From 753c9b7c19944c4709078b4cf76711ecbbf58263 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Sun, 26 Jan 2020 23:56:25 +0100
Subject: [PATCH 001/127] gnu: emacs-modus-themes: Update to 0.4.0.

* gnu/packages/emacs-xyz.scm (emacs-modus-themes): Update to 0.4.0.
---
 gnu/packages/emacs-xyz.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 9870964ec0..d2558707ef 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -20209,7 +20209,7 @@ Emacs that integrate with major modes like Org-mode.")
 (define-public emacs-modus-themes
   (package
     (name "emacs-modus-themes")
-    (version "0.3.0")
+    (version "0.4.0")
     (source
      (origin
        (method git-fetch)
@@ -20218,8 +20218,7 @@ Emacs that integrate with major modes like Org-mode.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32
-         "1xrrjhpdxi9bgx877gvq8xrc2ph5qp9y5j3ssdphy333x9km1px1"))))
+        (base32 "0c4y3y9mjf6x2b9087fk6nkxvgvm9f5l1p2vdwqny80vp4krsb8r"))))
     (build-system emacs-build-system)
     (home-page "https://gitlab.com/protesilaos/modus-themes")
     (synopsis "Emacs themes designed for colour-contrast accessibility")

From 406c7bc6cd16dc0a17e7edbe6594650db09d5032 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Sun, 26 Jan 2020 23:58:23 +0100
Subject: [PATCH 002/127] gnu: emacs-org: Update to 9.3.2.

* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.3.2.
---
 gnu/packages/emacs-xyz.scm | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index d2558707ef..fe1ed6837c 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -8053,14 +8053,13 @@ passive voice.")
     (name "emacs-org")
     ;; emacs-org-contrib inherits from this package.  Please update it as
     ;; well.
-    (version "9.3.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://elpa.gnu.org/packages/org-"
-                                  version ".tar"))
-              (sha256
-               (base32
-                "1n79h6ihhsaxxbnl9hw511aav0215m3pa51sa5fh3ddknjfplian"))))
+    (version "9.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://elpa.gnu.org/packages/org-" version ".tar"))
+       (sha256
+        (base32 "1275s3hzyka2wwxl6nc2sndnwyl7kbc1nnl0hrznxb3wpy2abfd6"))))
     (build-system emacs-build-system)
     (home-page "https://orgmode.org/")
     (synopsis "Outline-based notes management and organizer")

From 2e4ea249a120202878e96d95f519c1c6fc003cfb Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Mon, 27 Jan 2020 00:02:34 +0100
Subject: [PATCH 003/127] gnu: emacs-org-contrib: Update to 20200126.

* gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 20200126.
---
 gnu/packages/emacs-xyz.scm | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index fe1ed6837c..a528f373ad 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -8073,14 +8073,14 @@ programming and reproducible research.")
   (package
     (inherit emacs-org)
     (name "emacs-org-contrib")
-    (version "20191226")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://orgmode.org/elpa/"
-                                  "org-plus-contrib-" version ".tar"))
-              (sha256
-               (base32
-                "08h6qiplvm7rvrb1pv2arwdlv6p31p0a6h0fk64kb79g6br8rk8i"))))
+    (version "20200126")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://orgmode.org/elpa/"
+                           "org-plus-contrib-" version ".tar"))
+       (sha256
+        (base32 "08yik0i8ya2x5j4vsnwxdcdlcxbiq58lvy30vcbdbf0hqrd40kjv"))))
     (arguments
      `(#:modules ((guix build emacs-build-system)
                   (guix build utils)

From 4144eb195c28cbfd1ca2a131cf4b64afcad713ae Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 27 Jan 2020 00:47:57 +0100
Subject: [PATCH 004/127] gnu: sicp: Remove unused module import.

* gnu/packages/scheme.scm (sicp)[arguments]: Do not import (srfi srfi-1).
---
 gnu/packages/scheme.scm | 2 --
 1 file changed, 2 deletions(-)

diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm
index b0da2ac36b..c765125b85 100644
--- a/gnu/packages/scheme.scm
+++ b/gnu/packages/scheme.scm
@@ -638,12 +638,10 @@ threads.")
                        ("texinfo" ,texinfo)))
       (arguments
        `(#:modules ((guix build utils)
-                    (srfi srfi-1)
                     (srfi srfi-26))
          #:builder
          (begin
            (use-modules (guix build utils)
-                        (srfi srfi-1)
                         (srfi srfi-26))
            (let ((gzip (assoc-ref %build-inputs "gzip"))
                  (source (assoc-ref %build-inputs "source"))

From 1ef71f522577e8b796344e072463d87e5cbae889 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sun, 26 Jan 2020 19:01:00 -0500
Subject: [PATCH 005/127] gnu: pcsxr: Wrap with GSETTINGS_SCHEMA_DIR path
 variable.

Without setting this path variable, gtk+ must be installed in the user's
profile for pcsxr's GUI to work.

* gnu/packages/emulators.scm (pcsxr)[arguments]: Add 'wrap-program' phase and
return #t from 'cd-subdir' and 'fix-cdio-lookup' phases.
---
 gnu/packages/emulators.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 140a8087ec..23b5ad864f 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -1478,12 +1478,22 @@ functions.  The source code to MAME serves as this documentation.")
          #:phases
          (modify-phases %standard-phases
            (add-after 'unpack 'cd-subdir
-             (lambda _ (chdir "pcsxr")))
+             (lambda _ (chdir "pcsxr") #t))
            (add-before 'configure 'fix-cdio-lookup
              (lambda* (#:key inputs #:allow-other-keys)
                (substitute* "cmake/FindCdio.cmake"
                  (("/usr/include/cdio")
-                  (string-append (assoc-ref inputs "libcdio") "/include/cdio"))))))))
+                  (string-append (assoc-ref inputs "libcdio") "/include/cdio")))
+               #t))
+           (add-after 'install 'wrap-program
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (wrap-program (string-append (assoc-ref outputs "out")
+                                            "/bin/pcsxr")
+                 ;; For GtkFileChooserDialog.
+                 `("GSETTINGS_SCHEMA_DIR" =
+                   (,(string-append (assoc-ref inputs "gtk+")
+                                    "/share/glib-2.0/schemas"))))
+               #t)))))
       (native-inputs
        `(("pkg-config" ,pkg-config)
          ("intltool" ,intltool)

From 7a4780ce9dc9fcd4c7ecca1a9458350f06c9a064 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 23 Jan 2020 02:27:10 +0100
Subject: [PATCH 006/127] gnu: ocambuild: Update to 0.14.0.

* gnu/packages/ocaml.scm (ocamlbuild): Update to 0.14.0.
[build-system]: Use ocaml-build-system.
---
 gnu/packages/ocaml.scm | 29 ++++++++++-------------------
 1 file changed, 10 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index a278504ae0..f5becb6bf4 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -233,7 +233,7 @@ functional, imperative and object-oriented styles of programming.")
 (define-public ocamlbuild
   (package
     (name "ocamlbuild")
-    (version "0.13.1")
+    (version "0.14.0")
     (source
      (origin
        (method git-fetch)
@@ -242,31 +242,22 @@ functional, imperative and object-oriented styles of programming.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v37vjvdqw35yvj8ipmlzmwf1jhip0hbsmcbdcn9cnj12p3mr6k7"))))
-    (build-system gnu-build-system)
+        (base32 "1hb5mcdz4wv7sh1pj7dq9q4fgz5h3zg7frpiya6s8zd3ypwzq0kh"))))
+    (build-system ocaml-build-system)
     (arguments
-     `(#:test-target "test"
-       #:tests? #f; tests require findlib
-       #:make-flags
+     `(#:make-flags
        (list (string-append "OCAMLBUILD_PREFIX=" (assoc-ref %outputs "out"))
              (string-append "OCAMLBUILD_BINDIR=" (assoc-ref %outputs "out")
-                        "/bin")
+                            "/bin")
              (string-append "OCAMLBUILD_LIBDIR=" (assoc-ref %outputs "out")
-                        "/lib/ocaml/site-lib")
+                            "/lib/ocaml/site-lib")
              (string-append "OCAMLBUILD_MANDIR=" (assoc-ref %outputs "out")
-                        "/share/man"))
+                            "/share/man"))
        #:phases
        (modify-phases %standard-phases
-         (delete 'bootstrap)
-         (delete 'configure)
-         (add-before 'build 'findlib-environment
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out")))
-               (setenv "OCAMLFIND_DESTDIR" (string-append out "/lib/ocaml/site-lib"))
-               (setenv "OCAMLFIND_LDCONF" "ignore")
-               #t))))))
-    (native-inputs
-     `(("ocaml" ,ocaml)))
+         (delete 'configure))
+       ; some failures because of changes in OCaml's error message formating
+       #:tests? #f))
     (home-page "https://github.com/ocaml/ocamlbuild")
     (synopsis "OCaml build tool")
     (description "OCamlbuild is a generic build tool, that has built-in rules

From 73c26d572902c2c22b2581169826505957e728e7 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 23 Jan 2020 03:07:09 +0100
Subject: [PATCH 007/127] gnu: Add ocaml4.07-lablgtk.

