH 138/215] gnu: ikiwiki: Add missing inputs.

* gnu/packages/web.scm (ikiwiki)[inputs]: Add perl-authen-passphrase,
perl-file-mimeinfo, perl-mail-sendmail and perl-xml-twig.
---
 gnu/packages/web.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 21acfcea24..15410f945b 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4873,15 +4873,19 @@ NetSurf project.")
        ("mercurial" ,mercurial)))
     (inputs
      `(("python" ,python-wrapper)
+       ("perl-authen-passphrase" ,perl-authen-passphrase)
        ("perl-cgi-formbuilder" ,perl-cgi-formbuilder)
        ("perl-cgi-session" ,perl-cgi-session)
        ("perl-cgi-simple" ,perl-cgi-simple)
        ("perl-db-file" ,perl-db-file)
+       ("perl-file-mimeinfo" ,perl-file-mimeinfo)
        ("perl-html-tagset" ,perl-html-tagset)
        ("perl-image-magick" ,perl-image-magick)
+       ("perl-mail-sendmail" ,perl-mail-sendmail)
        ("perl-timedate" ,perl-timedate)
        ("perl-xml-sax" ,perl-xml-sax)
-       ("perl-xml-simple" ,perl-xml-simple)))
+       ("perl-xml-simple" ,perl-xml-simple)
+       ("perl-xml-twig" ,perl-xml-twig)))
     (propagated-inputs
      `(("perl-html-parser" ,perl-html-parser)
        ("perl-html-scrubber" ,perl-html-scrubber)

From 2933cdf88e2b978da7d3ea995931946a6581a8e7 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Tue, 28 Apr 2020 17:52:21 +0100
Subject: [PATCH 139/215] gnu: ikiwiki: Translate documentation.

* gnu/packages/web.scm (ikiwiki)[inputs]: Add po4a.
[arguments]<#:phases>[patch-Makefile]: Rename to...
[arguments]<#:phases>[patch-Makefiles]: ...this.  Add build environment
paths to the PERL5LIB environment variable that is used by the 'po2wiki'
script.
---
 gnu/packages/web.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 15410f945b..6bb8257c8d 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4840,10 +4840,13 @@ NetSurf project.")
                  "        addenv(\"PERL5LIB\", \""
                  (getenv "PERL5LIB")
                  "\");")))))
-         (add-after 'patch-source-shebangs 'patch-Makefile
+         (add-after 'patch-source-shebangs 'patch-Makefiles
            (lambda _
              (substitute* "Makefile.PL"
-               (("SYSCONFDIR\\?=") "SYSCONFDIR?=$(PREFIX)"))
+                          (("SYSCONFDIR\\?=") "SYSCONFDIR?=$(PREFIX)"))
+             (with-directory-excursion "po"
+               (substitute* "Makefile"
+                            (("PERL5LIB=") "PERL5LIB=${PERL5LIB}:")))
              #t))
          (add-before 'build 'set-modification-times
            ;; The wiki '--refresh' steps, which are executed during
@@ -4885,7 +4888,8 @@ NetSurf project.")
        ("perl-timedate" ,perl-timedate)
        ("perl-xml-sax" ,perl-xml-sax)
        ("perl-xml-simple" ,perl-xml-simple)
-       ("perl-xml-twig" ,perl-xml-twig)))
+       ("perl-xml-twig" ,perl-xml-twig)
+       ("po4a" ,po4a)))
     (propagated-inputs
      `(("perl-html-parser" ,perl-html-parser)
        ("perl-html-scrubber" ,perl-html-scrubber)

From da6539d17b6fe8c73ea06c2cad5327e1a91af6d3 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Tue, 28 Apr 2020 21:32:56 +0100
Subject: [PATCH 140/215] gnu: ikiwiki: Update to 3.20200202.3.

* gnu/packages/web.scm (ikiwiki): Update to 3.20200202.3.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 6bb8257c8d..092ff30148 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4810,7 +4810,7 @@ NetSurf project.")
 (define-public ikiwiki
   (package
     (name "ikiwiki")
-    (version "3.20190228")
+    (version "3.20200202.3")
     (source
      (origin
        (method git-fetch)
@@ -4820,7 +4820,7 @@ NetSurf project.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1c0i48jp2vpiwn2pacr6jbjdj26v7s9vzzs7j7gc16bx37dfgbbi"))
+         "0fphyqzlk9y8v9s89ypsmrnbhyymzrpc2w0liy0n4knc7kk2pabq"))
        (snippet
         '(begin
            ;; The POT file requires write permission during the build

From 4f0f46e4af0e342d84c5ad448258702029601e4b Mon Sep 17 00:00:00 2001
From: Alexandros Theodotou <alex@zrythm.org>
Date: Tue, 28 Apr 2020 15:55:13 +0100
Subject: [PATCH 141/215] gnu: zrythm: Update to 0.8.333.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/music.scm (zrythm): Update to 0.8.333.
[inputs]: Add new dependencies graphviz and gtksourceview.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
---
 gnu/packages/music.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 34d4adb33c..589f158afe 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -99,6 +99,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gpodder)
   #:use-module (gnu packages graphics)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
@@ -5158,7 +5159,7 @@ and as an LV2 plugin.")
 (define-public zrythm
   (package
     (name "zrythm")
-    (version "0.8.200")
+    (version "0.8.333")
     (source
       (origin
         (method url-fetch)
@@ -5166,7 +5167,7 @@ and as an LV2 plugin.")
                             version ".tar.xz"))
         (sha256
           (base32
-            "13ivxbrd44qnhyh46dcr94dvqxg8cn4bbd8xm77ljw0p9b4ks4zs"))))
+            "0x2kxr5zz058jpy6k6ymj0fi2gqfcgrlv4qkwz9443hjy5345iwb"))))
    (build-system meson-build-system)
    (arguments
     `(#:glib-or-gtk? #t
@@ -5190,7 +5191,9 @@ and as an LV2 plugin.")
       ("fftwf" ,fftwf)
       ("gettext" ,gettext-minimal)
       ("glibc" ,glibc)
+      ("graphviz" ,graphviz)
       ("gtk+" ,gtk+)
+      ("gtksourceview" ,gtksourceview)
       ("guile" ,guile-2.2)
       ("libcyaml" ,libcyaml)
       ("libsamplerate" ,libsamplerate)

From 8fe681b9ffc5c5b0056e3174fade2f9e0b58fb97 Mon Sep 17 00:00:00 2001
From: Brice Waegeneire <brice@waegenei.re>
Date: Tue, 28 Apr 2020 11:53:23 +0200
Subject: [PATCH 142/215] gnu: Add edid-decode.

* gnu/packages/hardware.scm (edid-decode): New variable.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
---
 gnu/packages/hardware.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm
index 7ee657a75a..114332455e 100644
--- a/gnu/packages/hardware.scm
+++ b/gnu/packages/hardware.scm
@@ -79,6 +79,43 @@ calibrated, and restored when the calibration is applied.")
     (license (list license:bsd-3        ; FindDDCUtil.cmake
                    license:gpl2+))))    ; everything else
 
+(define-public edid-decode
+  (let ((commit "74b64180d67bb009d8d9ea1b6f18ad41aaa16396") ; 2020-04-22
+        (revision "1"))
+    (package
+      (name "edid-decode")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (file-name (git-file-name name version))
+         (uri (git-reference
+               (url "git://linuxtv.org/edid-decode.git")
+               (commit commit)))
+         (sha256
+          (base32 "0nirp5bza08zj5d8bjgcm0p869hdg3qg3mwa7999pjdrzmn7s2ah"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                     ; No test suite
+         #:make-flags
+         (list (string-append "DESTDIR=" (assoc-ref %outputs "out"))
+               "bindir=/bin" "mandir=/share/man")
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'fix-cross-compilation
+             (lambda* (#:key native-inputs target #:allow-other-keys)
+               (when target
+                 (substitute* "Makefile"
+                   (("\\$\\(CXX\\)")
+                    (string-append target "-g++"))))
+               #t))
+           (delete 'configure))))
+      (home-page "https://git.linuxtv.org/edid-decode.git/")
+      (synopsis "Decode @dfn{EDID} data in human-readable format")
+      (description "edid-decode decodes @dfn{EDID} monitor description data in
+human-readable format and checks if it conforms to the standards.")
+      (license license:expat))))
+
 ;; Distinct from memtest86, which is obsolete.
 (define-public memtest86+
   (package

From 1228c2abcfd5b426385211e3b27379f27d655b17 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 13:34:22 +0200
Subject: [PATCH 143/215] gnu: kaldi-gstreamer-server: Update to 0-2.f68cab4.

* gnu/packages/machine-learning.scm (kaldi-gstreamer-server): Update to
0-2.f68cab4.
[inputs]: Replace python-2 with python-wrapper, python2-pygobject with
python-pygobject, python2-pyyaml with python-pyyaml, and python2-tornado with
python-tornado; remove python2-ws4py-for-kaldi-gstreamer-server and
python2-futures.
---
 gnu/packages/machine-learning.scm | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index f979a64d55..425961ee14 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1239,8 +1239,9 @@ automatically.")
       (license license:asl2.0))))
 
 (define-public kaldi-gstreamer-server
-  (let ((commit "1735ba49c5dc0ebfc184e45105fc600cd9f1f508")
-        (revision "1"))
+  ;; This is the tip of the py3 branch
+  (let ((commit "f68cab490be7eb0da2af1475fbc16655f50a60cb")
+        (revision "2"))
     (package
       (name "kaldi-gstreamer-server")
       (version (git-version "0" revision commit))
@@ -1252,7 +1253,7 @@ automatically.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0j701m7lbwmzqxsfanj882v7881hrbmpqybbczbxqpcbg8q34w0k"))))
+                  "17lh1368vkg8ngrcbn2phvigzlmalrqg6djx2gg61qq1a0nj87dm"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f ; there are no tests that can be run automatically
@@ -1268,6 +1269,10 @@ automatically.")
                ;; are reproducible.
                (setenv "PYTHONHASHSEED" "0")
                (with-directory-excursion "kaldigstserver"
+                 ;; This is a Python 2 file
+                 (delete-file "decoder_test.py")
+                 (delete-file "test-buffer.py")
+
                  (for-each (lambda (file)
                              (apply invoke
                                     `("python"
@@ -1318,12 +1323,10 @@ exec ~a ~a/~a \"$@\"~%"
                  #t))))))
       (inputs
        `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
-         ("python2" ,python-2)
-         ("python2-futures" ,python2-futures)
-         ("python2-pygobject" ,python2-pygobject)
-         ("python2-pyyaml" ,python2-pyyaml)
-         ("python2-tornado" ,python2-tornado)
-         ("python2-ws4py" ,python2-ws4py-for-kaldi-gstreamer-server)))
+         ("python" ,python-wrapper)
+         ("python-pygobject" ,python-pygobject)
+         ("python-pyyaml" ,python-pyyaml)
+         ("python-tornado" ,python-tornado)))
       (home-page "https://github.com/alumae/kaldi-gstreamer-server")
       (synopsis "Real-time full-duplex speech recognition server")
       (description "This is a real-time full-duplex speech recognition server,

From e979cea9052d45f2a3e703ebe4103f441190d087 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 13:35:51 +0200
Subject: [PATCH 144/215] gnu: Remove python2-ws4py-for-kaldi-gstreamer-server.

* gnu/packages/python-web.scm (python2-ws4py-for-kaldi-gstreamer-server):
Remove variable.
---
 gnu/packages/python-web.scm | 26 --------------------------
 1 file changed, 26 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 6b77a9d949..30cd22fddb 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3268,32 +3268,6 @@ such as IoT applications or multi-user database-driven business applications.")
 Python.")
     (license license:bsd-3)))
 
-;; kaldi-gstreamer-server does not yet work with python-ws4py > 0.3.2
-(define-public python2-ws4py-for-kaldi-gstreamer-server
-  (package (inherit python-ws4py)
-    (name "python2-ws4py")
-    (version "0.3.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "ws4py" version))
-       (sha256
-        (base32
-         "12ys3dv98awhrxd570vla3hqgzq3avjhq4yafhghhq3a942y1928"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         ;; We don't have a package for cherrypy.
-         (add-after 'unpack 'remove-cherrypy-support
-           (lambda _
-             (delete-file "ws4py/server/cherrypyserver.py")
-             #t)))))
-    (propagated-inputs
-     `(("python-gevent" ,python2-gevent)
-       ("python-tornado" ,python2-tornado)))))
-
 (define-public python-slugify
   (package
     (name "python-slugify")

From 27cb52a20b9c697131e3d51e7bf084d6af5b5a62 Mon Sep 17 00:00:00 2001
From: Raghav Gururajan <raghavgururajan@disroot.org>
Date: Fri, 10 Jan 2020 08:49:02 -0500
Subject: [PATCH 145/215] gnu: gnome-calendar: Propagate evolution-data-server.

* gnu/packages/gnome.scm (gnome-calendar)[inputs]: Move evolution-data-server
from here...
[propagated-inputs]: ...to here.