* gnu/packages/ocaml.scm (ocaml4.07-lablgtk): New variable.
(lablgtk)[properties]: Add variant.
---
 gnu/packages/ocaml.scm | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index f5becb6bf4..ebe2618e6e 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -811,6 +811,7 @@ Knuth’s LR(1) parser construction technique.")
                  (substitute* "config.make"
                    ((ocaml) out))
                  #t))))))
+    (properties `((ocaml4.07-variant . ,(delay ocaml4.07-lablgtk))))
     (home-page "http://lablgtk.forge.ocamlcore.org/")
     (synopsis "GTK+ bindings for OCaml")
     (description
@@ -824,6 +825,16 @@ libglade (and it an generate OCaml code from .glade files),
 libpanel, librsvg and quartz.")
     (license license:lgpl2.1)))
 
+(define-public ocaml4.07-lablgtk
+  (package
+    (inherit lablgtk)
+    (name "ocaml4.07-lablgtk")
+    (native-inputs
+     `(("ocaml" ,ocaml-4.07)
+       ("findlib" ,ocaml4.07-findlib)
+       ("pkg-config" ,pkg-config)))
+    (properties '())))
+
 (define-public unison
   (package
     (name "unison")

From 0ccd9463ec0be3bb225373575355e987664555d5 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 23 Jan 2020 03:23:38 +0100
Subject: [PATCH 008/127] gnu: Add ocaml4.07-dune.

* gnu/packages/ocaml.scm (ocaml4.07-dune): New variable.
---
 gnu/packages/ocaml.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index ebe2618e6e..f56658e253 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -1271,6 +1271,9 @@ release of Jane Street packages.  It reads metadata from @file{dune} files
 following a very simple s-expression syntax.")
     (license license:expat)))
 
+(define-public ocaml4.07-dune
+  (package-with-ocaml4.07 dune))
+
 (define-public ocaml-migrate-parsetree
   (package
     (name "ocaml-migrate-parsetree")

From 1e8da4cdefb089ac7d2453d71f72924540238d87 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 23 Jan 2020 03:24:01 +0100
Subject: [PATCH 009/127] guix: ocaml: Also replace dune when relevant in
 package-with-explicit-ocaml.

* guix/build-system/ocaml.scm (package-with-explicit-ocaml): Take a dune
argument and add it to transformed packages when relevant.
---
 guix/build-system/ocaml.scm | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/guix/build-system/ocaml.scm b/guix/build-system/ocaml.scm
index de3e71a5aa..c5996bf0cf 100644
--- a/guix/build-system/ocaml.scm
+++ b/guix/build-system/ocaml.scm
@@ -92,7 +92,11 @@
   (let ((module (resolve-interface '(gnu packages ocaml))))
     (module-ref module 'ocaml4.07-findlib)))
 
-(define* (package-with-explicit-ocaml ocaml findlib old-prefix new-prefix
+(define (default-ocaml4.07-dune)
+  (let ((module (resolve-interface '(gnu packages ocaml))))
+    (module-ref module 'ocaml4.07-dune)))
+
+(define* (package-with-explicit-ocaml ocaml findlib dune old-prefix new-prefix
                                        #:key variant-property)
   "Return a procedure of one argument, P.  The procedure creates a package
 with the same fields as P, which is assumed to use OCAML-BUILD-SYSTEM, such
@@ -100,6 +104,10 @@ that it is compiled with OCAML and FINDLIB instead.  The inputs are changed
 recursively accordingly.  If the name of P starts with OLD-PREFIX, this is
 replaced by NEW-PREFIX; otherwise, NEW-PREFIX is prepended to the name.
 
+When the package uses the DUNE-BUILD-SYSTEM, the procedure creates a package
+with the same fields as P, such that it is compiled with OCAML, FINDLIB and DUNE
+instead.
+
 When VARIANT-PROPERTY is present, it is used as a key to search for
 pre-defined variants of this transformation recorded in the 'properties' field
 of packages.  The property value must be the promise of a package.  This is a
@@ -132,10 +140,15 @@ pre-defined variants."
                                    name))))
         (arguments
          (let ((ocaml   (if (promise? ocaml) (force ocaml) ocaml))
-               (findlib (if (promise? findlib) (force findlib) findlib)))
+               (findlib (if (promise? findlib) (force findlib) findlib))
+               (dune (if (promise? dune) (force dune) dune)))
            (ensure-keyword-arguments (package-arguments p)
                                      `(#:ocaml   ,ocaml
-                                       #:findlib ,findlib))))))
+                                       #:findlib ,findlib
+                                       ,@(if (eq? (package-build-system p)
+                                                  (default-dune-build-system))
+                                             `(#:dune ,dune)
+                                             '())))))))
      (else p)))
 
   (define (cut? p)
@@ -148,6 +161,7 @@ pre-defined variants."
 (define package-with-ocaml4.07
   (package-with-explicit-ocaml (delay (default-ocaml4.07))
                                (delay (default-ocaml4.07-findlib))
+                               (delay (default-ocaml4.07-dune))
                                "ocaml-" "ocaml4.07-"
                                #:variant-property 'ocaml4.07-variant))
 

From 87858bc526a9d577760f55d05a51cb56630f845b Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 23 Jan 2020 04:39:52 +0100
Subject: [PATCH 010/127] gnu: ocaml: Switch to ocaml 4.09 by default.

Bap and earley cannot be updated as they do not support 4.09 yet. Bap requires
the janestreet packages, which cannot be upgraded as no version supports
4.09 and 4.07 at the same time. Moreover, newer versions of the
janestreet packages have a different dependency graph, which will
require a whole new set of packages. We cannot simply use
package-with-ocaml4.07 on them.

* gnu/packages/ocaml.scm (ocaml-sqlite3, ocaml-ppx-tools, ocaml-gen)
(ocaml-sedlex, ocaml-pcre, ocaml-expect, ocaml-ezjsonm, ocaml-uri)
(ocaml-piqilib, ocaml-piqi, ocaml-charinfo-width, ocaml-zed)
(ocaml-lambda-term, ocaml-utop, ocaml-ppx-inline-test, ocaml-earley)
(ocaml-merlin, ocaml-gsl, ocaml-gsl-1, ocaml-sexplib0, ocaml-parsexp)
(ocaml-sexplib, ocaml-base, ocaml-stdio, ocaml-ppxlib, ocaml-ppx-compare)
(ocaml-fieldslib, ocaml-variantslib, ocaml-ppx-fields-conv)
(ocaml-ppx-sexp-conv, ocaml-ppx-variants-conv, ocaml-ppx-custom-printf)
(ocaml-bin-prot, ocaml-ppx-hash, ocaml-ppx-enumerate, ocaml-ppx-bench)
(ocaml-ppx-here, ocaml-ppx-typerep, ocaml-ppx-sexp-value)
(ocaml-ppx-sexp-message, ocaml-ppx-pipebang, ocaml-ppx-optional)
(ocaml-ppx-optcomp, ocaml-ppx-fail, ocaml-ppx-let, ocaml-ppx-assert)
(ocaml-ppx-expect, ocaml-ppx-js-style, ocaml-ppx-typerep-conv)
(ocaml-ppx-base, ocaml-ppx-bin-prot, ocaml-ppx-jane)
(ocaml-splittable-random, ocaml-configurator, ocaml-spawn, ocaml-core)
(ocaml-core-kernel, ocaml-odoc, ocaml-fftw3, ocaml-lacaml): Rename to ...
(ocaml4.07-sqlite3, ocaml4.07-ppx-tools, ocaml4.07-gen, ocaml4.07-sedlex)
(ocaml4.07-pcre, ocaml4.07-expect, ocaml4.07-ezjsonm, ocaml4.07-uri)
(ocaml4.07-piqilib, ocaml4.07-piqi, ocaml4.07-charinfo-width)
(ocaml4.07-zed, ocaml4.07-lambda-term, ocaml4.07-utop)
(ocaml4.07-ppx-inline-test, ocaml4.07-earley, ocaml4.07-merlin)
(ocaml4.07-gsl, ocaml4.07-gsl-1, ocaml4.07-sexplib0, ocaml4.07-parsexp)
(ocaml4.07-sexplib, ocaml4.07-base, ocaml4.07-stdio, ocaml4.07-ppxlib)
(ocaml4.07-ppx-compare, ocaml4.07-fieldslib, ocaml4.07-variantslib)
(ocaml4.07-ppx-fields-conv, ocaml4.07-ppx-sexp-conv)
(ocaml4.07-ppx-variants-conv, ocaml4.07-ppx-custom-printf)
(ocaml4.07-bin-prot, ocaml4.07-ppx-hash, ocaml4.07-ppx-enumerate)
(ocaml4.07-ppx-bench, ocaml4.07-ppx-here, ocaml4.07-ppx-typerep)
(ocaml4.07-ppx-sexp-value, ocaml4.07-ppx-sexp-message)
(ocaml4.07-ppx-pipebang, ocaml4.07-ppx-optional, ocaml4.07-ppx-optcomp)
(ocaml4.07-ppx-fail, ocaml4.07-ppx-let, ocaml4.07-ppx-assert)
(ocaml4.07-ppx-expect, ocaml4.07-ppx-js-style)
(ocaml4.07-ppx-typerep-conv, ocaml4.07-ppx-base, ocaml4.07-ppx-bin-prot)
(ocaml4.07-ppx-jane, ocaml4.07-splittable-random)
(ocaml4.07-configurator, ocaml4.07-spawn, ocaml4.07-core)
(ocaml4.07-core-kernel, ocaml4.07-odoc, ocaml4.07-fftw3)
(ocaml4.07-lacaml): ... to this and use ocaml 4.07.
(bap, unison): Use ocaml-4.07.
* gnu/packages/bioinformatics.scm (pplacer): Use ocaml-4.07.
---
 gnu/packages/bioinformatics.scm |   22 +-
 gnu/packages/ocaml.scm          | 1049 ++++++++++++++++++-------------
 2 files changed, 626 insertions(+), 445 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e8dac2a12b..c71adbe98c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14626,21 +14626,23 @@ let before_space s =
                (let* ((out (assoc-ref outputs "out"))
                       (bin (string-append out "/bin")))
                  (copy-recursively "bin" bin))
-               #t)))))
+               #t)))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
       (inputs
        `(("zlib" ,zlib "static")
          ("gsl" ,gsl)
-         ("ocaml-ounit" ,ocaml-ounit)
-         ("ocaml-batteries" ,ocaml-batteries)
-         ("ocaml-camlzip" ,camlzip)
-         ("ocaml-csv" ,ocaml-csv)
-         ("ocaml-sqlite3" ,ocaml-sqlite3)
-         ("ocaml-xmlm" ,ocaml-xmlm)
-         ("ocaml-mcl" ,ocaml-mcl)
-         ("ocaml-gsl" ,ocaml-gsl-1)))
+         ("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit))
+         ("ocaml-batteries" ,(package-with-ocaml4.07 ocaml-batteries))
+         ("ocaml-camlzip" ,(package-with-ocaml4.07 camlzip))
+         ("ocaml-csv" ,(package-with-ocaml4.07 ocaml-csv))
+         ("ocaml-sqlite3" ,ocaml4.07-sqlite3)
+         ("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm))
+         ("ocaml-mcl" ,(package-with-ocaml4.07 ocaml-mcl))
+         ("ocaml-gsl" ,ocaml4.07-gsl-1)))
       (native-inputs
        `(("cddlib-src" ,(package-source cddlib))
-         ("ocamlbuild" ,ocamlbuild)
+         ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))
          ("pkg-config" ,pkg-config)))
       (propagated-inputs
        `(("pplacer-scripts" ,pplacer-scripts)))
diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index f56658e253..df998af1f5 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -228,7 +228,7 @@ functional, imperative and object-oriented styles of programming.")
                           "--prefix" out
                           "--mandir" mandir))))))))))
 