Fixes <https://bugs.gnu.org/40686>.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/gnome.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index d96a5f4643..e6b1942450 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -8094,13 +8094,14 @@ desktop.  It supports world clock, stop watch, alarms, and count down timer.")
        ("gtk+-bin" ,gtk+ "bin")         ; For gtk-update-icon-cache
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("evolution-data-server" ,evolution-data-server)
-       ("gnome-online-accounts:lib" ,gnome-online-accounts "lib")
+     `(("gnome-online-accounts:lib" ,gnome-online-accounts "lib")
        ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
        ("libdazzle" ,libdazzle)
        ("libedataserverui" ,evolution-data-server)
        ("libgweather" ,libgweather)
        ("geoclue" ,geoclue)))
+    (propagated-inputs
+     `(("evolution-data-server" ,evolution-data-server)))
     (home-page "https://wiki.gnome.org/Apps/Calendar")
     (synopsis "GNOME's calendar application")
     (description

From 39a96b99fe66c2cf7ff8ff023f3839647332ebd9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:37:22 +0200
Subject: [PATCH 146/215] gnu: Add python-restructuredtext-lint.

* gnu/packages/python-xyz.scm (python-restructuredtext-lint): New variable.
---
 gnu/packages/python-xyz.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 31cafd47d1..45789d7eb5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3212,6 +3212,38 @@ reStructuredText.")
                (base32
                 "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji"))))))
 
+(define-public python-restructuredtext-lint
+  (package
+    (name "python-restructuredtext-lint")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "restructuredtext-lint" version))
+       (sha256
+        (base32
+         "026rdy5h82ng4vqxk8fnprii9d6qxf7hkygiv0a8afjvdlsxmcwp"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "nosetests" "-v"))
+             #t)))))
+    (propagated-inputs
+     `(("python-docutils" ,python-docutils)))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "https://github.com/twolfson/restructuredtext-lint")
+    (synopsis "reStructuredText linter")
+    (description "This package provides a linter for the reStructuredText
+format.")
+    (license license:unlicense)))
+
 (define-public python-pygments
   (package
     (name "python-pygments")

From d08782d16c21998a493e50e2c90a183a3d4a53bb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:38:22 +0200
Subject: [PATCH 147/215] gnu: Add python-port-for.

* gnu/packages/python-web.scm (python-port-for): New variable.
---
 gnu/packages/python-web.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 30cd22fddb..c0be3fa5d1 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3595,3 +3595,35 @@ and rendering come directly from GitHub, so you'll know exactly how it will
 appear.  Changes you make to the file will be instantly reflected in the browser
 without requiring a page refresh.")
       (license license:expat))))
+
+(define-public python-port-for
+  (package
+    (name "python-port-for")
+    (version "0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "port-for" version))
+       (sha256
+        (base32
+         "1pncxlj25ggw99r0ijfbkq70gd7cbhqdx5ivsxy4jdp0z14cpda7"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-urllib3
+           (lambda _
+             (substitute* "port_for/_download_ranges.py"
+               (("urllib2") "urllib3"))
+             #t)))))
+    (propagated-inputs
+     `(("python-urllib3" ,python-urllib3)))
+    (native-inputs
+     `(("python-mock" ,python-mock)))
+    (home-page "https://github.com/kmike/port-for/")
+    (synopsis "TCP localhost port finder and association manager")
+    (description
+     "This package provides a utility that helps with local TCP ports
+management.  It can find an unused TCP localhost port and remember the
+association.")
+    (license license:expat)))

From d0e0b865e1e97679f718daf159e766c19bc09c91 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:40:54 +0200
Subject: [PATCH 148/215] gnu: Add python-livereload.

* gnu/packages/python-web.scm (python-livereload): New variable.
---
 gnu/packages/python-web.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index c0be3fa5d1..0dba566a77 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3627,3 +3627,26 @@ without requiring a page refresh.")
 management.  It can find an unused TCP localhost port and remember the
 association.")
     (license license:expat)))
+
+(define-public python-livereload
+  (package
+    (name "python-livereload")
+    (version "2.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "livereload" version))
+       (sha256
+        (base32
+         "0rhggz185bxc3zjnfpmhcvibyzi86i624za1lfh7x7ajsxw4y9c9"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-six" ,python-six)
+       ("python-tornado" ,python-tornado)))
+    (home-page "https://github.com/lepture/python-livereload")
+    (synopsis "Python LiveReload")
+    (description
+     "Python LiveReload provides a command line utility, @command{livereload},
+for starting a web server in a directory.  It can trigger arbitrary commands
+and serve updated contents upon changes to the directory.")
+    (license license:bsd-3)))

From ff5ca61d15e979f1a91d77f950af13c76dd9b00a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:41:13 +0200
Subject: [PATCH 149/215] gnu: Add python-doc8.

* gnu/packages/python-xyz.scm (python-doc8): New variable.
---
 gnu/packages/python-xyz.scm | 39 +++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 45789d7eb5..decc1ce8a6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3244,6 +3244,45 @@ reStructuredText.")
 format.")
     (license license:unlicense)))
 
+(define-public python-doc8
+  (package
+    (name "python-doc8")
+    (version "0.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "doc8" version))
+       (sha256
+        (base32
+         "0hw5w8mpgsp51qg8nnq28p7y1jiksvz7a0axnn5bkgss3af9zy1d"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "pytest" "-v"))
+             #t)))))
+    (propagated-inputs
+     `(("python-chardet" ,python-chardet)
+       ("python-docutils" ,python-docutils)
+       ("python-restructuredtext-lint" ,python-restructuredtext-lint)
+       ("python-six" ,python-six)
+       ("python-stevedore" ,python-stevedore)))
+    (native-inputs
+     `(("python-testtools" ,python-testtools)
+       ("python-pytest" ,python-pytest)))
+    (home-page "https://launchpad.net/doc8")
+    (synopsis
+     "Style checker for Sphinx (or other) RST documentation")
+    (description
+     "Doc8 is an opinionated style checker for reStructured Text and plain
+text styles of documentation.")
+    (license license:asl2.0)))
+
 (define-public python-pygments
   (package
     (name "python-pygments")

From e9f93cd5f78ffa234263e049e594fc57cd1e94f7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:41:52 +0200
Subject: [PATCH 150/215] gnu: Add python-sphinx-autobuild.

* gnu/packages/sphinx.scm (python-sphinx-autobuild): New variable.
---
 gnu/packages/sphinx.scm | 48 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 47 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index ff5d8e5de7..f27f9d0176 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 David Thompson <davet@gnu.org>
-;;; Copyright © 2015, 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke <mbakke@fastmail.com>
@@ -597,3 +597,49 @@ to be able to read and render the Doxygen xml output.")
      "A utility tool that provides several features that make it easy to
 translate and to apply translation to Sphinx generated document.")
     (license license:bsd-2)))
+
+(define-public python-sphinx-autobuild
+  (package
+    (name "python-sphinx-autobuild")
+    (version "0.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sphinx-autobuild" version))
+       (sha256
+        (base32
+         "0kn753dyh3b1s0h77lbk704niyqc7bamvq6v3s1f6rj6i20qyf36"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; See https://github.com/GaretJax/sphinx-autobuild/pull/72
+         (add-after 'unpack 'use-later-port-for
+           (lambda _
+             (substitute* "requirements.txt"
+               (("port_for==.*") "port_for\n"))
+             #t))
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "pytest" "-v"))
+             #t)))))
+    (propagated-inputs
+     `(("python-argh" ,python-argh)
+       ("python-livereload" ,python-livereload)
+       ("python-pathtools" ,python-pathtools)
+       ("python-port-for" ,python-port-for)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-tornado" ,python-tornado)
+       ("python-watchdog" ,python-watchdog)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "https://github.com/GaretJax/sphinx-autobuild")
+    (synopsis "Rebuild Sphinx documentation when a change is detected")
+    (description
+     "This package lets you watch a Sphinx directory and rebuild the
+documentation when a change is detected.  It also includes a livereload
+enabled web server.")
+    (license license:expat)))

From c537d2bcb7c652b4776435cd1e2a5119af43dd78 Mon Sep 17 00:00:00 2001
From: Mathieu Othacehe <m.othacehe@gmail.com>
Date: Wed, 29 Apr 2020 15:25:00 +0200
Subject: [PATCH 151/215] tests: install: Fix device usage.

This is a follow-up of a860eddbbddeae5d3b6fe084e29ac9fafd2d6f02. Guided
installation tests are now run from an ISO image. Hence the main block device
is vda and not vdb anymore.

* gnu/tests/install.scm (installation-target-os-for-gui-tests): Use
%minimal-os-on-vda instead of %minimal-os.
(%minimal-os-on-vda): Make sure that it replicates the config of %minimal-os.
---
 gnu/tests/install.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm
index 8650474fbc..019e21fd39 100644
--- a/gnu/tests/install.scm
+++ b/gnu/tests/install.scm
@@ -387,6 +387,7 @@ per %test-installed-os, this test is expensive in terms of CPU and storage.")
     (services (cons (service marionette-service-type
                              (marionette-configuration
                               (imported-modules '((gnu services herd)
+                                                  (guix build utils)
                                                   (guix combinators)))))
                     %base-services))))
 
@@ -1058,7 +1059,7 @@ build (current-guix) and then store a couple of full system images.")
 (define* (installation-target-os-for-gui-tests
           #:key (encrypted? #f))
   (operating-system
-    (inherit %minimal-os)
+    (inherit %minimal-os-on-vda)
     (users (append (list (user-account
                           (name "alice")
                           (comment "Bob's sister")
@@ -1076,7 +1077,7 @@ build (current-guix) and then store a couple of full system images.")
     ;; encryption support.
     (swap-devices (if encrypted? '() '("/dev/vda2")))
     (services (cons (service dhcp-client-service-type)
-                    (operating-system-user-services %minimal-os)))))
+                    (operating-system-user-services %minimal-os-on-vda)))))
 
 (define* (installation-target-desktop-os-for-gui-tests
           #:key (encrypted? #f))

From 373c0dc95ce0dc65f378432d0cb1a29bda2f12e5 Mon Sep 17 00:00:00 2001
From: Masaya Tojo <masaya@tojo.tokyo>
Date: Wed, 29 Apr 2020 16:26:21 +0200
Subject: [PATCH 152/215] gnu: Add emacs-twittering-mode.

* gnu/packages/emacs-xyz.scm (emacs-twittering-mode): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 2c61c4189d..650a573542 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2632,6 +2632,27 @@ Stack Overflow, Super User, and other StackExchange sites.")
 Tom's Obvious, Minimal Language} data format.")
       (license license:gpl3+))))
 
+(define-public emacs-twittering-mode
+  (package
+    (name "emacs-twittering-mode")
+    (version "3.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/twmode"
+                           "/twittering-mode-" version
+                           "/twittering-mode-" version ".tar.xz"))
+       (sha256
+        (base32 "02imis1gxz90lah0b5n37j2hlsaw5igss11d85vpsm5d1bgw8j28"))))
+    (build-system emacs-build-system)
+    (home-page "http://twmode.sourceforge.net")
+    (synopsis "Emacs major mode for Twitter")
+    (description
+     "Twittering mode is an Emacs major mode for Twitter.
+You can check timelines, tweet, mark posts as favorites and so on with
+Emacs.")
+    (license license:gpl2+)))
+
 (define-public emacs-f
   (package
     (name "emacs-f")

From 6d25f29143b8ebe7f627a32418a369a1c5f8625f Mon Sep 17 00:00:00 2001
From: pinoaffe <pinoaffe@airmail.cc>
Date: Wed, 29 Apr 2020 16:29:53 +0200
Subject: [PATCH 153/215] gnu: Add emacs-ryo-modal.

* gnu/packages/emacs-xyz.scm (emacs-ryo-modal): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 650a573542..56cd298c28 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -68,6 +68,7 @@
 ;;; Copyright © 2020 John Soo <jsoo1@asu.edu>
 ;;; Copyright © 2020 Jérémy Korwin-Zmijowski <jeremy@korwin-zmijowski.fr>
 ;;; Copyright © 2020 Alberto Eleuterio Flores Guerrero <barbanegra+guix@posteo.mx>
+;;; Copyright © 2020 pinoaffe <pinoaffe@airmail.cc>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -7312,6 +7313,30 @@ of its name.")
 names, e.g. #0000ff is displayed in white with a blue background.")
     (license license:gpl3+)))
 
+(define-public emacs-ryo-modal
+  ;; Package has no release.  Version is extracted from "Version:" keyword in
+  ;; main file.
+  (let ((commit "3a54312eea7023a86ca3f8eb3c03c872554bff2f")
+        (revision "0"))
+    (package
+      (name "emacs-ryo-modal")
+      (version (git-version "0.4" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/Kungsgeten/ryo-modal.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1cyvp3bi6yhckbdnq98xvghmhdzghya5y9wd7hxjawibs75rza95"))))
+      (build-system emacs-build-system)
+      (home-page "http://github.com/Kungsgeten/ryo-modal")
+      (synopsis "Emacs minor mode for defining modal editing environments")
+      (description "RYO modal provides a convenient way of defining modal
+keybindings in Emacs, and does not come with any predefined bindings.")
+      (license license:expat))))
+
 (define-public emacs-visual-fill-column
   (package
     (name "emacs-visual-fill-column")

From 1cc9947a53adc36d0767c1854f54178d91eb872d Mon Sep 17 00:00:00 2001
From: pinoaffe <pinoaffe@airmail.cc>
Date: Wed, 29 Apr 2020 16:33:35 +0200
Subject: [PATCH 154/215] gnu: Add emacs-kakoune.

* gnu/packages/emacs-xyz.scm (emacs-kakoune): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 56cd298c28..9200122b77 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2479,6 +2479,37 @@ create an Extempore REPL, connect the current @code{extempore-mode} buffer to a
 running Extempore process, and more.")
       (license license:bsd-2))))
 
+(define-public emacs-kakoune
+  ;; Package has no release.  Version is extracted from "Version:" keyword in
+  ;; main file.
+  (let ((commit "d73d14e69ea38076af50cc69f846808383ff539d")
+        (revision "0"))
+    (package
+      (name "emacs-kakoune")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/jmorag/kakoune.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0nk6jdy1y5mc3ryd0smiqghrk6iv34d5grc7f7migmshlbq0np92"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-expand-region"    ,emacs-expand-region)
+         ("emacs-multiple-cursors" ,emacs-multiple-cursors)
+         ("emacs-ryo-modal"        ,emacs-ryo-modal)))
+      (home-page "https://github.com/jmorag/kakoune.el")
+      (synopsis "Emacs simple simulation, but not emulation, of Kakoune")
+      (description "This package provides many, but not all of the editing
+primitives in the Kakoune editor.  Unlike Evil mode for Vim, this is a very
+shallow emulation, which seeks to do as little work as possible, leveraging
+Emacs native editing commmands and the work of other packages wherever
+possible.")
+      (license license:expat))))
+
 (define-public emacs-keyfreq
   (package
     (name "emacs-keyfreq")

From 587ccf4c793973dcde1abd3ef207a9ee58b9f0e5 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Wed, 29 Apr 2020 19:36:30 +0300
Subject: [PATCH 155/215] gnu: emacs-vterm: Update to 0-1.e63bd65.

* gnu/packages/emacs-xyz.scm (emacs-vterm): Update to 0-1.e63bd65.
---
 gnu/packages/emacs-xyz.scm | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 9200122b77..79f7126ed7 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -18241,7 +18241,7 @@ stored playlists.")
 (define-public emacs-vterm
   (let ((version "0")
         (revision "1")
-        (commit "7d7381fa8104b55b70148cf147523d9ab7f01fcd"))
+        (commit "e63bd65eece7c5de3a534b7e2fdbe58256ec2da0"))
     (package
       (name "emacs-vterm")
       (version (git-version version revision commit))
@@ -18253,7 +18253,7 @@ stored playlists.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "04a2jlhmr20ipgzpnba3yryw3ly7qdxjgaw10dwn9wxy1yqmapz1"))))
+                  "0iq857w54qmazxh23fipz85fb9i6dav3f63g0ghpmi6mybfp6i5v"))))
       (build-system emacs-build-system)
       (arguments
        `(#:modules ((guix build emacs-build-system)
@@ -18264,14 +18264,11 @@ stored playlists.")
                              (guix build cmake-build-system))
          #:phases
          (modify-phases %standard-phases
-           (add-before 'add-source-to-load-path 'remove-vterm-module-make
+           (add-before 'add-source-to-load-path 'substitute-vterm-module-path
              (lambda* (#:key outputs #:allow-other-keys)
-               ;; Remove the Emacs Lisp file.
-               (delete-file "vterm-module-make.el")
-               ;; Remove references to the removed file.
-               (make-file-writable "vterm.el")
+               (chmod "vterm.el" #o644)
                (emacs-substitute-sexps "vterm.el"
-                 ("(or (require 'vterm-module nil t)"
+                 ("(require 'vterm-module nil t)"
                   `(module-load
                     ,(string-append (assoc-ref outputs "out")
                                     "/lib/vterm-module.so"))))

From 19987f5efe0acb65918802681f3a18cbb6a07c2a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 29 Apr 2020 16:57:09 +0200
Subject: [PATCH 156/215] gnu: foo2zjs: Update to 20200426.

* gnu/packages/cups.scm (foo2zjs): Update to 20200426.
---
 gnu/packages/cups.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index 1db2f101f1..f24ea6c02a 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -673,14 +673,14 @@ printer/driver specific, but spooler-independent PPD file.")
 (define-public foo2zjs
   (package
     (name "foo2zjs")
-    (version "20200207")
+    (version "20200426")
     (source (origin
               (method url-fetch)
               ;; XXX: This is an unversioned URL!
               (uri "http://foo2zjs.rkkda.com/foo2zjs.tar.gz")
               (sha256
                (base32
-                "0pf1sm29gnrhhpyvq95jskvr874h5r4kls9w10gc24z23fjmr5zx"))))
+                "0wwh29ddd59q18r1jpi3166lgnwr8zn9lry82vahc2g96l97isp7"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases

From f224a8bb79cc3c9e5960227ffea5524eb666d34a Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 28 Apr 2020 15:59:16 -0400
Subject: [PATCH 157/215] gnu: OpenLDAP: Update to 2.4.50 [fixes
 CVE-2019-{13057,13565}].

* gnu/packages/openldap.scm (openldap)[replacement]: Use openldap-2.4.50.
(openldap/fixed): Replace with ...
(openldap-2.4.50): ... new variable.
* gnu/packages/patches/openldap-CVE-2020-12243.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                  |   1 -
 gnu/packages/openldap.scm                     |  16 ++-
 .../patches/openldap-CVE-2020-12243.patch     | 125 ------------------
 3 files changed, 11 insertions(+), 131 deletions(-)
 delete mode 100644 gnu/packages/patches/openldap-CVE-2020-12243.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 67bf04547c..9426ee30a0 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1276,7 +1276,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/opencv-rgbd-aarch64-test-fix.patch	\
   %D%/packages/patches/openfoam-4.1-cleanup.patch			\
   %D%/packages/patches/openjdk-10-idlj-reproducibility.patch	\
-  %D%/packages/patches/openldap-CVE-2020-12243.patch		\
   %D%/packages/patches/openmpi-mtl-priorities.patch		\
   %D%/packages/patches/openocd-nrf52.patch			\
   %D%/packages/patches/openssl-runpath.patch			\
diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm
index aa51520654..53c57e846f 100644
--- a/gnu/packages/openldap.scm
+++ b/gnu/packages/openldap.scm
@@ -58,8 +58,8 @@
 
 (define-public openldap
   (package
-   (replacement openldap/fixed)
    (name "openldap")
+   (replacement openldap-2.4.50)
    (version "2.4.47")
    (source (origin
             (method url-fetch)
@@ -112,12 +112,18 @@
    (license openldap2.8)
    (home-page "https://www.openldap.org/")))
 
-(define openldap/fixed
+(define openldap-2.4.50
   (package
     (inherit openldap)
-    (source
-      (origin (inherit (package-source openldap))
-              (patches (search-patches "openldap-CVE-2020-12243.patch"))))))
+    (version "2.4.50")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://www.openldap.org/software/download/"
+                                  "OpenLDAP/openldap-release/openldap-" version
+                                  ".tgz"))
+              (sha256
+               (base32
+                "1f46nlfwmys110j36sifm7ah8m8f3s10c3vaiikmmigmifapvdaw"))))))
 
 (define-public nss-pam-ldapd
   (package
diff --git a/gnu/packages/patches/openldap-CVE-2020-12243.patch b/gnu/packages/patches/openldap-CVE-2020-12243.patch
deleted file mode 100644
index 6321998198..0000000000
--- a/gnu/packages/patches/openldap-CVE-2020-12243.patch
+++ /dev/null
@@ -1,125 +0,0 @@
-From 98464c11df8247d6a11b52e294ba5dd4f0380440 Mon Sep 17 00:00:00 2001
-From: Howard Chu <hyc@openldap.org>
-Date: Thu, 16 Apr 2020 01:08:19 +0100
-Subject: [PATCH] ITS#9202 limit depth of nested filters
-
-Using a hardcoded limit for now; no reasonable apps
-should ever run into it.
----
- servers/slapd/filter.c | 41 ++++++++++++++++++++++++++++++++---------
- 1 file changed, 32 insertions(+), 9 deletions(-)
-
-diff --git a/servers/slapd/filter.c b/servers/slapd/filter.c
-index 3252cf2a7..ed57bbd7b 100644
---- a/servers/slapd/filter.c
-+++ b/servers/slapd/filter.c
-@@ -37,11 +37,16 @@
- const Filter *slap_filter_objectClass_pres;
- const struct berval *slap_filterstr_objectClass_pres;
- 
-+#ifndef SLAPD_MAX_FILTER_DEPTH
-+#define SLAPD_MAX_FILTER_DEPTH	5000
-+#endif
-+
- static int	get_filter_list(
- 	Operation *op,
- 	BerElement *ber,
- 	Filter **f,
--	const char **text );
-+	const char **text,
-+	int depth );
- 
- static int	get_ssa(
- 	Operation *op,
-@@ -80,12 +85,13 @@ filter_destroy( void )
- 	return;
- }
- 
--int
--get_filter(
-+static int
-+get_filter0(
- 	Operation *op,
- 	BerElement *ber,
- 	Filter **filt,
--	const char **text )
-+	const char **text,
-+	int depth )
- {
- 	ber_tag_t	tag;
- 	ber_len_t	len;
-@@ -126,6 +132,11 @@ get_filter(
- 	 *
- 	 */
- 
-+	if( depth > SLAPD_MAX_FILTER_DEPTH ) {
-+		*text = "filter nested too deeply";
-+		return SLAPD_DISCONNECT;
-+	}
-+
- 	tag = ber_peek_tag( ber, &len );
- 
- 	if( tag == LBER_ERROR ) {
-@@ -221,7 +232,7 @@ get_filter(
- 
- 	case LDAP_FILTER_AND:
- 		Debug( LDAP_DEBUG_FILTER, "AND\n", 0, 0, 0 );
--		err = get_filter_list( op, ber, &f.f_and, text );
-+		err = get_filter_list( op, ber, &f.f_and, text, depth+1 );
- 		if ( err != LDAP_SUCCESS ) {
- 			break;
- 		}
-@@ -234,7 +245,7 @@ get_filter(
- 
- 	case LDAP_FILTER_OR:
- 		Debug( LDAP_DEBUG_FILTER, "OR\n", 0, 0, 0 );
--		err = get_filter_list( op, ber, &f.f_or, text );
-+		err = get_filter_list( op, ber, &f.f_or, text, depth+1 );
- 		if ( err != LDAP_SUCCESS ) {
- 			break;
- 		}
-@@ -248,7 +259,7 @@ get_filter(
- 	case LDAP_FILTER_NOT:
- 		Debug( LDAP_DEBUG_FILTER, "NOT\n", 0, 0, 0 );
- 		(void) ber_skip_tag( ber, &len );
--		err = get_filter( op, ber, &f.f_not, text );
-+		err = get_filter0( op, ber, &f.f_not, text, depth+1 );
- 		if ( err != LDAP_SUCCESS ) {
- 			break;
- 		}
-@@ -311,10 +322,22 @@ get_filter(
- 	return( err );
- }
- 
-+int
-+get_filter(
-+	Operation *op,
-+	BerElement *ber,
-+	Filter **filt,
-+	const char **text )
-+{
-+	return get_filter0( op, ber, filt, text, 0 );
-+}
-+
-+
- static int
- get_filter_list( Operation *op, BerElement *ber,
- 	Filter **f,
--	const char **text )
-+	const char **text,
-+	int depth )
- {
- 	Filter		**new;
- 	int		err;
-@@ -328,7 +351,7 @@ get_filter_list( Operation *op, BerElement *ber,
- 		tag != LBER_DEFAULT;
- 		tag = ber_next_element( ber, &len, last ) )
- 	{
--		err = get_filter( op, ber, new, text );
-+		err = get_filter0( op, ber, new, text, depth );
- 		if ( err != LDAP_SUCCESS )
- 			return( err );
- 		new = &(*new)->f_next;
--- 
-2.26.2
-

From 4b800bff8039ca718aa70db814dc51b5de18da8e Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 21 Apr 2020 10:34:30 +0200
Subject: [PATCH 158/215] gnu: python-aiosqlite: Update to 0.12.0.

* gnu/packages/databases.scm (python-aiosqlite): Update to 0.12.0.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/databases.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 606594e005..bf5398d87b 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2743,14 +2743,14 @@ translate the complete SQLite API into Python.")
 (define-public python-aiosqlite
   (package
     (name "python-aiosqlite")
-    (version "0.11.0")
+    (version "0.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "aiosqlite" version))
        (sha256
         (base32
-         "1f3zdldp9zgrw6qz5fsp3wa5zw73cjf139pj4vf24ryv895320jg"))))
+         "1w8248yz85xyzvvh4jaxnc59fqil45aka6h82kn1rcih4rjxbnn1"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-aiounittest" ,python-aiounittest)))

From 510472f865a9a21cce4ed8b1f16236ed513dbccc Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 21 Apr 2020 10:35:33 +0200
Subject: [PATCH 159/215] gnu: python-pypika: Update to 0.37.2.