-(define-public ocaml ocaml-4.07)
+(define-public ocaml ocaml-4.09)
 
 (define-public ocamlbuild
   (package
@@ -852,7 +852,7 @@ libpanel, librsvg and quartz.")
     (outputs '("out"
                "doc"))                  ; 1.9 MiB of documentation
     (native-inputs
-     `(("ocaml" ,ocaml)
+     `(("ocaml" ,ocaml-4.07)
        ;; For documentation
        ("ghostscript" ,ghostscript)
        ("texlive" ,texlive-tiny)
@@ -1444,9 +1444,9 @@ to operate on the result type available from OCaml 4.03 in the standard
 library.")
     (license license:isc)))
 
-(define-public ocaml-sqlite3
+(define-public ocaml4.07-sqlite3
   (package
-    (name "ocaml-sqlite3")
+    (name "ocaml4.07-sqlite3")
     (version "4.4.1")
     (source
      (origin
@@ -1459,9 +1459,12 @@ library.")
         (base32
          "1536agm5fgcqysszhpd3kmw7lkc5n5ni7gmlyglrbvmnmrwf3av2"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (native-inputs
-     `(("ocaml-base" ,ocaml-base)
-       ("ocaml-stdio" ,ocaml-stdio)
+     `(("ocaml-base" ,ocaml4.07-base)
+       ("ocaml-stdio" ,ocaml4.07-stdio)
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("sqlite" ,sqlite)))
@@ -1671,9 +1674,9 @@ displayed at the end of the run (with the full logs ready to inspect), with a
 simple (yet expressive) query language to select the tests to run.")
     (license license:isc)))
 
-(define-public ocaml-ppx-tools
+(define-public ocaml4.07-ppx-tools
   (package
-    (name "ocaml-ppx-tools")
+    (name "ocaml4.07-ppx-tools")
     (version "5.1+4.06.0")
     (source
      (origin
@@ -1687,7 +1690,9 @@ simple (yet expressive) query language to select the tests to run.")
     (build-system ocaml-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases (delete 'configure))
-       #:tests? #f))
+       #:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (properties `((upstream-name . "ppx_tools")))
     (home-page "https://github.com/alainfrisch/ppx_tools")
     (synopsis "Tools for authors of ppx rewriters and other syntactic tools")
@@ -1987,9 +1992,9 @@ format.  It can process XML documents without a complete in-memory
 representation of the data.")
     (license license:isc)))
 
-(define-public ocaml-gen
+(define-public ocaml4.07-gen
   (package
-    (name "ocaml-gen")
+    (name "ocaml4.07-gen")
     (version "0.5.2")
     (source (origin
               (method git-fetch)
@@ -2003,21 +2008,23 @@ representation of the data.")
     (build-system dune-build-system)
     (arguments
      `(#:tests? #f; no tests
-       #:package "gen"))
+       #:package "gen"
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-     `(("ocaml-odoc" ,ocaml-odoc)))
+     `(("ocaml-odoc" ,ocaml4.07-odoc)))
     (native-inputs
-     `(("ocaml-qtest" ,ocaml-qtest)
-       ("ocaml-qcheck" ,ocaml-qcheck)))
+     `(("ocaml-qtest" ,(package-with-ocaml4.07 ocaml-qtest))
+       ("ocaml-qcheck" ,(package-with-ocaml4.07 ocaml-qcheck))))
     (home-page "https://github.com/c-cube/gen/")
     (synopsis "Iterators for OCaml, both restartable and consumable")
     (description "Gen implements iterators of OCaml, that are both restartable
 and consumable.")
     (license license:bsd-2)))
 
-(define-public ocaml-sedlex
+(define-public ocaml4.07-sedlex
   (package
-    (name "ocaml-sedlex")
+    (name "ocaml4.07-sedlex")
     (version "2.1")
     (source (origin
               (method git-fetch)
@@ -2046,13 +2053,16 @@ and consumable.")
          (add-before 'build 'chmod
            (lambda _
              (for-each (lambda (file) (chmod file #o644)) (find-files "." ".*"))
-             #t)))))
+             #t)))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (native-inputs
-     `(("ocamlbuild" ,ocamlbuild)))
+     `(("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))))
     (propagated-inputs
-     `(("ocaml-gen" ,ocaml-gen)
-       ("ocaml-ppx-tools-versioned" ,ocaml-ppx-tools-versioned)
-       ("ocaml-uchar" ,ocaml-uchar)))
+     `(("ocaml-gen" ,ocaml4.07-gen)
+       ("ocaml-ppx-tools-versioned"
+        ,(package-with-ocaml4.07 ocaml-ppx-tools-versioned))
+       ("ocaml-uchar" ,(package-with-ocaml4.07 ocaml-uchar))))
     ;; These three files are needed by src/generator/data/dune, but would be
     ;; downloaded using curl at build time.
     (inputs
@@ -2358,9 +2368,9 @@ every compliant installation of OCaml and organize these libraries into a
 hierarchy of modules.")
     (license license:lgpl2.1+)))
 
-(define-public ocaml-pcre
+(define-public ocaml4.07-pcre
   (package
-    (name "ocaml-pcre")
+    (name "ocaml4.07-pcre")
     (version "7.4.1")
     (source (origin
               (method git-fetch)
@@ -2373,9 +2383,12 @@ hierarchy of modules.")
                 "11sd8g668h48790lamz0riw9jgnfkaif5qdfa0akcndwa6aj07jf"))))
     (build-system dune-build-system)
     (arguments
-     `(#:test-target "."))
+     `(#:test-target "."
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib
+       #:dune ,ocaml4.07-dune))
     (native-inputs
-     `(("ocaml-base" ,ocaml-base)
+     `(("ocaml-base" ,ocaml4.07-base)
        ("pcre:bin" ,pcre "bin")))
     (propagated-inputs `(("pcre" ,pcre)))
     (home-page "https://mmottl.github.io/pcre-ocaml")
@@ -2385,9 +2398,9 @@ matching and substitution, similar to the functionality offered by the Perl
 language.")
     (license license:lgpl2.1+))); with the OCaml link exception
 
-(define-public ocaml-expect
+(define-public ocaml4.07-expect
   (package
-    (name "ocaml-expect")
+    (name "ocaml4.07-expect")
     (version "0.0.6")
     (source (origin
               (method url-fetch)
@@ -2396,14 +2409,17 @@ language.")
                (base32
                 "098qvg9d4yrqzr5ax291y3whrpax0m3sx4gi6is0mblc96r9yqk0"))))
     (arguments
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (build-system ocaml-build-system)
     (native-inputs
-     `(("ocamlbuild" ,ocamlbuild)
-       ("ocaml-num" ,ocaml-num)
-       ("ocaml-pcre" ,ocaml-pcre)
-       ("ounit" ,ocaml-ounit)))
-    (propagated-inputs `(("batteries" ,ocaml-batteries)))
+     `(("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))
+       ("ocaml-num" ,(package-with-ocaml4.07 ocaml-num))
+       ("ocaml-pcre" ,ocaml4.07-pcre)
+       ("ounit" ,(package-with-ocaml4.07 ocaml-ounit))))
+    (propagated-inputs
+     `(("batteries" ,(package-with-ocaml4.07 ocaml-batteries))))
     (home-page "https://forge.ocamlcore.org/projects/ocaml-expect/")
     (synopsis "Simple implementation of expect")
     (description "Help building unitary testing of interactive program.  You
@@ -2712,9 +2728,9 @@ writing to these structures, and they are accessed via the Bigarray module.")
     (description "Hex is a minimal library providing hexadecimal converters.")
     (license license:isc)))
 
-(define-public ocaml-ezjsonm
+(define-public ocaml4.07-ezjsonm
   (package
-    (name "ocaml-ezjsonm")
+    (name "ocaml4.07-ezjsonm")
     (version "1.1.0")
     (source
      (origin
@@ -2728,13 +2744,15 @@ writing to these structures, and they are accessed via the Bigarray module.")
     (build-system dune-build-system)
     (arguments
      `(#:package "ezjsonm"
-       #:test-target "."))
+       #:test-target "."
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (native-inputs
-     `(("ocaml-alcotest" ,ocaml-alcotest)))
+     `(("ocaml-alcotest" ,(package-with-ocaml4.07 ocaml-alcotest))))
     (propagated-inputs
-     `(("ocaml-hex" ,ocaml-hex)
-       ("ocaml-jsonm" ,ocaml-jsonm)
-       ("ocaml-sexplib" ,ocaml-sexplib)))
+     `(("ocaml-hex" ,(package-with-ocaml4.07 ocaml-hex))
+       ("ocaml-jsonm" ,(package-with-ocaml4.07 ocaml-jsonm))
+       ("ocaml-sexplib" ,ocaml4.07-sexplib)))
     (home-page "https://github.com/mirage/ezjsonm/")
     (synopsis "Read and write JSON data")
     (description "Ezjsonm provides more convenient (but far less flexible) input
@@ -2743,9 +2761,9 @@ the need to write signal code, which is useful for quick scripts that manipulate
 JSON.")
     (license license:isc)))
 
-(define-public ocaml-uri
+(define-public ocaml4.07-uri
   (package
-    (name "ocaml-uri")
+    (name "ocaml4.07-uri")
     (version "2.2.0")
     (source
      (origin
@@ -2764,14 +2782,16 @@ JSON.")
          (add-before 'build 'update-deprecated
            (lambda _
              (substitute* "lib/uri.ml"
-               (("Re.get") "Re.Group.get")))))))
+               (("Re.get") "Re.Group.get")))))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (native-inputs
-     `(("ocaml-ounit" ,ocaml-ounit)
-       ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)))
+     `(("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit))
+       ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)))
     (propagated-inputs
-     `(("ocaml-re" ,ocaml-re)
-       ("ocaml-sexplib0" ,ocaml-sexplib0)
-       ("ocaml-stringext" ,ocaml-stringext)))
+     `(("ocaml-re" ,(package-with-ocaml4.07 ocaml-re))
+       ("ocaml-sexplib0" ,ocaml4.07-sexplib0)
+       ("ocaml-stringext" ,(package-with-ocaml4.07 ocaml-stringext))))
     (home-page "https://github.com/mirage/ocaml-uri")
     (synopsis "RFC3986 URI/URL parsing library")
     (description "OCaml-uri is a library for parsing URI/URL in the RFC3986 format.")
@@ -2808,9 +2828,9 @@ JSON.")
 Format module of the OCaml standard library.")
     (license license:bsd-3)))
 
-(define-public ocaml-piqilib
+(define-public ocaml4.07-piqilib
   (package
-    (name "ocaml-piqilib")
+    (name "ocaml4.07-piqilib")
     (version "0.6.15")
     (source
      (origin
@@ -2854,14 +2874,16 @@ Format module of the OCaml standard library.")
              (mkdir-p stubs)
              (symlink (string-append lib "/dllpiqilib_stubs.so")
                       (string-append stubs "/dllpiqilib_stubs.so"))
-             #t))))))
+             #t))))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (native-inputs
      `(("which" ,which)))
     (propagated-inputs
-     `(("ocaml-xmlm" ,ocaml-xmlm)
-       ("ocaml-sedlex" ,ocaml-sedlex)
-       ("ocaml-easy-format" ,ocaml-easy-format)
-       ("ocaml-base64" ,ocaml-base64)))
+     `(("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm))
+       ("ocaml-sedlex" ,ocaml4.07-sedlex)
+       ("ocaml-easy-format" ,(package-with-ocaml4.07 ocaml-easy-format))
+       ("ocaml-base64" ,(package-with-ocaml4.07 ocaml-base64))))
     (home-page "http://piqi.org")
     (synopsis "Data serialization and conversion library")
     (description "Piqilib is the common library used by the piqi command-line
@@ -2927,9 +2949,9 @@ and 4 (random based) according to RFC 4122.")
     (description "OCamlgraph is a generic graph library for OCaml.")
     (license license:lgpl2.1)))
 
-(define-public ocaml-piqi
+(define-public ocaml4.07-piqi
   (package
-    (name "ocaml-piqi")
+    (name "ocaml4.07-piqi")
     (version "0.7.7")
     (source (origin
               (method url-fetch)
@@ -2947,14 +2969,16 @@ and 4 (random based) according to RFC 4122.")
                             "/bin/sh"))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure))))
+         (delete 'configure))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (native-inputs
      `(("which" ,which)
        ("protobuf" ,protobuf))) ; for tests
     (propagated-inputs
-     `(("ocaml-num" ,ocaml-num)
-       ("ocaml-piqilib" ,ocaml-piqilib)
-       ("ocaml-stdlib-shims" ,ocaml-stdlib-shims)))
+     `(("ocaml-num" ,(package-with-ocaml4.07 ocaml-num))
+       ("ocaml-piqilib" ,ocaml4.07-piqilib)
+       ("ocaml-stdlib-shims" ,(package-with-ocaml4.07 ocaml-stdlib-shims))))
     (home-page "https://github.com/alavrik/piqi-ocaml")
     (synopsis "Protocol serialization system for OCaml")
     (description "Piqi is a multi-format data serialization system for OCaml.
@@ -2978,24 +3002,24 @@ XML and Protocol Buffers formats.")
                 "0ryf2xb37pj2f9mc3p5prqgqrylph9qgq7q9jnbx8b03nzzpa6h6"))))
    (build-system ocaml-build-system)
    (native-inputs
-    `(("ocaml-oasis" ,ocaml-oasis)
+    `(("ocaml-oasis" ,(package-with-ocaml4.07 ocaml-oasis))
       ("clang" ,clang-3.8)
-      ("ocaml-ounit" ,ocaml-ounit)))
+      ("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit))))
    (propagated-inputs
-    `(("camlzip" ,camlzip)
-      ("ocaml-bitstring" ,ocaml-bitstring)
-      ("ocaml-cmdliner" ,ocaml-cmdliner)
-      ("ocaml-core-kernel" ,ocaml-core-kernel)
-      ("ocaml-ezjsonm" ,ocaml-ezjsonm)
-      ("ocaml-fileutils" ,ocaml-fileutils)
-      ("ocaml-frontc" ,ocaml-frontc)
-      ("ocaml-graph" ,ocaml-graph)
-      ("ocaml-ocurl" ,ocaml-ocurl)
-      ("ocaml-piqi" ,ocaml-piqi)
-      ("ocaml-ppx-jane" ,ocaml-ppx-jane)
-      ("ocaml-uuidm" ,ocaml-uuidm)
-      ("ocaml-uri" ,ocaml-uri)
-      ("ocaml-zarith" ,ocaml-zarith)))
+    `(("camlzip" ,(package-with-ocaml4.07 camlzip))
+      ("ocaml-bitstring" ,(package-with-ocaml4.07 ocaml-bitstring))
+      ("ocaml-cmdliner" ,(package-with-ocaml4.07 ocaml-cmdliner))
+      ("ocaml-core-kernel" ,ocaml4.07-core-kernel)
+      ("ocaml-ezjsonm" ,ocaml4.07-ezjsonm)
+      ("ocaml-fileutils" ,(package-with-ocaml4.07 ocaml-fileutils))
+      ("ocaml-frontc" ,(package-with-ocaml4.07 ocaml-frontc))
+      ("ocaml-graph" ,(package-with-ocaml4.07 ocaml-graph))
+      ("ocaml-ocurl" ,(package-with-ocaml4.07 ocaml-ocurl))
+      ("ocaml-piqi" ,ocaml4.07-piqi)
+      ("ocaml-ppx-jane" ,ocaml4.07-ppx-jane)
+      ("ocaml-uuidm" ,(package-with-ocaml4.07 ocaml-uuidm))
+      ("ocaml-uri" ,ocaml4.07-uri)
+      ("ocaml-zarith" ,(package-with-ocaml4.07 ocaml-zarith))))
    (inputs
     `(("llvm" ,llvm-3.8)
       ("gmp" ,gmp)))
@@ -3019,7 +3043,9 @@ XML and Protocol Buffers formats.")
                       "/lib/ocaml/site-lib")
                     "--with-llvm-version=3.8"
                     "--with-llvm-config=llvm-config"
-                    "--enable-everything"))))))
+                    "--enable-everything"))))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
    (synopsis "Binary Analysis Platform")
    (description "Binary Analysis Platform is a framework for writing program
 analysis tools, that target binary files.  The framework consists of a plethora
@@ -3059,9 +3085,9 @@ library is currently designed for Unicode Standard 3.2.")
     ;; with an exception for linked libraries to use a different license
     (license license:lgpl2.0+)))
 
-(define-public ocaml-charinfo-width
+(define-public ocaml4.07-charinfo-width
   (package
-    (name "ocaml-charinfo-width")
+    (name "ocaml4.07-charinfo-width")
     (version "1.1.0")
     (source (origin
               (method url-fetch)
@@ -3072,11 +3098,14 @@ library is currently designed for Unicode Standard 3.2.")
                (base32
                 "00bv4p1yqs8y0z4z07wd9w9yyv669dikp9b04dcjbwpiy2wy0086"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-     `(("ocaml-result" ,ocaml-result)
-       ("ocaml-camomile" ,ocaml-camomile)))
+     `(("ocaml-result" ,(package-with-ocaml4.07 ocaml-result))
+       ("ocaml-camomile" ,(package-with-ocaml4.07 ocaml-camomile))))
     (native-inputs
-     `(("ocaml-ppx-expect" ,ocaml-ppx-expect)))
+     `(("ocaml-ppx-expect" ,ocaml4.07-ppx-expect)))
     (properties
      `((upstream-name . "charInfo_width")))
     (home-page "https://bitbucket.org/zandoye/charinfo_width/")
@@ -3085,9 +3114,9 @@ library is currently designed for Unicode Standard 3.2.")
 function that follows the prototype of POSIX's wcwidth.")
     (license license:expat)))
 