* gnu/packages/databases.scm (python-pypika): Update to 0.37.2.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/databases.scm | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index bf5398d87b..57a5128e9e 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3074,14 +3074,16 @@ transforms idiomatic python function calls to well-formed SQL queries.")
 (define-public python-pypika
   (package
     (name "python-pypika")
-    (version "0.36.0")
+    (version "0.37.2")
     (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "PyPika" version))
-       (sha256
-        (base32
-         "0qzn5vygirg52dlizm6ayzdc5llq8p2krrx0kymr236lrz89wqp8"))))
+     (origin (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/kayak/pypika.git")
+                   (commit (string-append "v" version))))
+             (file-name (git-file-name name version))
+             (sha256
+              (base32
+               "089z1c778q1fwhzsc88ws8j5gm2hgxknibabn4wpax8rz2bfs3ck"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-parameterized" ,python-parameterized)))

From b9d96ed77343e3f158f7ee1c758270bf4f059a74 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 21 Apr 2020 10:36:29 +0200
Subject: [PATCH 160/215] gnu: python-tortoise-orm: Update to 0.16.7 [security
 fixes].

* gnu/packages/databases.scm (python-tortoise-orm)[source]: Update to 0.16.7.
[propagated-inputs]: Propagate python-ciso8601, which is required in setup.py.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/databases.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 57a5128e9e..23b8f14c54 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2197,24 +2197,24 @@ can autogenerate peewee models using @code{pwiz}, a model generator.")
 (define-public python-tortoise-orm
   (package
     (name "python-tortoise-orm")
-    (version "0.16.3")
+    (version "0.16.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "tortoise-orm" version))
        (sha256
         (base32
-         "01hbvfyxs2qd1mjc96aipwsdxxhydw8ww686r4gsf87bl6f98dvz"))))
+         "0wr7p4v0b16ypm9fcpwpl99kf491m6w3jkd13xcsgq13fy73fbqc"))))
     (build-system python-build-system)
     ;; Disable tests for now. They pull in a lot of dependencies.
     (arguments `(#:tests? #f))
     (native-inputs
-     `(("python-ciso8601" ,python-ciso8601)
-       ("python-asynctest" ,python-asynctest)
+     `(("python-asynctest" ,python-asynctest)
        ("python-nose2" ,python-nose2)))
     (propagated-inputs
      `(("python-aiosqlite" ,python-aiosqlite)
        ("python-pypika" ,python-pypika)
+       ("python-ciso8601" ,python-ciso8601)
        ("python-typing-extensions"
         ,python-typing-extensions)))
     (home-page

From e118837ede3f96bc76c7db22f1fc2cc348099507 Mon Sep 17 00:00:00 2001
From: Marcin Karpezo <sirmacik@wioo.waw.pl>
Date: Wed, 29 Apr 2020 16:49:36 +0200
Subject: [PATCH 161/215] gnu: Add aspell-dict-pl.

* gnu/packages/aspell.scm (aspell-dict-pl): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/aspell.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm
index b11a2dbe6b..689fe64ec1 100644
--- a/gnu/packages/aspell.scm
+++ b/gnu/packages/aspell.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2016, 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
 ;;; Copyright © 2020 Timotej Lazar <timotej.lazar@araneo.si>
+;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -298,6 +299,13 @@ dictionaries, including personal ones.")
                      (base32
                       "0w2k5l5rbqpliripgqwiqixz5ghnjf7i9ggbrc4ly4vy1ia10rmc")))
 
+(define-public aspell-dict-pl
+  (aspell-dictionary "pl" "Polish"
+                     #:version "0.51-0"
+                     #:sha256
+                     (base32
+                      "1a3ccji6k5gys7l3ilr2lh5pzxgzb7ipc5vb737svl6nqgdy8757")))
+
 (define-public aspell-dict-pt-br
   (aspell-dictionary "pt_BR" "Brazilian Portuguese"
                      #:version "20131030-12-0"

From c5c25b39ebe68dd89bf3913d2766df3a8a77dff1 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 29 Apr 2020 16:14:55 -0400
Subject: [PATCH 162/215] gnu: magic-wormhole-mailbox-server: Update to 0.4.1.

* gnu/packages/magic-wormhole.scm (magic-wormhole-mailbox-server): Update to
0.4.1.
---
 gnu/packages/magic-wormhole.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/magic-wormhole.scm b/gnu/packages/magic-wormhole.scm
index bdfc1162b6..85b25bc0e5 100644
--- a/gnu/packages/magic-wormhole.scm
+++ b/gnu/packages/magic-wormhole.scm
@@ -29,14 +29,14 @@
 (define-public magic-wormhole-mailbox-server
   (package
     (name "magic-wormhole-mailbox-server")
-    (version "0.3.1")
+    (version "0.4.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "magic-wormhole-mailbox-server" version))
         (sha256
          (base32
-          "1q6zhbx8fcpk7rchclm7yqcxdsc1x97hki2ji61sa544r5xvxv55"))))
+          "1yw8i8jv5iv1kkz1aqimskw7fpichjn6ww0fq0czbalwj290bw8s"))))
     (build-system python-build-system)
     (arguments
      '(#:phases

From 718c8837f94f792d93b4fe1f8259f02718755f49 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 29 Apr 2020 16:15:19 -0400
Subject: [PATCH 163/215] gnu: magic-wormhole-transit-relay: Update to 0.2.1.

* gnu/packages/magic-wormhole.scm (magic-wormhole-transit-relay): Update to
0.2.1.
---
 gnu/packages/magic-wormhole.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/magic-wormhole.scm b/gnu/packages/magic-wormhole.scm
index 85b25bc0e5..4456f95d99 100644
--- a/gnu/packages/magic-wormhole.scm
+++ b/gnu/packages/magic-wormhole.scm
@@ -68,14 +68,14 @@ connection, or through a transit-relay.")
 (define-public magic-wormhole-transit-relay
   (package
     (name "magic-wormhole-transit-relay")
-    (version "0.1.2")
+    (version "0.2.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "magic-wormhole-transit-relay" version))
         (sha256
          (base32
-          "11w5gdc6am2ph5rns60x0694sx4zrlzxj540jljhn5cmnbx1ngxi"))))
+          "0ppsx2s1ysikns1h053x67z2zmficbn3y3kf52bzzslhd2s02j6b"))))
     (build-system python-build-system)
     (arguments
      `(#:phases

From fb5bb6bd9e451aa672e67573bf2911a5fc7b4d6d Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 29 Apr 2020 16:15:40 -0400
Subject: [PATCH 164/215] gnu: Magic Wormhole: Update to 0.12.0.

* gnu/packages/magic-wormhole.scm (magic-wormhole): Update to 0.12.0.
---
 gnu/packages/magic-wormhole.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/magic-wormhole.scm b/gnu/packages/magic-wormhole.scm
index 4456f95d99..465e6aced6 100644
--- a/gnu/packages/magic-wormhole.scm
+++ b/gnu/packages/magic-wormhole.scm
@@ -107,14 +107,14 @@ together, allowing them to pretend they have a direct connection.")
 (define-public magic-wormhole
   (package
     (name "magic-wormhole")
-    (version "0.11.2")
+    (version "0.12.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "magic-wormhole" version))
         (sha256
          (base32
-          "01fr4bi6kc6fz9n3c4qq892inrc3nf6p2djy65yvm7xkvdxncydf"))))
+          "0q41j99718y7m95zg1vaybnsp31lp6lhyqkbv4yqz5ys6jixh3qv"))))
     (build-system python-build-system)
     (arguments
      '(#:phases

From fd65311cf4ee043290c594900b99ddeb9d8dff3a Mon Sep 17 00:00:00 2001
From: Marcin Karpezo <sirmacik@wioo.waw.pl>
Date: Wed, 29 Apr 2020 14:51:33 +0200
Subject: [PATCH 165/215] gnu: Add sbcl-stumpwm-pass.

* gnu/packages/wm.scm (sbcl-stumpwm-pass): New variable.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
---
 gnu/packages/wm.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 4d1b6b3fd4..9f64f206af 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -34,6 +34,7 @@
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020 Boris A. Dekshteyn <harlequin78@gmail.com>
+;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1730,6 +1731,36 @@ productive, customizable lisp based systems.")
 rendering.")
       (license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
 
+(define-public sbcl-stumpwm-pass
+  (let ((commit "dd5b037923ec7d3cc27c55806bcec5a1b8cf4e91")
+        (revision "1"))
+    (package
+      (name "sbcl-pass")
+      (version (git-version "0.0.1" revision commit)) ;no upstream release
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/stumpwm/stumpwm-contrib.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0ahxdj9f884afpzxczx6mx7l4nwg4kw6afqaq7lwhf7lxcwylldn"))))
+      (inputs
+       `(("stumpwm" ,stumpwm "lib")))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       '(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'chdir
+             (lambda _
+               (chdir "util/pass"))))))
+      (home-page "https://github.com/stumpwm/stumpwm-contrib")
+      (synopsis "Integrate @code{pass} wih StumpWM")
+      (description "This package provides an interface which integrates
+password-store into StumpWM.")
+      (license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
+
 (define-public sbcl-stumpwm-globalwindows
   (let ((commit "dd5b037923ec7d3cc27c55806bcec5a1b8cf4e91")
         (revision "1"))

From 145df67b25dbabc31fba8a152bee639c34f1a44f Mon Sep 17 00:00:00 2001
From: Marcin Karpezo <sirmacik@wioo.waw.pl>
Date: Wed, 29 Apr 2020 15:26:11 +0200
Subject: [PATCH 166/215] doc: cookbook: Rename stumpwm package to current
 state.

* doc/guix-cookbook.texi (StumpWM): Rename STUMPWM package to current state.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
---
 doc/guix-cookbook.texi | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/doc/guix-cookbook.texi b/doc/guix-cookbook.texi
index 82700a48ad..f58d18d47c 100644
--- a/doc/guix-cookbook.texi
+++ b/doc/guix-cookbook.texi
@@ -13,6 +13,7 @@ Copyright @copyright{} 2019 Efraim Flashner@*
 Copyright @copyright{} 2019 Pierre Neidhardt@*
 Copyright @copyright{} 2020 Oleg Pykhalov@*
 Copyright @copyright{} 2020 Matthew Brooks@*
+Copyright @copyright{} 2020 Marcin Karpezo@*
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -1575,7 +1576,7 @@ available for inclusion into the initrd.
 @cindex stumpwm
 
 You could install StumpWM with a Guix system by adding
-@code{stumpwm-checkout} and optionally @code{`(,stumpwm-checkout "lib")}
+@code{stumpwm} and optionally @code{`(,stumpwm "lib")}
 packages to a system configuration file, e.g.@: @file{/etc/config.scm}.
 
 An example configuration can look like this:
@@ -1586,7 +1587,7 @@ An example configuration can look like this:
 
 (operating-system
   ;; …
-  (packages (append (list sbcl stumpwm-checkout `(,stumpwm-checkout "lib"))
+  (packages (append (list sbcl stumpwm `(,stumpwm "lib"))
                     %base-packages)))
 @end lisp
 
@@ -1601,7 +1602,7 @@ module @code{sbcl-stumpwm-ttf-fonts}, adding it to Guix system packages:
 
 (operating-system
   ;; …
-  (packages (append (list sbcl stumpwm-checkout `(,stumpwm-checkout "lib"))
+  (packages (append (list sbcl stumpwm `(,stumpwm "lib"))
                     sbcl-stumpwm-ttf-fonts font-dejavu %base-packages)))
 @end lisp
 

From ad2736717a475fa696b4fe637d722f31ed520a8d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 13:41:38 +0200
Subject: [PATCH 167/215] gnu: python-psutil: Update to 5.7.0.

* gnu/packages/python-xyz.scm (python-psutil): Update to 5.7.0.
---
 gnu/packages/python-xyz.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index decc1ce8a6..6f881161fd 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -412,16 +412,17 @@ data for video and audio files.")
 (define-public python-psutil
   (package
     (name "python-psutil")
-    (version "5.6.5")
+    (version "5.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psutil" version))
        (sha256
-        (base32 "0isil5jxwwd8awz54qk28rpgjg43i5l6yl70g40vxwa4r4m56lfh"))))
+        (base32 "03jykdi3dgf1cdal9bv4fq9zjvzj9l9bs99gi5ar81sdl5nc2pk8"))))
     (build-system python-build-system)
     (arguments
-     ;; FIXME: some tests does not return and times out.
+     ;; FIXME: some tests do not return and time out.  Some tests fail because
+     ;; some processes survive kill().
      '(#:tests? #f))
     (home-page "https://www.github.com/giampaolo/psutil")
     (synopsis "Library for retrieving information on running processes")

From 88f8a7c6100302e66e9a0058ae018042cdd27b62 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 14:12:37 +0200
Subject: [PATCH 168/215] gnu: Add python-voluptuous.