-(define-public ocaml-zed
+(define-public ocaml4.07-zed
   (package
-    (name "ocaml-zed")
+    (name "ocaml4.07-zed")
     (version "2.0.3")
     (source
      (origin
@@ -3101,11 +3130,13 @@ function that follows the prototype of POSIX's wcwidth.")
     (build-system dune-build-system)
     (arguments
      `(#:jbuild? #t
-       #:test-target "."))
+       #:test-target "."
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-     `(("ocaml-camomile" ,ocaml-camomile)
-       ("ocaml-charinfo-width" ,ocaml-charinfo-width)
-       ("ocaml-react" ,ocaml-react)))
+     `(("ocaml-camomile" ,(package-with-ocaml4.07 ocaml-camomile))
+       ("ocaml-charinfo-width" ,ocaml4.07-charinfo-width)
+       ("ocaml-react" ,(package-with-ocaml4.07 ocaml-react))))
     (home-page "https://github.com/diml/zed")
     (synopsis "Abstract engine for text editing in OCaml")
     (description "Zed is an abstract engine for text edition.  It can be used
@@ -3113,9 +3144,9 @@ to write text editors, edition widgets, readlines, etc.  You just have to
 connect an engine to your inputs and rendering functions to get an editor.")
     (license license:bsd-3)))
 
-(define-public ocaml-lambda-term
+(define-public ocaml4.07-lambda-term
   (package
-    (name "ocaml-lambda-term")
+    (name "ocaml4.07-lambda-term")
     (version "2.0.2")
     (source
      (origin
@@ -3129,12 +3160,14 @@ connect an engine to your inputs and rendering functions to get an editor.")
     (build-system dune-build-system)
     (arguments
      `(#:build-flags (list "--profile" "release")
-       #:tests? #f))
+       #:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-     `(("ocaml-lwt" ,ocaml-lwt)
-       ("ocaml-lwt-log" ,ocaml-lwt-log)
-       ("ocaml-lwt-react" ,ocaml-lwt-react)
-       ("ocaml-zed" ,ocaml-zed)))
+     `(("ocaml-lwt" ,(package-with-ocaml4.07 ocaml-lwt))
+       ("ocaml-lwt-log" ,(package-with-ocaml4.07 ocaml-lwt-log))
+       ("ocaml-lwt-react" ,(package-with-ocaml4.07 ocaml-lwt-react))
+       ("ocaml-zed" ,ocaml4.07-zed)))
     (inputs
      `(("libev" ,libev)))
     (home-page "https://github.com/diml/lambda-term")
@@ -3147,9 +3180,9 @@ manipulation than, for example, ncurses, by providing a native OCaml interface
 instead of bindings to a C library.")
     (license license:bsd-3)))
 
-(define-public ocaml-utop
+(define-public ocaml4.07-utop
   (package
-    (name "ocaml-utop")
+    (name "ocaml4.07-utop")
     (version "2.4.3")
     (source
      (origin
@@ -3163,15 +3196,17 @@ instead of bindings to a C library.")
     (build-system dune-build-system)
     (arguments
      `(#:jbuild? #t
-       #:test-target "."))
+       #:test-target "."
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (native-inputs
-     `(("cppo" ,ocaml-cppo)))
+     `(("cppo" ,(package-with-ocaml4.07 ocaml-cppo))))
     (propagated-inputs
-     `(("lambda-term" ,ocaml-lambda-term)
-       ("lwt" ,ocaml-lwt)
-       ("react" ,ocaml-react)
-       ("camomile" ,ocaml-camomile)
-       ("zed" ,ocaml-zed)))
+     `(("lambda-term" ,ocaml4.07-lambda-term)
+       ("lwt" ,(package-with-ocaml4.07 ocaml-lwt))
+       ("react" ,(package-with-ocaml4.07 ocaml-react))
+       ("camomile" ,(package-with-ocaml4.07 ocaml-camomile))
+       ("zed" ,ocaml4.07-zed)))
     (home-page "https://github.com/ocaml-community/utop")
     (synopsis "Improved interface to the OCaml toplevel")
     (description "UTop is an improved toplevel for OCaml.  It can run in a
@@ -3437,9 +3472,9 @@ Dedukti files.")
 syntax checking on dedukti files.")
       (license license:cecill-b))))
 
-(define-public ocaml-ppx-inline-test
+(define-public ocaml4.07-ppx-inline-test
   (package
-    (name "ocaml-ppx-inline-test")
+    (name "ocaml4.07-ppx-inline-test")
     (version "0.12.0")
     (home-page "https://github.com/janestreet/ppx_inline_test")
     (source
@@ -3455,14 +3490,17 @@ syntax checking on dedukti files.")
     (build-system dune-build-system)
     (arguments
      ;see home page README for further information
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (inputs
-     `(("ocaml-base" ,ocaml-base)
-       ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-       ("ocaml-compiler-libs" ,ocaml-compiler-libs)
-       ("ocaml-sexplib0" ,ocaml-sexplib0)
-       ("ocaml-stdio" ,ocaml-stdio)
-       ("ocaml-ppxlib" ,ocaml-ppxlib)))
+     `(("ocaml-base" ,ocaml4.07-base)
+       ("ocaml-migrate-parsetree"
+        ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+       ("ocaml-compiler-libs" ,(package-with-ocaml4.07 ocaml-compiler-libs))
+       ("ocaml-sexplib0" ,ocaml4.07-sexplib0)
+       ("ocaml-stdio" ,ocaml4.07-stdio)
+       ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_inline_test")))
     (synopsis "Syntax extension for writing in-line tests in ocaml code")
     (description "This package contains a syntax extension for writing
@@ -3508,9 +3546,9 @@ for programming languages, but also for manipulating terms of the λ-calculus
 or quantified formulas.")
     (license license:gpl3+)))
 
-(define-public ocaml-earley
+(define-public ocaml4.07-earley
   (package
-    (name "ocaml-earley")
+    (name "ocaml4.07-earley")
     (version "2.0.0")
     (home-page "https://github.com/rlepigre/ocaml-earley")
     (source
@@ -3525,7 +3563,9 @@ or quantified formulas.")
          "18k7bi7krc4bvqnhijz1q0pfr0nfahghfjifci8rh1q4i5zd0xz5"))))
     (build-system dune-build-system)
     (arguments
-     `(#:test-target "."))
+     `(#:test-target "."
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (synopsis "Parsing library based on Earley Algorithm")
     (description "Earley is a parser combinator library base on Earley's
 algorithm.  It is intended to be used in conjunction with an OCaml syntax
@@ -3675,9 +3715,9 @@ Mercurial's @code{https://www.selenic.com/blog/?p=663, unified test
 format}.  @code{craml} is released as a single binary (called @code{craml}).")
     (license license:isc)))
 
-(define-public ocaml-merlin
+(define-public ocaml4.07-merlin
   (package
-    (name "ocaml-merlin")
+    (name "ocaml4.07-merlin")
     (version "3.2.2")
     (home-page "https://ocaml.github.io/merlin/")
     (source
@@ -3692,14 +3732,16 @@ format}.  @code{craml} is released as a single binary (called @code{craml}).")
          "15ssgmwdxylbwhld9p1cq8x6kadxyhll5bfyf11dddj6cldna3hb"))))
     (build-system dune-build-system)
     (inputs
-     `(("ocaml-biniou" ,ocaml-biniou)
-       ("ocaml-yojson" ,ocaml-yojson)
-       ("ocaml-easy-format" ,ocaml-easy-format)))
+     `(("ocaml-biniou" ,(package-with-ocaml4.07 ocaml-biniou))
+       ("ocaml-yojson" ,(package-with-ocaml4.07 ocaml-yojson))
+       ("ocaml-easy-format" ,(package-with-ocaml4.07 ocaml-easy-format))))
     (native-inputs
      `(("ocaml-findlib" ,ocaml-findlib)))
     (arguments
-     '(#:jbuild? #t
-       #:tests? #f)) ;; Errors in tests in version 3.2.2
+     `(#:jbuild? #t
+       #:tests? #f ;; Errors in tests in version 3.2.2
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (synopsis "Context sensitive completion for OCaml in Vim and Emacs")
     (description "Merlin is an editor service that provides modern IDE
 features for OCaml.  Emacs and Vim support is provided out-of-the-box.
@@ -3707,9 +3749,9 @@ External contributors added support for Visual Studio Code, Sublime Text and
 Atom.")
     (license license:expat)))
 
-(define-public ocaml-gsl
+(define-public ocaml4.07-gsl
   (package
-    (name "ocaml-gsl")
+    (name "ocaml4.07-gsl")
     (version "1.24.0")
     (source
      (origin
@@ -3730,12 +3772,15 @@ Atom.")
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "src/config/discover.ml"
                (("/usr") (assoc-ref inputs "gsl")))
-             #t)))))
+             #t)))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib
+       #:dune ,ocaml4.07-dune))
     (inputs
      `(("gsl" ,gsl)))
     (propagated-inputs
-     `(("ocaml-base" ,ocaml-base)
-       ("ocaml-stdio" ,ocaml-stdio)))
+     `(("ocaml-base" ,ocaml4.07-base)
+       ("ocaml-stdio" ,ocaml4.07-stdio)))
     (home-page "https://mmottl.github.io/gsl-ocaml")
     (synopsis "Bindings to the GNU Scientific Library")
     (description
@@ -3743,9 +3788,9 @@ Atom.")
 the OCaml language.")
     (license license:gpl3+)))
 
-(define-public ocaml-gsl-1
+(define-public ocaml4.07-gsl-1
   (package
-    (inherit ocaml-gsl)
+    (inherit ocaml4.07-gsl)
     (version "1.19.3")
     (source (origin
               (method url-fetch)
@@ -3759,8 +3804,10 @@ the OCaml language.")
     (inputs
      `(("gsl" ,gsl)))
     (native-inputs
-     `(("ocamlbuild" ,ocamlbuild)))
-    (arguments '())
+     `(("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))))
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs '())))
 
 (define-public cubicle
@@ -3821,9 +3868,9 @@ an arbitrary number of processes.  Cache coherence protocols and mutual
 exclusion algorithms are typical examples of such systems.")
     (license license:asl2.0)))
 
-(define-public ocaml-sexplib0
+(define-public ocaml4.07-sexplib0
   (package
-    (name "ocaml-sexplib0")
+    (name "ocaml4.07-sexplib0")
     (version "0.11.0")
     (home-page "https://github.com/janestreet/sexplib0")
     (source
@@ -3838,7 +3885,9 @@ exclusion algorithms are typical examples of such systems.")
          "07v3ggyss7xhfv14bjk1n87sr42iqwj4cgjiv2lcdfkqk49i2bmi"))))
     (build-system dune-build-system)
     (arguments
-     '(#:tests? #f)) ;no tests
+     `(#:tests? #f ;no tests
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (synopsis "Library containing the definition of S-expressions and some
 base converters")
     (description "Part of Jane Street's Core library The Core suite of
@@ -3846,9 +3895,9 @@ libraries is an industrial strength alternative to OCaml's standard library
 that was developed by Jane Street, the largest industrial user of OCaml.")
 (license license:expat)))
 
-(define-public ocaml-parsexp
+(define-public ocaml4.07-parsexp
   (package
-    (name "ocaml-parsexp")
+    (name "ocaml4.07-parsexp")
     (version "0.11.0")
     (home-page "https://github.com/janestreet/parsexp")
     (source
@@ -3862,8 +3911,11 @@ that was developed by Jane Street, the largest industrial user of OCaml.")
         (base32
          "1nyq23s5igd8cf3n4qxprjvhbmb6ighb3fy5mw7hxl0mdgsw5fvz"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (inputs
-     `(("ocaml-sexplib0" ,ocaml-sexplib0)))
+     `(("ocaml-sexplib0" ,ocaml4.07-sexplib0)))
     (synopsis "S-expression parsing library")
     (description
      "This library provides generic parsers for parsing S-expressions from
@@ -3892,9 +3944,9 @@ s-expressions from files or other external sources, you should use
 parsexp_io.")
     (license license:expat)))
 
-(define-public ocaml-sexplib
+(define-public ocaml4.07-sexplib
   (package
-    (name "ocaml-sexplib")
+    (name "ocaml4.07-sexplib")
     (version "0.11.0")
     (home-page "https://github.com/janestreet/sexplib")
     (source
@@ -3908,10 +3960,13 @@ parsexp_io.")
         (base32
          "1qfl0m04rpcjvc4yw1hzh6r16jpwmap0sa9ax6zjji67dz4szpyb"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-     `(("ocaml-num" ,ocaml-num)
-       ("ocaml-parsexp" ,ocaml-parsexp)
-       ("ocaml-sexplib0" ,ocaml-sexplib0)))
+     `(("ocaml-num" ,(package-with-ocaml4.07 ocaml-num))
+       ("ocaml-parsexp" ,ocaml4.07-parsexp)
+       ("ocaml-sexplib0" ,ocaml4.07-sexplib0)))
     (synopsis
      "Library for serializing OCaml values to and from S-expressions")
     (description
@@ -3919,9 +3974,9 @@ parsexp_io.")
 functionality for parsing and pretty-printing s-expressions.")
     (license license:expat)))
 
-(define-public ocaml-base
+(define-public ocaml4.07-base
   (package
-    (name "ocaml-base")
+    (name "ocaml4.07-base")
     (version "0.11.1")
     (home-page "https://github.com/janestreet/base")
     (source
@@ -3936,14 +3991,16 @@ functionality for parsing and pretty-printing s-expressions.")
          "0j6xb4265jr41vw4fjzak6yr8s30qrnzapnc6rl1dxy8bjai0nir"))))
     (build-system dune-build-system)
     (propagated-inputs
-     `(("ocaml-sexplib0" ,ocaml-sexplib0)))
+     `(("ocaml-sexplib0" ,ocaml4.07-sexplib0)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'build
            ;; make warnings non fatal (jbuilder behaviour)
            (lambda _
-             (invoke "dune" "build" "@install" "--profile=release"))))))
+             (invoke "dune" "build" "@install" "--profile=release"))))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
   (synopsis
     "Full standard library replacement for OCaml")
   (description
@@ -3983,9 +4040,9 @@ so they don't expose everything at toplevel.  For instance, @code{Ast_helper}
 is now @code{Ocaml_common.Ast_helper}.")
     (license license:expat)))
 
-(define-public ocaml-stdio
+(define-public ocaml4.07-stdio
   (package
-    (name "ocaml-stdio")
+    (name "ocaml4.07-stdio")
     (version "0.11.0")
     (home-page "https://github.com/janestreet/stdio")
     (source
@@ -4000,10 +4057,12 @@ is now @code{Ocaml_common.Ast_helper}.")
          "1facajqhvq34g2wrg368y0ajxd6lrj5b3lyzyj0jhdmraxajjcwn"))))
     (build-system dune-build-system)
     (propagated-inputs
-     `(("ocaml-base" ,ocaml-base)
-       ("ocaml-sexplib0" ,ocaml-sexplib0)))
+     `(("ocaml-base" ,ocaml4.07-base)
+       ("ocaml-sexplib0" ,ocaml4.07-sexplib0)))
     (arguments
-     '(#:tests? #f)) ;no tests
+     `(#:tests? #f ;no tests
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (synopsis "Standard IO library for OCaml")
     (description
      "Stdio implements simple input/output functionalities for OCaml.  It
@@ -4038,9 +4097,9 @@ ppx_deriving and ppx_type_conv to inter-operate gracefully when linked
 as part of the same ocaml-migrate-parsetree driver.")
     (license license:bsd-3)))
 
-(define-public ocaml-ppxlib
+(define-public ocaml4.07-ppxlib
   (package
-    (name "ocaml-ppxlib")
+    (name "ocaml4.07-ppxlib")
     (version "0.6.0")
     (home-page "https://github.com/ocaml-ppx/ppxlib")
     (source
@@ -4055,15 +4114,16 @@ as part of the same ocaml-migrate-parsetree driver.")
          "0my9x7sxb329h0lzshppdaawiyfbaw6g5f41yiy7bhl071rnlvbv"))))
     (build-system dune-build-system)
     (propagated-inputs
-     `(("ocaml-base" ,ocaml-base)
-       ("ocaml-compiler-libs" ,ocaml-compiler-libs)
-       ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-       ("ocaml-ppx-derivers" ,ocaml-ppx-derivers)
-       ("ocaml-stdio" ,ocaml-stdio)
-       ("ocaml-result" ,ocaml-result)
-       ("ocaml-sexplib0" ,ocaml-sexplib0)))
+     `(("ocaml-base" ,ocaml4.07-base)
+       ("ocaml-compiler-libs" ,(package-with-ocaml4.07 ocaml-compiler-libs))
+       ("ocaml-migrate-parsetree"
+        ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+       ("ocaml-ppx-derivers" ,(package-with-ocaml4.07 ocaml-ppx-derivers))
+       ("ocaml-stdio" ,ocaml4.07-stdio)
+       ("ocaml-result" ,(package-with-ocaml4.07 ocaml-result))
+       ("ocaml-sexplib0" ,ocaml4.07-sexplib0)))
     (arguments
-     '(#:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-before 'check 'set-topfind
            (lambda* (#:key inputs #:allow-other-keys)
@@ -4081,7 +4141,9 @@ as part of the same ocaml-migrate-parsetree driver.")
                  (("#use \"topfind\";;" all)
                   (string-append "#directory \"" findlib-libdir "\"\n"
                                  all))))
-             #t)))))
+             #t)))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (synopsis
      "Base library and tools for ppx rewriters")
     (description
@@ -4099,9 +4161,9 @@ OCaml AST in the OCaml syntax;
 @end itemize")
     (license license:expat)))
 
-(define-public ocaml-ppx-compare
+(define-public ocaml4.07-ppx-compare
   (package
-    (name "ocaml-ppx-compare")
+    (name "ocaml4.07-ppx-compare")
     (version "0.11.1")
     (source (origin
               (method git-fetch)
@@ -4114,9 +4176,13 @@ OCaml AST in the OCaml syntax;
                 "06bq4m1bsm4jlx4g7wh5m99qky7xm4c2g52kaz6pv25hdn5agi2m"))))
     (build-system dune-build-system)
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (properties `((upstream-name . "ppx_compare")))
     (home-page "https://github.com/janestreet/ppx_compare")
     (synopsis "Generation of comparison functions from types")
@@ -4128,9 +4194,9 @@ flexibility by allowing you to override them for a specific type and more safety
 by making sure that you only compare comparable values.")
     (license license:asl2.0)))
 
-(define-public ocaml-fieldslib
+(define-public ocaml4.07-fieldslib
   (package
-    (name "ocaml-fieldslib")
+    (name "ocaml4.07-fieldslib")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4143,11 +4209,14 @@ by making sure that you only compare comparable values.")
     (build-system dune-build-system)
     (arguments
      ;; No tests
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "fieldslib")))
     (home-page "https://github.com/janestreet/fieldslib")
     (synopsis "Syntax extension to record fields")
@@ -4156,9 +4225,9 @@ record fields, to get and set record fields, iterate and fold over all fields
 of a record and create new record values.")
     (license license:asl2.0)))
 