* gnu/packages/python-xyz.scm (python-voluptuous): New variable.
---
 gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6f881161fd..e6088bd6ce 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -19660,3 +19660,24 @@ workspace...")
 dependencies.  It implements the @uref{http://opensoundcontrol.org/spec-1_0,
 Open Sound Control 1.0} specification.")
     (license license:unlicense)))
+
+(define-public python-voluptuous
+  (package
+    (name "python-voluptuous")
+    (version "0.11.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "voluptuous" version))
+        (sha256
+          (base32
+            "0mplkcpb5d8wjf8vk195fys4y6a3wbibiyf708imw33lphfk9g1a"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "https://github.com/alecthomas/voluptuous")
+    (synopsis "Python data validation library")
+    (description
+     "Voluptuous is a Python data validation library.  It is primarily
+intended for validating data coming into Python as JSON, YAML, etc.")
+    (license license:bsd-3)))

From 7e3ddb6904e27b18f364b7c3b161f2927017155c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 14:12:49 +0200
Subject: [PATCH 169/215] gnu: Add python-cmd2.

* gnu/packages/python-xyz.scm (python-cmd2): New variable.
---
 gnu/packages/python-xyz.scm | 46 +++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e6088bd6ce..c37ed2bfa0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -19681,3 +19681,49 @@ Open Sound Control 1.0} specification.")
      "Voluptuous is a Python data validation library.  It is primarily
 intended for validating data coming into Python as JSON, YAML, etc.")
     (license license:bsd-3)))
+
+(define-public python-cmd2
+  (package
+    (name "python-cmd2")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cmd2" version))
+       (sha256
+        (base32
+         "1f18plbc9yyvhn0js3d2bii9yld8zfl775gxsaw9jza5pmlg9ss2"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-attrs" ,python-attrs)
+       ("python-colorama" ,python-colorama)
+       ("python-pyperclip" ,python-pyperclip)
+       ("python-wcwidth" ,python-wcwidth)))
+    (native-inputs
+     `(("python-codecov" ,python-codecov)
+       ("python-coverage" ,python-coverage)
+       ("python-doc8" ,python-doc8)
+       ("python-flake8" ,python-flake8)
+       ("python-invoke" ,python-invoke)
+       ("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-mock" ,python-pytest-mock)
+       ("python-setuptools-scm" ,python-setuptools-scm)
+       ("python-sphinx" ,python-sphinx)
+       ("python-sphinx-autobuild" ,python-sphinx-autobuild)
+       ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)
+       ("python-tox" ,python-tox)
+       ("python-twine" ,python-twine)
+       ("which" ,which)))
+    (home-page "https://github.com/python-cmd2/cmd2")
+    (synopsis "Tool for building interactive command line applications")
+    (description
+     "Cmd2 is a tool for building interactive command line applications in
+Python.  Its goal is to make it quick and easy for developers to build
+feature-rich and user-friendly interactive command line applications.  It
+provides a simple API which is an extension of Python's built-in @code{cmd}
+module.  @code{cmd2} provides a wealth of features on top of @code{cmd} to
+make your life easier and eliminates much of the boilerplate code which would
+be necessary when using @code{cmd}.")
+    (license license:expat)))

From 37130eccd23eccfdc6653c3e73321fea4000d51d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:16:31 +0200
Subject: [PATCH 170/215] gnu: Remove python2-pyflakes-0.8.1.

* gnu/packages/python-xyz.scm (python2-pyflakes-0.8.1): Remove variable.
---
 gnu/packages/python-xyz.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c37ed2bfa0..c6c6bf2c3e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7454,9 +7454,6 @@ complexity of Python source code.")
      ;; XXX Tests not compatible with Python 3.5.
      '(#:tests? #f))))
 
-(define-public python2-pyflakes-0.8.1
-  (package-with-python2 python-pyflakes-0.8.1))
-
 (define-public python-flake8
   (package
     (name "python-flake8")

From a6559240098d8b8ff7f799f57aecf96a53a88401 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:19:25 +0200
Subject: [PATCH 171/215] gnu: Replace python-pyflakes-0.8.1 with
 python-pyflakes-1.2.

* gnu/packages/python-xyz.scm (python-pyflakes-0.8.1): Remove variable.
(python-pyflakes-1.2): New variable.
* gnu/packages/openstack.scm (python-hacking)[propagated-inputs]: Replace
python-pyflakes-0.8.1 with python-pyflakes-1.2.
---
 gnu/packages/openstack.scm  |  2 +-
 gnu/packages/python-xyz.scm | 37 +++++++++++++++++++++----------------
 2 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 8dd8c1907c..6c81454150 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -144,7 +144,7 @@ manner.")
        ("python-mccabe-0.2.1" ,python-mccabe-0.2.1)
        ("python-pbr" ,python-pbr)
        ("python-pep8-1.5.7" ,python-pep8-1.5.7)
-       ("python-pyflakes-0.8.1" ,python-pyflakes-0.8.1)
+       ("python-pyflakes-1.2" ,python-pyflakes-1.2)
        ("python-six" ,python-six)))
     (native-inputs
      `( ;; Tests
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c6c6bf2c3e..80185f49e0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7380,6 +7380,27 @@ PEP 8.")
 (define-public python2-pyflakes
   (package-with-python2 python-pyflakes))
 
+;; Flake8 2.6 requires an older version of pyflakes.
+;; This should be removed ASAP.
+(define-public python-pyflakes-1.2
+  (package (inherit python-pyflakes)
+    (version "1.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyflakes" version))
+       (sha256
+        (base32
+         "17hkw8yd44cr8fz13phy4aih3r5j2p7ild4zlvqdh2c8dmiinjif"))))
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         ;; This one test fails.
+         (replace 'check
+           (lambda _ (invoke "pytest" "-vv" "-k" "not test_f_string"))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))))
+
 (define-public python-mccabe
   (package
     (name "python-mccabe")
@@ -7438,22 +7459,6 @@ complexity of Python source code.")
 (define-public python2-pep8-1.5.7
   (package-with-python2 python-pep8-1.5.7))
 
-;; Flake8 2.4.1 requires an older version of pyflakes.
-;; This should be removed ASAP.
-(define-public python-pyflakes-0.8.1
-  (package (inherit python-pyflakes)
-    (version "0.8.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pyflakes" version))
-       (sha256
-        (base32
-         "0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z"))))
-    (arguments
-     ;; XXX Tests not compatible with Python 3.5.
-     '(#:tests? #f))))
-
 (define-public python-flake8
   (package
     (name "python-flake8")

From 7fea8e076fd2405c0d53d7ee5d7a36936215ffcc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:23:19 +0200
Subject: [PATCH 172/215] gnu: Remove python2-flake8-2.5.

* gnu/packages/python-xyz.scm (python2-flake8-2.5): Remove variable.
(python-flake8-2.5)[properties]: Remove.
---
 gnu/packages/python-xyz.scm | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 80185f49e0..1110360afd 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7519,18 +7519,7 @@ complexity of Python source code.")
                 "1snylqwbmrylbx3r1wpz8ggk98f6bcag4441ag8mm2l7wyn58sij"))))
     (propagated-inputs
      `(("python-pep8" ,python-pep8)
-       ,@(package-propagated-inputs python-flake8)))
-    (properties `((python2-variant . ,(delay python2-flake8-2.5))))))
-
-(define-public python2-flake8-2.5
-  (package
-    (inherit python2-flake8)
-    (version (package-version python-flake8-2.5))
-    (source (origin
-              (inherit (package-source python-flake8-2.5))))
-    (propagated-inputs
-     `(("python2-pep8" ,python2-pep8)
-       ,@(package-propagated-inputs python2-flake8)))))
+       ,@(package-propagated-inputs python-flake8)))))
 
 (define-public python-flake8-polyfill
   (package

From 7b0e0fd5a2f963758d4c9161e9f2844e56289dad Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:24:49 +0200
Subject: [PATCH 173/215] gnu: python-flake8-2.5: Update to 2.6.2.

* gnu/packages/python-xyz.scm (python-flake8-2.5): Update to 2.6.2; rename
it...
(python-flake8-2.6): ...to this.
[arguments]: Add phase "use-later-pycodestyles", and move "check" phase after
"install".
[propagated-inputs]: Explicitly list python-pycodestyle, python-entrypoints,
python-pyflakes-1.2, and python-mccabe.
---
 gnu/packages/python-xyz.scm | 29 ++++++++++++++++++++++++-----
 1 file changed, 24 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1110360afd..0f4351d152 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7506,20 +7506,39 @@ complexity of Python source code.")
          ("python2-typing" ,python2-typing)
           ,@(package-propagated-inputs base))))))
 
-;; python-hacking requires flake8 <2.6.0.
-(define-public python-flake8-2.5
+;; python-hacking requires flake8 <2.7.0.
+(define-public python-flake8-2.6
   (package
     (inherit python-flake8)
-    (version "2.5.5")
+    (version "2.6.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "flake8" version))
               (sha256
                (base32
-                "1snylqwbmrylbx3r1wpz8ggk98f6bcag4441ag8mm2l7wyn58sij"))))
+                "0y57hzal0j84dh9i1g1g6dc4aywvrnhy2fjmmbglpv5ajihxh713"))))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-later-pycodestyles
+           (lambda __
+             (substitute* '("flake8.egg-info/requires.txt"
+                            "setup.py")
+               (("pycodestyle >= 2.0, < 2.1")
+                "pycodestyle >= 2.0"))
+             #t))
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-v")
+             #t)))))
     (propagated-inputs
      `(("python-pep8" ,python-pep8)
-       ,@(package-propagated-inputs python-flake8)))))
+       ("python-pycodestyle" ,python-pycodestyle)
+       ("python-entrypoints" ,python-entrypoints)
+       ("python-pyflakes" ,python-pyflakes-1.2)
+       ("python-mccabe" ,python-mccabe)))))
 
 (define-public python-flake8-polyfill
   (package

From 851a3a779a7173807683e0a3c4e118ef4d8eb0b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:28:07 +0200
Subject: [PATCH 174/215] gnu: python-hacking: Update to 1.1.0.

* gnu/packages/openstack.scm (python-hacking): Update to 1.1.0.
[arguments]: Add "delete-broken-test" phase.
[propagated-inputs]: Replace python-flake8-2.5 with python-flake8-2.6.
---
 gnu/packages/openstack.scm | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 6c81454150..a1e21d8872 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016, 2017, 2019 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -130,17 +131,27 @@ manner.")
 (define-public python-hacking
   (package
     (name "python-hacking")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "hacking" version))
        (sha256
         (base32
-         "0s9l99s64jsyvm28fa4hzllbdi21sb7jn4gzdf1pd5ckvy7p4b0k"))))
+         "1vlgh81v4vsw3q3cf7qggsp043vq16knp203lrll82h7l7rhd8r3"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'delete-broken-test
+           (lambda _
+             ;; TODO: Just one test fails:
+             ;; hacking.tests.test_doctest.HackingTestCase.test_pycodestyle
+             ;;   (H403-hacking_docstring_multiline_end-line-5)
+             (delete-file "hacking/tests/test_doctest.py")
+             #t)))))
     (propagated-inputs
-     `(("python-flake8" ,python-flake8-2.5)
+     `(("python-flake8" ,python-flake8-2.6)
        ("python-mccabe-0.2.1" ,python-mccabe-0.2.1)
        ("python-pbr" ,python-pbr)
        ("python-pep8-1.5.7" ,python-pep8-1.5.7)

From 5bc78570b28806b12485dc9863cd7d2c06d5883a Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 29 Apr 2020 22:12:10 -0400
Subject: [PATCH 175/215] gnu: linux-libre@4.19: Update to 4.19.119.

* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.119.
(linux-libre-4.19-pristine-source): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 12cb39ff9b..b5400d8a83 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -385,10 +385,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))
 
-(define-public linux-libre-4.19-version "4.19.118")
+(define-public linux-libre-4.19-version "4.19.119")
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "15lcq3xky59v88vb8vvnmgcsmm1fadz0m4jyrii6rynsz5jr6x49")))
+        (hash (base32 "1klvdzz8sndg2zsr1anfy9p5fc1aapjqvc249myrbndyf55bk91b")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))

From 09b87e503d3af1db309fdb3ea5617986013751f3 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 29 Apr 2020 22:13:15 -0400
Subject: [PATCH 176/215] gnu: linux-libre@5.6: Update to 5.6.8.

* gnu/packages/linux.scm (linux-libre-5.6-version): Update to 5.6.8.
(linux-libre-5.6-pristine-source): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b5400d8a83..dd16cdc17d 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -369,10 +369,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
     (sha256 hash)))
 
 
-(define-public linux-libre-5.6-version "5.6.7")
+(define-public linux-libre-5.6-version "5.6.8")
 (define-public linux-libre-5.6-pristine-source
   (let ((version linux-libre-5.6-version)
-        (hash (base32 "1jljcva3gxg1yc2kw3jjgmhzzdm16nylzxl63zbndjza547l5813")))
+        (hash (base32 "1pw2q9509jzp84b6qasaais2ws25v2wrjh072q0x3j520zzl5q8r")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.6)))

From 89ea0415b33bc3382ead3755fc2fc27c11920878 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 29 Apr 2020 22:13:56 -0400
Subject: [PATCH 177/215] gnu: linux-libre: Update to 5.4.36.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.36.
(linux-libre-5.4-pristine-source): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index dd16cdc17d..70d2163fee 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -377,10 +377,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.6)))
 
-(define-public linux-libre-5.4-version "5.4.35")
+(define-public linux-libre-5.4-version "5.4.36")
 (define-public linux-libre-5.4-pristine-source
   (let ((version linux-libre-5.4-version)
-        (hash (base32 "1m06k19pbb3wz8z2dgf03jvzbbdh6q8jwwdz509s902a53vxasz1")))
+        (hash (base32 "13avfvimjyg4lhj9micgib9bb5qpx11cja5liypid0rf2acfmymr")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))

From f03e5ca59f2f099693def2c8e6ff409e5b4ed40a Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Thu, 30 Apr 2020 10:09:15 +0200
Subject: [PATCH 178/215] gnu: gnuradio: Fix runtime python environment for
 plugins.