-(define-public ocaml-variantslib
+(define-public ocaml4.07-variantslib
   (package
-    (name "ocaml-variantslib")
+    (name "ocaml4.07-variantslib")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4171,11 +4240,14 @@ of a record and create new record values.")
     (build-system dune-build-system)
     (arguments
      ;; No tests
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "variantslib")))
     (home-page "https://github.com/janestreet/variantslib")
     (synopsis "OCaml variants as first class values")
@@ -4183,9 +4255,9 @@ of a record and create new record values.")
 standard library.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-fields-conv
+(define-public ocaml4.07-ppx-fields-conv
   (package
-    (name "ocaml-ppx-fields-conv")
+    (name "ocaml4.07-ppx-fields-conv")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4197,10 +4269,14 @@ standard library.")
                 "07zrd3qky2ppbfl55gpm90rvqa5860xgwcsvihrjmkrw6d0jirkc"))))
     (build-system dune-build-system)
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-fieldslib" ,ocaml-fieldslib)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-fieldslib" ,ocaml4.07-fieldslib)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (properties `((upstream-name . "ppx_fields_conv")))
     (home-page "https://github.com/janestreet/ppx_fields_conv")
     (synopsis "Generation of accessor and iteration functions for ocaml records")
@@ -4210,9 +4286,9 @@ and set record fields, iterate and fold over all fields of a record and create
 new record values.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-sexp-conv
+(define-public ocaml4.07-ppx-sexp-conv
   (package
-    (name "ocaml-ppx-sexp-conv")
+    (name "ocaml4.07-ppx-sexp-conv")
     (version "0.11.2")
     (source (origin
               (method git-fetch)
@@ -4225,9 +4301,13 @@ new record values.")
                 "0pqwnqy1xp309wvdcaax4lg02yk64lq2w03mbgfvf6ps5ry4gis9"))))
     (build-system dune-build-system)
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (properties `((upstream-name . "ppx_sexp_conv")))
     (home-page "https://github.com/janestreet/ppx_sexp_conv")
     (synopsis "Generation of S-expression conversion functions from type definitions")
@@ -4235,9 +4315,9 @@ new record values.")
 definitions.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-variants-conv
+(define-public ocaml4.07-ppx-variants-conv
   (package
-    (name "ocaml-ppx-variants-conv")
+    (name "ocaml4.07-ppx-variants-conv")
     (version "0.11.1")
     (source (origin
               (method git-fetch)
@@ -4250,10 +4330,14 @@ definitions.")
                 "1yc0gsds5m2nv39zga8nnrca2n75rkqy5dz4xj1635ybz20hhbjd"))))
     (build-system dune-build-system)
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-variantslib" ,ocaml-variantslib)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-variantslib" ,ocaml4.07-variantslib)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (properties
       `((upstream-name . "ppx_variants_conv")))
     (home-page
@@ -4264,9 +4348,9 @@ definitions.")
 variant types.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-custom-printf
+(define-public ocaml4.07-ppx-custom-printf
   (package
-    (name "ocaml-ppx-custom-printf")
+    (name "ocaml4.07-ppx-custom-printf")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4278,10 +4362,14 @@ variant types.")
                 "11b73smf3g3bpd9lg014pr4rx285nk9mnk6g6464ph51jv0sqzhj"))))
     (build-system dune-build-system)
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (properties `((upstream-name . "ppx_custom_printf")))
     (home-page "https://github.com/janestreet/ppx_custom_printf")
     (synopsis "Printf-style format-strings for user-defined string conversion")
@@ -4289,9 +4377,9 @@ variant types.")
 string conversion.")
     (license license:asl2.0)))
 
-(define-public ocaml-bin-prot
+(define-public ocaml4.07-bin-prot
   (package
-    (name "ocaml-bin-prot")
+    (name "ocaml4.07-bin-prot")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4303,13 +4391,17 @@ string conversion.")
                 "1rsd91gx36prj4whi76nsiz1bzpgal9nzyw3pxdz1alv4ilk2il6"))))
     (build-system dune-build-system)
     (inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-ppx-compare" ,ocaml-ppx-compare)
-        ("ocaml-ppx-custom-printf" ,ocaml-ppx-custom-printf)
-        ("ocaml-ppx-fields-conv" ,ocaml-ppx-fields-conv)
-        ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)
-        ("ocaml-ppx-variants-conv" ,ocaml-ppx-variants-conv)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare)
+        ("ocaml-ppx-custom-printf" ,ocaml4.07-ppx-custom-printf)
+        ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv)
+        ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)
+        ("ocaml-ppx-variants-conv" ,ocaml4.07-ppx-variants-conv)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))))
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (properties `((upstream-name . "bin_prot")))
     (home-page "https://github.com/janestreet/bin_prot")
     (synopsis "Binary protocol generator")
@@ -4343,9 +4435,9 @@ storage of large amounts of data.")
     (description "Octavius is a library to parse the `ocamldoc` comment syntax.")
     (license license:isc)))
 
-(define-public ocaml-ppx-hash
+(define-public ocaml4.07-ppx-hash
   (package
-    (name "ocaml-ppx-hash")
+    (name "ocaml4.07-ppx-hash")
     (version "0.11.1")
     (source (origin
               (method git-fetch)
@@ -4358,11 +4450,15 @@ storage of large amounts of data.")
                 "1p0ic6aijxlrdggpmycj12q3cy9xksbq2vq727215maz4snvlf5p"))))
     (build-system dune-build-system)
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-ppx-compare" ,ocaml-ppx-compare)
-        ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare)
+        ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (properties `((upstream-name . "ppx_hash")))
     (home-page "https://github.com/janestreet/ppx_hash")
     (synopsis "Generation of hash functions from type expressions and definitions")
@@ -4370,9 +4466,9 @@ storage of large amounts of data.")
 hash functions from type exrpessions and definitions.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-enumerate
+(define-public ocaml4.07-ppx-enumerate
   (package
-    (name "ocaml-ppx-enumerate")
+    (name "ocaml4.07-ppx-enumerate")
     (version "0.11.1")
     (source (origin
               (method git-fetch)
@@ -4385,11 +4481,14 @@ hash functions from type exrpessions and definitions.")
                 "0spx9k1v7vjjb6sigbfs69yndgq76v114jhxvzjmffw7q989cyhr"))))
     (build-system dune-build-system)
     (arguments
-     `(#:tests? #f))                    ; no test suite
+     `(#:tests? #f; no test suite
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_enumerate")))
     (home-page "https://github.com/janestreet/ppx_enumerate")
     (synopsis "Generate a list containing all values of a finite type")
@@ -4398,9 +4497,9 @@ for the list of all values of a type (for a type which only has finitely
 many values).")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-bench
+(define-public ocaml4.07-ppx-bench
   (package
-    (name "ocaml-ppx-bench")
+    (name "ocaml4.07-ppx-bench")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4413,20 +4512,23 @@ many values).")
     (build-system dune-build-system)
     (arguments
      ;; No tests
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-ppx-inline-test" ,ocaml-ppx-inline-test)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_bench")))
     (home-page "https://github.com/janestreet/ppx_bench")
     (synopsis "Syntax extension for writing in-line benchmarks in ocaml code")
     (description "Syntax extension for writing in-line benchmarks in ocaml code.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-here
+(define-public ocaml4.07-ppx-here
   (package
-    (name "ocaml-ppx-here")
+    (name "ocaml4.07-ppx-here")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4439,11 +4541,14 @@ many values).")
     (build-system dune-build-system)
     (arguments
      ;; broken tests
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_here")))
     (home-page "https://github.com/janestreet/ppx_here")
     (synopsis "Expands [%here] into its location")
@@ -4451,9 +4556,9 @@ many values).")
       "Part of the Jane Street's PPX rewriters collection.")
     (license license:asl2.0)))
 