* gnu/packages/radio.scm (gnuradio)[native-search-paths]: Add PYTHONPATH.
  [native-inputs]: Move python ...
  [inputs]: ... here.
---
 gnu/packages/radio.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 935880780f..30567431bf 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -26,6 +26,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix utils)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
@@ -266,7 +267,6 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).")
        ("ghostscript" ,ghostscript)
        ("orc" ,orc)
        ("pkg-config" ,pkg-config)
-       ("python" ,python)
        ("python-cheetah" ,python-cheetah)
        ("python-mako" ,python-mako)
        ("python-pyzmq" ,python-pyzmq)
@@ -293,6 +293,7 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).")
        ("log4cpp" ,log4cpp)
        ("pango" ,pango)
        ("portaudio" ,portaudio)
+       ("python" ,python)
        ("python-click" ,python-click)
        ("python-click-plugins" ,python-click-plugins)
        ("python-lxml" ,python-lxml)
@@ -364,9 +365,16 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).")
                  `("GI_TYPELIB_PATH" ":" prefix ,(filter identity paths))))
              #t)))))
     (native-search-paths
+     ;; Variables required to find third-party plugins at runtime.
      (list (search-path-specification
             (variable "GRC_BLOCKS_PATH")
-            (files '("/share/gnuradio/grc/blocks")))))
+            (files '("share/gnuradio/grc/blocks")))
+           (search-path-specification
+            (variable "PYTHONPATH")
+            (files (list (string-append "lib/python"
+                                        (version-major+minor
+                                         (package-version python))
+                                        "/site-packages"))))))
     (synopsis "Toolkit for software-defined radios")
     (description
      "GNU Radio is a development toolkit that provides signal processing blocks

From 1b73fbdf5e3be0d1a90432b63c5eea2cde8c456d Mon Sep 17 00:00:00 2001
From: Eric Brown <ecbrown@ericcbrown.com>
Date: Wed, 22 Apr 2020 06:04:59 -0500
Subject: [PATCH 179/215] gnu: Add r-rserve.

* gnu/packages/cran.scm (r-rserve): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index baf1e0c18a..18829537e8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21633,3 +21633,40 @@ infinite-precision rational arithmetic.")
 Archive Toolkit.  Rxnat uses the XNAT REST API to perform data queries and
 download images.")
     (license license:gpl2)))
+
+(define-public r-rserve
+  (package
+    (name "r-rserve")
+    (version "1.8-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-checkmate" ,r-checkmate)
+       ("r-mime" ,r-mime)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-knitr" ,r-knitr)
+       ("r-r6" ,r-r6)
+       ("r-rcpp" ,r-rcpp)
+       ("r-uuid" ,r-uuid)))
+    (inputs
+     `(("openssl" ,openssl)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/s-u/Rserve")
+    (synopsis
+     "Server providing access to R from many languages and systems")
+    (description
+     "Rserve acts as a socket server (TCP/IP or local sockets) which allows
+binary requests to be sent to R.  Every connection has a separate workspace
+and working directory.  Client-side implementations are available for popular
+languages such as C/C++ and Java, allowing any application to use facilities
+of R without the need of linking to R code.  Rserve supports remote
+connection, user authentication and file transfer.  A simple R client is
+included in this package as well.")
+    (license license:gpl2)))

From ed33317893812715bf37005fb0ba5192b651b14f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:00:40 +0200
Subject: [PATCH 180/215] gnu: Add python2-weave.

* gnu/packages/python-science.scm (python2-weave): New variable.
---
 gnu/packages/python-science.scm | 35 ++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 530a2478f3..2f7516b9f6 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -162,6 +162,39 @@ routines such as routines for numerical integration and optimization.")
         (base32
          "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
 
+(define-public python2-weave
+  (package
+    (name "python2-weave")
+    (version "0.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "weave" version))
+       (sha256
+        (base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (invoke "nosetests" "-v"
+                     "--exclude"
+                     "test_(user|incorrect_ownership|char_fail|obj_fail)"))))))
+    (propagated-inputs
+     `(("python-numpy" ,python2-numpy)))
+    (native-inputs
+     `(("python-nose" ,python2-nose)))
+    (home-page "https://www.scipy.org/")
+    (synopsis "Tools for including C/C++ code within Python code")
+    (description "Weave is the stand-alone version of the obsolete Scipy
+submodule @code{scipy.weave}.  It is Python 2.x only, and is provided for
+users that need new versions of Scipy but have existing code that still
+depends on @code{scipy.weave}.  For new code, users are recommended to use
+Cython.")
+    (license license:bsd-3)))
+
 (define-public python-scikit-image
   (package
     (name "python-scikit-image")

From 4a148c6da37b55b22842ddbf0ec0ba56132c44ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:00:50 +0200
Subject: [PATCH 181/215] gnu: python2-warpedlmm: Fix build.

* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add
python2-weave.
[arguments]: Disable tests and add "use-weave" phase.
---
 gnu/packages/bioinformatics.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f90a0bf90c..740ed66972 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4942,14 +4942,24 @@ files and writing bioinformatics applications.")
          "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2))  ; requires Python 2.7
+     `(#:python ,python-2  ; requires Python 2.7
+       #:tests? #f ; test data are not included
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-weave
+           (lambda _
+             (substitute* "warpedlmm/util/linalg.py"
+               (("from scipy import linalg, weave")
+                "from scipy import linalg\nimport weave"))
+             #t)))))
     (propagated-inputs
      `(("python-scipy" ,python2-scipy)
        ("python-numpy" ,python2-numpy)
        ("python-matplotlib" ,python2-matplotlib)
        ("python-fastlmm" ,python2-fastlmm)
        ("python-pandas" ,python2-pandas)
-       ("python-pysnptools" ,python2-pysnptools)))
+       ("python-pysnptools" ,python2-pysnptools)
+       ("python-weave" ,python2-weave)))
     (native-inputs
      `(("python-mock" ,python2-mock)
        ("python-nose" ,python2-nose)

From 7395047017a6c210a47e9d0144fd3ebabf156da1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:03:52 +0200
Subject: [PATCH 182/215] gnu: Add python-tornado-6.

* gnu/packages/python-web.scm (python-tornado-6): New variable.
---
 gnu/packages/python-web.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 0dba566a77..76a2c57701 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -869,6 +869,37 @@ connection to each user.")
     (license license:asl2.0)
     (properties `((python2-variant . ,(delay python2-tornado))))))
 
+(define-public python-tornado-6
+  (package
+    (name "python-tornado")
+    (version "6.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "tornado" version))
+       (sha256
+        (base32
+         "1p5n7sw4580pkybywg93p8ddqdj9lhhy72rzswfa801vlidx9qhg"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (invoke "python" "-m" "tornado.test.runtests")
+             #t)))))
+    (native-inputs
+     `(("python-certifi" ,python-certifi)))
+    (home-page "https://www.tornadoweb.org/")
+    (synopsis "Python web framework and asynchronous networking library")
+    (description
+     "Tornado is a Python web framework and asynchronous networking library,
+originally developed at FriendFeed.  By using non-blocking network I/O,
+Tornado can scale to tens of thousands of open connections, making it ideal
+for long polling, WebSockets, and other applications that require a long-lived
+connection to each user.")
+    (license license:asl2.0)))
+
 (define-public python2-tornado
   (let ((tornado (package-with-python2 (strip-python2-variant python-tornado))))
     (package (inherit tornado)

From cb44af24c8308dd7e17e991ed6ee803f3cb8a1c2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:03:59 +0200
Subject: [PATCH 183/215] gnu: kaldi-gstreamer-server: Use Tornado 6.

* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[inputs]: Replace
python-tornado with python-tornado-6.
---
 gnu/packages/machine-learning.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 425961ee14..df2943167d 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1326,7 +1326,7 @@ exec ~a ~a/~a \"$@\"~%"
          ("python" ,python-wrapper)
          ("python-pygobject" ,python-pygobject)
          ("python-pyyaml" ,python-pyyaml)
-         ("python-tornado" ,python-tornado)))
+         ("python-tornado" ,python-tornado-6)))
       (home-page "https://github.com/alumae/kaldi-gstreamer-server")
       (synopsis "Real-time full-duplex speech recognition server")
       (description "This is a real-time full-duplex speech recognition server,

From 46d07f8472f09813be287fa5a10afb50c959dcb1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:04:55 +0200
Subject: [PATCH 184/215] gnu: kaldi-gstreamer-server: Fix bug.

* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[arguments]: Patch
master_server.py before build.
---
 gnu/packages/machine-learning.scm | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index df2943167d..8c817d3e3b 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1269,6 +1269,10 @@ automatically.")
                ;; are reproducible.
                (setenv "PYTHONHASHSEED" "0")
                (with-directory-excursion "kaldigstserver"
+                 ;; See https://github.com/alumae/kaldi-gstreamer-server/issues/232
+                 (substitute* "master_server.py"
+                   (("\\.replace\\('\\\\.*") ")"))
+
                  ;; This is a Python 2 file
                  (delete-file "decoder_test.py")
                  (delete-file "test-buffer.py")

From cf1ae793753e9da0d774f4a5495648f15d400b49 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:06:01 +0200
Subject: [PATCH 185/215] gnu: python2-pysnptools: Update to 0.4.11.

* gnu/packages/python-xyz.scm (python2-pysnptools): Update to 0.4.11;
implement in terms of...
(python-pysnptools): ...this new variable.
[propagated-inputs]: Add python-dill, python-h5py, and python-psutil.
---
 gnu/packages/python-xyz.scm | 34 ++++++++++++++++++++++++----------
 1 file changed, 24 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0f4351d152..74280befea 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4876,27 +4876,38 @@ toolkits.")
 three-way Venn diagrams in @code{matplotlib}.")
     (license license:expat)))
 
-(define-public python2-pysnptools
+(define-public python-pysnptools
   (package
-    (name "python2-pysnptools")
-    (version "0.3.13")
+    (name "python-pysnptools")
+    (version "0.4.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pysnptools" version))
        (sha256
         (base32
-         "0lnis5xsl7bi0hz4f7gbicahzi5zlxkc21nk3g374xv8fb5hb3qm"))))
+         "0gxr0bjix307wvk0qh7vkafbxbzfpdmq0wlswpxyyaymy0fwcypv"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2 ; only Python 2.7 is supported
-       #:tests? #f))      ; test files (e.g. examples/toydata.bim) not included
+     `(#:tests? #f ; no test data are included
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (if tests?
+                 (begin
+                   (add-installed-pythonpath inputs outputs)
+                   (invoke "python3" "pysnptools/test.py"))
+                 #t))))))
     (propagated-inputs
-     `(("python2-numpy" ,python2-numpy)
-       ("python2-scipy" ,python2-scipy)
-       ("python2-pandas" ,python2-pandas)))
+     `(("python-dill" ,python-dill)
+       ("python-h5py" ,python-h5py)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-psutil" ,python-psutil)
+       ("python-scipy" ,python-scipy)))
     (native-inputs
-     `(("python2-cython" ,python2-cython)))
+     `(("python-cython" ,python-cython)))
     (home-page "http://microsoftgenomics.github.io/PySnpTools/")
     (synopsis "Library for reading and manipulating genetic data")
     (description
@@ -4906,6 +4917,9 @@ those files.  It can also efficiently manipulate ranges of integers using set
 operators such as union, intersection, and difference.")
     (license license:asl2.0)))
 
+(define-public python2-pysnptools
+  (package-with-python2 python-pysnptools))
+
 (define-public python-socksipy-branch
   (package
     (name "python-socksipy-branch")

From 61fc72d3ac949d0c65690ee25bb1daf01f39bb42 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Fri, 10 Apr 2020 14:58:47 +0200
Subject: [PATCH 186/215] gnu: Add zbackup.

* gnu/packages/backup.scm (zbackup): New variable.
---
 gnu/packages/backup.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index d80359f8f1..23860ec821 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -976,6 +977,42 @@ precious backup space.
 @end itemize")
     (license license:bsd-2)))
 
+(define-public zbackup
+  (package
+    (name "zbackup")
+    (version "1.4.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/zbackup/zbackup.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "14l1kyxg7pccpax3d6qcpmdycb70kn3fxp1a59w64hqy2493hngl"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f))                    ;no test
+    (inputs
+     `(("lzo" ,lzo)
+       ("libressl" ,libressl)
+       ("protobuf" ,protobuf)
+       ("xz" ,xz)
+       ("zlib" ,zlib)))
+    (home-page "http://zbackup.org")
+    (synopsis "Versatile deduplicating backup tool")
+    (description
+     "ZBackup is a globally-deduplicating backup tool, based on the
+ideas found in Rsync.  Feed a large @file{.tar} into it, and it will
+store duplicate regions of it only once, then compress and optionally
+encrypt the result.  Feed another @file{.tar} file, and it will also
+re-use any data found in any previous backups.  This way only new
+changes are stored, and as long as the files are not very different,
+the amount of storage required is very low.  Any of the backup files
+stored previously can be read back in full at any time.  The program
+is format-agnostic, so you can feed virtually any files to it.")
+    (license license:gpl2+)))
+
 (define-public burp
   (package
     (name "burp")

From 4ac399603616b1fa5e2639ba2c587219f366ef6e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 14:41:53 +0200
Subject: [PATCH 187/215] gnu: Add missing module import.

This is a follow-up to commit 61fc72d3ac949d0c65690ee25bb1daf01f39bb42.

* gnu/packages/backup.scm: Add missing import of (guix build-system cmake).
---
 gnu/packages/backup.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 23860ec821..692795ce11 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -11,7 +11,7 @@
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
@@ -37,6 +37,7 @@
   #:use-module (guix git-download)
   #:use-module (guix download)
   #:use-module (guix utils)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system python)

From e17423186323829dff925d2f0fdbd8f494206a6e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 14:44:45 +0200
Subject: [PATCH 188/215] gnu: Add one more missing module import.

This is a follow-up to commit 61fc72d3ac949d0c65690ee25bb1daf01f39bb42.

* gnu/packages/backup.scm: Add missing import of (gnu packages protobuf).
---
 gnu/packages/backup.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 692795ce11..00986a328d 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -65,6 +65,7 @@
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)

From eca648b65b51d1154363dd63dd602ebb9797d478 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 30 Apr 2020 15:30:16 +0200
Subject: [PATCH 189/215] gnu: Add miniasm.

* gnu/packages/bioinformatics.scm (miniasm): New variable.
---
 gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 740ed66972..65b44568e0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13312,6 +13312,42 @@ cases include:
 @end enumerate\n")
     (license license:expat)))
 
+(define-public miniasm
+  (package
+   (name "miniasm")
+   (version "0.3")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://github.com/lh3/miniasm/archive/v"
+                  version ".tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
+            (sha256
+               (base32
+                "0g89pa98dvh34idv7w1zv12bsbyr3a11c4qb1cdcz68gyda88s4v"))))
+   (build-system gnu-build-system)
+   (inputs
+    `(("zlib" ,zlib)))
+   (arguments
+    `(#:tests? #f ; There are no tests.
+      #:phases
+      (modify-phases %standard-phases
+        (delete 'configure)
+        (replace 'install
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+              (install-file "miniasm" bin)
+              (install-file "minidot" bin)))))))
+   (home-page "https://github.com/lh3/miniasm")
+   (synopsis "Ultrafast de novo assembly for long noisy reads")
+   (description "Miniasm is a very fast OLC-based de novo assembler for noisy
+long reads.  It takes all-vs-all read self-mappings (typically by minimap) as
+input and outputs an assembly graph in the GFA format.  Different from
+mainstream assemblers, miniasm does not have a consensus step.  It simply
+concatenates pieces of read sequences to generate the final unitig sequences.
+Thus the per-base error rate is similar to the raw input reads.")
+   (license license:expat)))
+
 (define-public r-circus
   (package
     (name "r-circus")

From 0590673090d5fd76074977451a7f7e800e1698c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:25:32 +0200
Subject: [PATCH 190/215] gnu: r-pkgbuild: Update to 1.0.7.

* gnu/packages/cran.scm (r-pkgbuild): Update to 1.0.7.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 18829537e8..94bb1aa4bc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1771,13 +1771,13 @@ processes.  Most of its code is based on the @code{psutil} Python package.")
 (define-public r-pkgbuild
   (package
     (name "r-pkgbuild")
-    (version "1.0.6")
+    (version "1.0.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgbuild" version))
        (sha256
-        (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
+        (base32 "0wd9678yp6yi73n92f58wi9jc19gdq5cmbj65l6pifh2haikifr9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)

From 0ec790f82d0afe1baab5d24a0c94fbd77dc006ab Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:25:45 +0200
Subject: [PATCH 191/215] gnu: r-proxy: Update to 0.4-24.

* gnu/packages/cran.scm (r-proxy): Update to 0.4-24.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 94bb1aa4bc..f581cf462b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2272,14 +2272,14 @@ plot networks.")
 (define-public r-proxy
   (package
     (name "r-proxy")
-    (version "0.4-23")
+    (version "0.4-24")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "proxy" version))
        (sha256
         (base32
-         "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
+         "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/proxy")
     (synopsis "Distance and similarity measures")

From 78b686824d8b5605a6203d0da760288f601b8f37 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:25:50 +0200
Subject: [PATCH 192/215] gnu: r-rootsolve: Update to 1.8.2.1.

* gnu/packages/cran.scm (r-rootsolve): Update to 1.8.2.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f581cf462b..ddab6c9830 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7084,14 +7084,14 @@ bootstrap.  Confidence intervals can be computed for (p)AUC or ROC curves.")
 (define-public r-rootsolve
   (package
     (name "r-rootsolve")
-    (version "1.8.2")
+    (version "1.8.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rootSolve" version))
        (sha256
         (base32
-         "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
+         "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
     (properties `((upstream-name . "rootSolve")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))

From b5ea7affcfd6bfaa7a9f62862f5379f6f1bbda0e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:25:57 +0200
Subject: [PATCH 193/215] gnu: r-usethis: Update to 1.6.1.

* gnu/packages/cran.scm (r-usethis): Update to 1.6.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ddab6c9830..99d1c416d1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8920,14 +8920,14 @@ terminals that do not support Unicode.")
 (define-public r-usethis
   (package
     (name "r-usethis")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "usethis" version))
        (sha256
         (base32
-         "12iyimqyza752anj29wpfisl8nz5r25kfcqbssybg24nb4wyy146"))))
+         "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)

From 1514fa85e49f3a31a75e7174a34678cb799efb8d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:03 +0200
Subject: [PATCH 194/215] gnu: r-arm: Update to 1.11-1.

* gnu/packages/cran.scm (r-arm): Update to 1.11-1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 99d1c416d1..304cddca83 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9655,14 +9655,14 @@ features (e.g. local modes).")
 (define-public r-arm
   (package
     (name "r-arm")
-    (version "1.10-1")
+    (version "1.11-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "arm" version))
        (sha256
         (base32
-         "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
+         "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-abind" ,r-abind)

From 7d1e02c872fe5dd6dc3180dc50b0bd8288f033b0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:07 +0200
Subject: [PATCH 195/215] gnu: r-dalex: Update to 1.2.1.

* gnu/packages/cran.scm (r-dalex): Update to 1.2.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 304cddca83..a0ee26e8b5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15435,14 +15435,14 @@ classification and regression models.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "0mfcci54622gnk8al9fl2jhs9i2vfly7lam04y5rdacbyiam49j6"))))
+         "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs

From 8dfa9ab05a4fe4bde615d569486396a1c0d3a8fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:13 +0200
Subject: [PATCH 196/215] gnu: r-ggfortify: Update to 0.4.10.

* gnu/packages/cran.scm (r-ggfortify): Update to 0.4.10.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a0ee26e8b5..55ffb2787a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15510,14 +15510,14 @@ includes data sets from oceanography.")
 (define-public r-ggfortify
   (package
     (name "r-ggfortify")
-    (version "0.4.9")
+    (version "0.4.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggfortify" version))
        (sha256
         (base32
-         "1p6knrbyaynaqwd939w09hpf1zz1gn95cb46sfgppl8l98krb2h5"))))
+         "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)

From aa180e9e031a001228c74c34fe6516e75bcb719f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:18 +0200
Subject: [PATCH 197/215] gnu: r-systemfonts: Update to 0.2.1.

* gnu/packages/cran.scm (r-systemfonts): Update to 0.2.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 55ffb2787a..1eddb459fe 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16026,14 +16026,14 @@ both R code and compiled C/C++/FORTRAN code.")
 (define-public r-systemfonts
   (package
     (name "r-systemfonts")
-    (version "0.2.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "systemfonts" version))
        (sha256
         (base32
-         "1aba07djvxqdmnsdbwvzcsbm2fddnhrssa54xyrlviiwsv2c1qsd"))))
+         "0dna00xai0pw76b4830yy4r5j1hq7f7kla67v0iz39cjm4rq4ygq"))))
     (properties `((upstream-name . "systemfonts")))
     (build-system r-build-system)
     (inputs

From d7a29bd586bf4d8f7af926ef9287f4e88890ff2e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:24 +0200
Subject: [PATCH 198/215] gnu: r-graphlayouts: Update to 0.7.0.

* gnu/packages/cran.scm (r-graphlayouts): Update to 0.7.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1eddb459fe..92902d0a73 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16055,14 +16055,14 @@ be used further by e.g. graphic devices.")
 (define-public r-graphlayouts
   (package
     (name "r-graphlayouts")
-    (version "0.6.0")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "graphlayouts" version))
        (sha256
         (base32
-         "1la016m37kp79zk8p1yx9kaha8y6d4w52w39h0mzv1mfsi6d75w0"))))
+         "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
     (properties `((upstream-name . "graphlayouts")))
     (build-system r-build-system)
     (propagated-inputs

From 2a749c859633c314a5b29f75b1d96836cda2fa2f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:30 +0200
Subject: [PATCH 199/215] gnu: r-univoutl: Update to 0.2.

* gnu/packages/cran.scm (r-univoutl): Update to 0.2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 92902d0a73..6d1cc8dbfe 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18795,14 +18795,14 @@ functions.")
 (define-public r-univoutl
   (package
     (name "r-univoutl")
-    (version "0.1-5")
+    (version "0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "univOutl" version))
        (sha256
         (base32
-         "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
+         "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
     (properties `((upstream-name . "univOutl")))
     (build-system r-build-system)
     (propagated-inputs

From c54b41093dd02254517df5b12cd059ab4ebad510 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:35 +0200
Subject: [PATCH 200/215] gnu: r-kutils: Update to 1.70.

* gnu/packages/cran.scm (r-kutils): Update to 1.70.
[propagated-inputs]: Remove r-lavaan.
---
 gnu/packages/cran.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6d1cc8dbfe..965ab2949d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20219,19 +20219,18 @@ estimate parameters given observed data.")
 (define-public r-kutils
   (package
     (name "r-kutils")
-    (version "1.69")
+    (version "1.70")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "kutils" version))
        (sha256
         (base32
-         "12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8"))))
+         "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
     (properties `((upstream-name . "kutils")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreign" ,r-foreign)
-       ("r-lavaan" ,r-lavaan)
        ("r-openxlsx" ,r-openxlsx)
        ("r-plyr" ,r-plyr)
        ("r-runit" ,r-runit)

From 1b6434a324f7ad8fca4d63107b28fa95de6017a4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:52 +0200
Subject: [PATCH 201/215] gnu: r-boot: Update to 1.3-25.

* gnu/packages/statistics.scm (r-boot): Update to 1.3-25.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6bf952734c..a599e2f432 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -407,14 +407,14 @@ available, greatly increasing its breadth and scope.")
 (define-public r-boot
   (package
     (name "r-boot")
-    (version "1.3-24")
+    (version "1.3-25")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "boot" version))
        (sha256
         (base32
-         "0yv0l55kjmlfdx1xhgyjdi0bskxhfal74wr5jxaib1qj99nmkm49"))))
+         "1gpvi1h3nqhnnsfy96rlhakdpj84iqqsxr29rr3261sknky3aj26"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/boot")
     (synopsis "Bootstrap functions for R")

From b2c95239e0d7ebb61b3bf5b056556517308ef99b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:01 +0200
Subject: [PATCH 202/215] gnu: r-mass: Update to 7.3-51.6.

* gnu/packages/statistics.scm (r-mass): Update to 7.3-51.6.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index a599e2f432..d8be4fbade 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -428,14 +428,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-51.5")
+    (version "7.3-51.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "1k0m7pa4gb5apzrrkb5kx5d7bmkm2pl5g15vwb6j067hrqahck26"))))
+         "1viyxy22qp8abzzzlbck55b0i81rrdygim1dq2pm52s2v13mq0z2"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")

From 175ec5eff4cdb92c01213de45c600eb5f2fd1742 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:09 +0200
Subject: [PATCH 203/215] gnu: r-class: Update to 7.3-17.

* gnu/packages/statistics.scm (r-class): Update to 7.3-17.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d8be4fbade..059747d031 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -449,14 +449,14 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
 (define-public r-class
   (package
     (name "r-class")
-    (version "7.3-16")
+    (version "7.3-17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "class" version))
        (sha256
         (base32
-         "1jpdgj0lsi60q0mqbhfw809w8d66whix27y6wpdzll6775g3j3ll"))))
+         "04qk8qia0qr8893fizmkbd5hsqn6m8383c0cyn9xnmkmvyv8a7xy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)))

From 1cf9a5cd759bed08b65d40e9cbdbe406c6565430 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:15 +0200
Subject: [PATCH 204/215] gnu: r-foreign: Update to 0.8-79.

* gnu/packages/statistics.scm (r-foreign): Update to 0.8-79.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 059747d031..e749afd4b3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -512,14 +512,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-78")
+    (version "0.8-79")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "01anirfbfa3ip5pyqv72cg4x7p0jsppmbvxrllw7bm28fl1hgiyq"))))
+         "1d5rk4k3khjrir1b4ciridd6vdpcgzi35r7p7ra4ky7vbaabcdmg"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")

From 9c313889f10b8f877fbf12a743a940e825c27ffe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:19 +0200
Subject: [PATCH 205/215] gnu: r-kernsmooth: Update to 2.23-17.

* gnu/packages/statistics.scm (r-kernsmooth): Update to 2.23-17.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e749afd4b3..8d8e2dacbb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -532,14 +532,14 @@ for reading and writing some dBase files.")
 (define-public r-kernsmooth
   (package
     (name "r-kernsmooth")
-    (version "2.23-16")
+    (version "2.23-17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "KernSmooth" version))
        (sha256
         (base32
-         "1acrkbdn3a74y4dndkcdl1njnpfqz7gk3bsz03g8lfj8l7z53hmq"))))
+         "11g6b0q67vasxag6v9m4px33qqxpmnx47c73yv1dninv2pz76g9b"))))
     (properties `((upstream-name . "KernSmooth")))
     (build-system r-build-system)
     (native-inputs

From aad9233c1dded6618c10228e8c21fa6ca550b4b9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:24 +0200
Subject: [PATCH 206/215] gnu: r-nnet: Update to 7.3-14.

* gnu/packages/statistics.scm (r-nnet): Update to 7.3-14.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8d8e2dacbb..15098331e0 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -643,14 +643,14 @@ distributions beyond the exponential family.")
 (define-public r-nnet
   (package
     (name "r-nnet")
-    (version "7.3-13")
+    (version "7.3-14")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nnet" version))
        (sha256
         (base32
-         "1z0rj5cm4ycw1y0gd5wwwg8c2298v90iybgqdqh17967jbi2125f"))))
+         "1bzl62p5awva5kxcncs6lrdrkqp9ljd993zia731ckfpcjbrw6sx"))))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
     (synopsis "Feed-forward neural networks and multinomial log-linear models")

From 599f2b50dee740af8cbc37f59726ba1ecf14b0ec Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:30 +0200
Subject: [PATCH 207/215] gnu: r-spatial: Update to 7.3-12.

* gnu/packages/statistics.scm (r-spatial): Update to 7.3-12.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 15098331e0..030701a22f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -681,14 +681,14 @@ classification, regression and survival trees.")
 (define-public r-spatial
   (package
     (name "r-spatial")
-    (version "7.3-11")
+    (version "7.3-12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatial" version))
        (sha256
         (base32
-         "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
+         "0qrdhzd5r78iwi46nk8jr56dzz5l5imkflxjw64d0ys0wyg06fbn"))))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
     (synopsis "Functions for kriging and point pattern analysis")

From 0ffd9701f583a05db92e7cc883a20d1c4b3a1c17 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:40 +0200
Subject: [PATCH 208/215] gnu: r-rcpparmadillo: Update to 0.9.870.2.0.

* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.870.2.0.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 030701a22f..18eb38ff29 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2588,13 +2588,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.860.2.0")
+    (version "0.9.870.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1rg9ak0zbv8d9cyj10jq52nrcbk1pvfz28kbkhpx79mpjhrl7pb5"))))
+                "1r7iajxvbyvslsy16rqacc95azmjciw9lvcq31xl97fl09kmsq5v"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (propagated-inputs

From 24599740e7e0910fdc2b859d2e0eff0411abbc3a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:45 +0200
Subject: [PATCH 209/215] gnu: r-vgam: Update to 1.1-3.

* gnu/packages/statistics.scm (r-vgam): Update to 1.1-3.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
---
 gnu/packages/statistics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 18eb38ff29..00b648a54c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4957,16 +4957,16 @@ groupings.")
 (define-public r-vgam
   (package
     (name "r-vgam")
-    (version "1.1-2")
+    (version "1.1-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "VGAM" version))
        (sha256
-        (base32 "0kyan3a4ys2xbg9kf167cyf1gk7g963id62cjm2ij4i7y4wi61zq"))))
+        (base32 "1hwlrdx3nhdp83pvy1h23i16vbbhi4kizdhr58c8nvg7kqdzb7qc"))))
     (properties `((upstream-name . "VGAM")))
     (build-system r-build-system)
-    (inputs
+    (native-inputs
      `(("gfortran" ,gfortran)))
     (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
     (synopsis "Vector generalized linear and additive models")

From 192177b04974f456a081e7cb9177e7d9147f822c Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Thu, 30 Apr 2020 16:56:44 +0200
Subject: [PATCH 210/215] gnu: sbcl-osicat: Fix library path.

* gnu/packages/lisp-xyz.scm (sbcl-osicat)[arguments]: Replace 'cleanup phase
  to preserve the location of libosicat.so so that it can be found when
  loading the system.
---
 gnu/packages/lisp-xyz.scm | 24 +++++++++++-------------
 1 file changed, 11 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index c2029d940e..b032346a30 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -11533,21 +11533,19 @@ MOP easier to use.")
       (arguments
        `(#:phases
          (modify-phases %standard-phases
-           (add-before 'validate-runpath 'cleanup-files
+           ;; The cleanup phase moves files around but we need to keep the
+           ;; directory structure for the grovel-generated library.
+           (replace 'cleanup
              (lambda* (#:key outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
-                      (lib (string-append out "/lib/sbcl")))
-                 (for-each
-                  delete-file
-                  (filter (lambda (file)
-                            (not (member (basename file)
-                                         '("basic-unixint__grovel"
-                                           "libosicat.so"
-                                           "osicat--system.fasl"
-                                           "osicat.asd"
-                                           "unixint__grovel"))))
-                          (find-files lib ".*")))
-                 #t))))))
+                      (lib (string-append out "/lib/sbcl/")))
+                 (delete-file-recursively (string-append lib "src"))
+                 (delete-file-recursively (string-append lib "tests"))
+                 (for-each delete-file
+                           (filter (lambda (file)
+                                     (not (member (basename file) '("libosicat.so"))))
+                                   (find-files (string-append lib "posix") ".*"))))
+               #t)))))
       (inputs
        `(("alexandria" ,sbcl-alexandria)
          ("cffi" ,sbcl-cffi)

From 194cb75d85a2d282419b2a618c8e124f140859f3 Mon Sep 17 00:00:00 2001
From: Simon Josefsson <simon@josefsson.org>
Date: Thu, 30 Apr 2020 11:02:08 +0200
Subject: [PATCH 211/215] gnu: libntlm: Update to 1.6 [fixes CVE-2019-17455].

* gnu/packages/gsasl.scm (libntlm): Update to 1.6.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/gsasl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/gsasl.scm b/gnu/packages/gsasl.scm
index a796f9aa82..98acc3c756 100644
--- a/gnu/packages/gsasl.scm
+++ b/gnu/packages/gsasl.scm
@@ -35,14 +35,14 @@
 (define-public libntlm
   (package
     (name "libntlm")
-    (version "1.5")
+    (version "1.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.nongnu.org/libntlm/releases/"
                                   "libntlm-" version ".tar.gz"))
               (sha256
                (base32
-                "1gcvv7f9rggpxay81qv6kw5hr6gd4qiyzkbwhzz02fx9jvv9kmsk"))))
+                "08b83nss16jsn213j326yhn1vnrz10k15fwq6jm5b1vdn23nndzj"))))
     (build-system gnu-build-system)
     (synopsis "Library that implements NTLM authentication")
     (description

From 2a94f72adef710af481a5abefdddb6cde04b5526 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 30 Apr 2020 14:17:32 -0400
Subject: [PATCH 212/215] gnu: MPD: Update to 0.21.23.

* gnu/packages/mpd.scm (mpd): Update to 0.21.23.
---
 gnu/packages/mpd.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm
index 303af32983..755fa5d482 100644
--- a/gnu/packages/mpd.scm
+++ b/gnu/packages/mpd.scm
@@ -92,7 +92,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
 (define-public mpd
   (package
     (name "mpd")
-    (version "0.21.22")
+    (version "0.21.23")
     (source (origin
               (method url-fetch)
               (uri
@@ -101,7 +101,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
                               "/mpd-" version ".tar.xz"))
               (sha256
                (base32
-                "18lvyv3crijki5nxjdhf1byayyavdvj07dk6rm856n4vi78qfmjn"))))
+                "18q72b9baj5cdpq0yn60qm7q4g8vwqqyqndl9xg3f3w0m4n557s3"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags '("-Ddocumentation=true"))) ;the default is 'false'...

From ac4fefb2983aff5e5972b4279aee5296a08aab6a Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@reproducible-builds.org>
Date: Thu, 30 Apr 2020 18:46:30 +0000
Subject: [PATCH 213/215] gnu: diffoscope: Update to 143.

* gnu/packages/diffoscope (diffoscope): Update to 143.
  [native-inputs]: Add openssl and python-h5py.
  [arguments] Add openssl to add-known-tools phase.
  [arguments] Remove hdf5 from add-known-tools phase, added upstream.
---
 gnu/packages/diffoscope.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index 71c0039dfb..1df8552a30 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -57,6 +57,7 @@
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages textutils)
+  #:use-module (gnu packages tls)
   #:use-module (gnu packages video)
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
@@ -69,7 +70,7 @@
   #:use-module (ice-9 match))
 
 (define-public diffoscope
-  (let ((version "141"))
+  (let ((version "143"))
     (package
       (name "diffoscope")
       (version version)
@@ -81,7 +82,7 @@
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0pls2jryx394ysaz0g8h959lhrsdqak9bkxjd5r6sdckgiikplkj"))))
+                  "0j58dqdk8ln8y0bcnfy37ljs37nkl56lzxqns396300ysln0qiwm"))))
       (build-system python-build-system)
       (arguments
        `(#:phases (modify-phases %standard-phases
@@ -96,8 +97,8 @@
                     (add-after 'unpack 'add-known-tools
                       (lambda _
                         (substitute* "diffoscope/external_tools.py"
-                          (("'debian': 'hdf5-tools'")
-                           "'debian': 'hdf5-tools', 'guix': 'hdf5'"))))
+                          (("'debian': 'openssl'")
+                           "'debian': 'openssl', 'guix': 'openssl'"))))
                     ;; This test is broken because our `file` package has a
                     ;; bug in berkeley-db file type detection.
                     (add-after 'unpack 'remove-berkeley-test
@@ -161,6 +162,7 @@
       (native-inputs `(("python-pytest" ,python-pytest)
                        ("python-chardet" ,python-chardet)
                        ("python-binwalk" ,python-binwalk)
+                       ("python-h5py" ,python-h5py)
                        ("python-pypdf2" ,python-pypdf2)
                        ("python-progressbar33" ,python-progressbar33)
                        ;; test suite skips tests when tool is missing
@@ -205,6 +207,7 @@
                        ("ocaml" ,ocaml)
                        ("odt2txt" ,odt2txt)
                        ("openssh" ,openssh)
+                       ("openssl" ,openssl)
                        ("pgpdump" ,pgpdump)
                        ("poppler" ,poppler)
                        ("python-jsbeautifier" ,python-jsbeautifier)

From 6c7a39c45e8b31279e0dc9d85f0af71f9a225f85 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 30 Apr 2020 17:17:46 -0400
Subject: [PATCH 214/215] doc: Bootloader Configuration: Fix an obsolete
 example.

Reported by rawmat on #guix.

* doc/guix.texi (Bootloader Configuration): Replace 'grub-configuration' with
'bootloader-configuration'.
---
 doc/guix.texi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index d0592220a7..26b4652f67 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -26599,7 +26599,7 @@ like
 
 @lisp
 (bootloader
- (grub-configuration
+ (bootloader-configuration
  ;; @dots{}
  (theme (grub-theme
          (inherit %default-theme)

From 229f4fa9522fb56b014ee9c0d8111e8fb6da764d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 30 Apr 2020 23:31:53 +0200
Subject: [PATCH 215/215] gnu: emacs-toml-mode: Fix syntax error in
 description.

* gnu/packages/emacs-xyz.scm (emacs-toml-mode)[description]: Replace usage of
@acronym with @dfn to work around a Guile Texinfo limitation.
---
 gnu/packages/emacs-xyz.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 79f7126ed7..776dcbb897 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2660,8 +2660,11 @@ Stack Overflow, Super User, and other StackExchange sites.")
       (home-page "https://github.com/dryman/toml-mode.el")
       (synopsis "Emacs major mode for editing TOML files")
       (description
-       "This package provides a major mode for editing files in @acronym{TOML,
-Tom's Obvious, Minimal Language} data format.")
+       ;; XXX: Ideally we'd use @acronym for "TOML", but Guile's Texinfo
+       ;; parser does not currently support @comma{}, making it impossible
+       ;; to use commas in the @acronym arguments.
+       "This package provides a major mode for editing files in @dfn{TOML}
+(Tom's Obvious, Minimal Language) data format.")
       (license license:gpl3+))))
 
 (define-public emacs-twittering-mode