-(define-public ocaml-typerep
+(define-public ocaml4.07-typerep
   (package
-    (name "ocaml-typerep")
+    (name "ocaml4.07-typerep")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4465,16 +4570,18 @@ many values).")
                 "1zi7hy0prpgzqhr4lkacr04wvlvbp21jfbdfvffhrm6cd400rb5v"))))
     (build-system dune-build-system)
     (arguments
-     `(#:tests? #f))
-    (propagated-inputs `(("ocaml-base" ,ocaml-base)))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
+    (propagated-inputs `(("ocaml-base" ,ocaml4.07-base)))
     (home-page "https://github.com/janestreet/typerep")
     (synopsis "Typerep is a library for runtime types")
     (description "Typerep is a library for runtime types.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-sexp-value
+(define-public ocaml4.07-ppx-sexp-value
   (package
-    (name "ocaml-ppx-sexp-value")
+    (name "ocaml4.07-ppx-sexp-value")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4485,12 +4592,16 @@ many values).")
                (base32
                 "1xnalfrln6k5khsyxvxkg6v32q8fpr4cqamsjqfih29jdv486xrs"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-ppx-here" ,ocaml-ppx-here)
-        ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-ppx-here" ,ocaml4.07-ppx-here)
+        ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_sexp_value")))
     (home-page "https://github.com/janestreet/ppx_sexp_value")
     (synopsis "Simplify building s-expressions from ocaml values")
@@ -4498,9 +4609,9 @@ many values).")
 ocaml values.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-sexp-message
+(define-public ocaml4.07-ppx-sexp-message
   (package
-    (name "ocaml-ppx-sexp-message")
+    (name "ocaml4.07-ppx-sexp-message")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4511,12 +4622,16 @@ ocaml values.")
                (base32
                 "1yh440za0w9cvrbxbmqacir8715kdaw6sw24ys9xj80av9nqpiw7"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-ppx-here" ,ocaml-ppx-here)
-        ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-ppx-here" ,ocaml4.07-ppx-here)
+        ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_sexp_message")))
     (home-page "https://github.com/janestreet/ppx_sexp_message")
     (synopsis "A ppx rewriter for easy construction of s-expressions")
@@ -4526,9 +4641,9 @@ where one needs to construct a s-expression based on various element of the
 context such as function arguments.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-pipebang
+(define-public ocaml4.07-ppx-pipebang
   (package
-    (name "ocaml-ppx-pipebang")
+    (name "ocaml4.07-ppx-pipebang")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4541,10 +4656,13 @@ context such as function arguments.")
     (build-system dune-build-system)
     (arguments
      ;; No tests
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_pipebang")))
     (home-page "https://github.com/janestreet/ppx_pipebang")
     (synopsis "Inline reverse application operators `|>` and `|!`")
@@ -4552,9 +4670,9 @@ context such as function arguments.")
 @code{|>} and @code{|!}.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-optional
+(define-public ocaml4.07-ppx-optional
   (package
-    (name "ocaml-ppx-optional")
+    (name "ocaml4.07-ppx-optional")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4567,11 +4685,14 @@ context such as function arguments.")
     (build-system dune-build-system)
     (arguments
      ;; No tests
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_optional")))
     (home-page "https://github.com/janestreet/ppx_optional")
     (synopsis "Pattern matching on flat options")
@@ -4580,9 +4701,9 @@ context such as function arguments.")
 else expression.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-optcomp
+(define-public ocaml4.07-ppx-optcomp
   (package
-    (name "ocaml-ppx-optcomp")
+    (name "ocaml4.07-ppx-optcomp")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4593,10 +4714,13 @@ else expression.")
                (base32
                 "1bb52p2j2h4s9f06vrcpla80rj93jinnzq6jzilapyx9q068929i"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-stdio" ,ocaml-stdio)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-stdio" ,ocaml4.07-stdio)
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_optcomp")))
     (home-page "https://github.com/janestreet/ppx_optcomp")
     (synopsis "Optional compilation for OCaml")
@@ -4605,9 +4729,9 @@ used to handle optional compilations of pieces of code depending of the word
 size, the version of the compiler, ...")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-let
+(define-public ocaml4.07-ppx-let
   (package
-    (name "ocaml-ppx-let")
+    (name "ocaml4.07-ppx-let")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4618,10 +4742,14 @@ size, the version of the compiler, ...")
                (base32
                 "1wdfw6w4xbg97a35yg6bif9gggxniy9ddnrjfw1a0inkl2yamxkj"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_let")))
     (home-page "https://github.com/janestreet/ppx_let")
     (synopsis "Monadic let-bindings")
@@ -4629,9 +4757,9 @@ size, the version of the compiler, ...")
 match expressions, and if expressions.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-fail
+(define-public ocaml4.07-ppx-fail
   (package
-    (name "ocaml-ppx-fail")
+    (name "ocaml4.07-ppx-fail")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4642,11 +4770,15 @@ match expressions, and if expressions.")
                (base32
                 "07plqsvljiwvngggfypwq55g46s5my55y45mvlmalrxyppzr03s8"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-ppx-here" ,ocaml-ppx-here)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-ppx-here" ,ocaml4.07-ppx-here)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_fail")))
     (home-page "https://github.com/janestreet/ppx_fail")
     (synopsis "Add location to calls to failwiths")
@@ -4654,9 +4786,9 @@ match expressions, and if expressions.")
 position.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-assert
+(define-public ocaml4.07-ppx-assert
   (package
-    (name "ocaml-ppx-assert")
+    (name "ocaml4.07-ppx-assert")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4667,13 +4799,17 @@ position.")
                (base32
                 "17kd311n0l9f72gblf9kv8i5rghr106w37x4f0m5qwh6nlgl0j9k"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-ppx-compare" ,ocaml-ppx-compare)
-        ("ocaml-ppx-here" ,ocaml-ppx-here)
-        ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare)
+        ("ocaml-ppx-here" ,ocaml4.07-ppx-here)
+        ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_assert")))
     (home-page "https://github.com/janestreet/ppx_assert")
     (synopsis "Assert-like extension nodes that raise useful errors on failure")
@@ -4681,9 +4817,9 @@ position.")
 useful errors on failure.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-expect
+(define-public ocaml4.07-ppx-expect
   (package
-    (name "ocaml-ppx-expect")
+    (name "ocaml4.07-ppx-expect")
     (version "0.12.0")
     (source (origin
               (method git-fetch)
@@ -4696,21 +4832,24 @@ useful errors on failure.")
                 "1wawsbjfkri4sw52n8xqrzihxc3xfpdicv3ahz83a1rsn4lb8j5q"))))
     (build-system dune-build-system)
     (arguments
-     `(#:jbuild? #t))
+     `(#:jbuild? #t
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-ppx-assert" ,ocaml-ppx-assert)
-        ("ocaml-ppx-compare" ,ocaml-ppx-compare)
-        ("ocaml-ppx-custom-printf" ,ocaml-ppx-custom-printf)
-        ("ocaml-ppx-fields-conv" ,ocaml-ppx-fields-conv)
-        ("ocaml-ppx-here" ,ocaml-ppx-here)
-        ("ocaml-ppx-inline-test" ,ocaml-ppx-inline-test)
-        ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)
-        ("ocaml-ppx-variants-conv" ,ocaml-ppx-variants-conv)
-        ("ocaml-stdio" ,ocaml-stdio)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)
-        ("ocaml-re" ,ocaml-re)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-ppx-assert" ,ocaml4.07-ppx-assert)
+        ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare)
+        ("ocaml-ppx-custom-printf" ,ocaml4.07-ppx-custom-printf)
+        ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv)
+        ("ocaml-ppx-here" ,ocaml4.07-ppx-here)
+        ("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test)
+        ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)
+        ("ocaml-ppx-variants-conv" ,ocaml4.07-ppx-variants-conv)
+        ("ocaml-stdio" ,ocaml4.07-stdio)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)
+        ("ocaml-re" ,(package-with-ocaml4.07 ocaml-re))))
     (properties `((upstream-name . "ppx_expect")))
     (home-page "https://github.com/janestreet/ppx_expect")
     (synopsis "Cram like framework for OCaml")
@@ -4721,9 +4860,9 @@ output-generating code, interleaved with @code{%expect} extension expressions
 to denote the expected output.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-js-style
+(define-public ocaml4.07-ppx-js-style
   (package
-    (name "ocaml-ppx-js-style")
+    (name "ocaml4.07-ppx-js-style")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4736,12 +4875,15 @@ to denote the expected output.")
     (build-system dune-build-system)
     (arguments
      ;; No tests
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-octavius" ,ocaml-octavius)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-octavius" ,(package-with-ocaml4.07 ocaml-octavius))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_js_style")))
     (home-page "https://github.com/janestreet/ppx_js_style")
     (synopsis "Code style checker for Jane Street Packages")
@@ -4750,9 +4892,9 @@ to denote the expected output.")
 packages.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-typerep-conv
+(define-public ocaml4.07-ppx-typerep-conv
   (package
-    (name "ocaml-ppx-typerep-conv")
+    (name "ocaml4.07-ppx-typerep-conv")
     (version "0.11.1")
     (source (origin
               (method git-fetch)
@@ -4765,12 +4907,15 @@ packages.")
                 "0a13dpfrrg0rsm8qni1bh7pqcda30l70z8r6yzi5a64bmwk7g5ah"))))
     (build-system dune-build-system)
     (arguments
-     `(#:test-target "."))
+     `(#:test-target "."
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-typerep" ,ocaml-typerep)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-typerep" ,ocaml4.07-typerep)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_typerep_conv")))
     (home-page "https://github.com/janestreet/ppx_typerep_conv")
     (synopsis "Generation of runtime types from type declarations")
@@ -4778,9 +4923,9 @@ packages.")
 from type definitions.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-base
+(define-public ocaml4.07-ppx-base
   (package
-    (name "ocaml-ppx-base")
+    (name "ocaml4.07-ppx-base")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4792,15 +4937,18 @@ from type definitions.")
                 "0aq206pg330jmj7lhcagiiwm3a0b3gsqm801m8ajd4ysyw7idkym"))))
     (build-system dune-build-system)
     (arguments
-     `(#:test-target "."))
+     `(#:test-target "."
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-ppx-compare" ,ocaml-ppx-compare)
-        ("ocaml-ppx-enumerate" ,ocaml-ppx-enumerate)
-        ("ocaml-ppx-hash" ,ocaml-ppx-hash)
-        ("ocaml-ppx-js-style" ,ocaml-ppx-js-style)
-        ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-ppx-compare" ,ocaml4.07-ppx-compare)
+        ("ocaml-ppx-enumerate" ,ocaml4.07-ppx-enumerate)
+        ("ocaml-ppx-hash" ,ocaml4.07-ppx-hash)
+        ("ocaml-ppx-js-style" ,ocaml4.07-ppx-js-style)
+        ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_base")))
     (home-page "https://github.com/janestreet/ppx_base")
     (synopsis "Base set of ppx rewriters")
@@ -4810,9 +4958,9 @@ Note that Base doesn't need ppx to build, it is only used as a
 verification tool.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-bin-prot
+(define-public ocaml4.07-ppx-bin-prot
   (package
-    (name "ocaml-ppx-bin-prot")
+    (name "ocaml4.07-ppx-bin-prot")
     (version "0.11.1")
     (source (origin
               (method git-fetch)
@@ -4826,13 +4974,16 @@ verification tool.")
     (build-system dune-build-system)
     (arguments
      ;; Cyclic dependency with ocaml-ppx-jane
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-bin-prot" ,ocaml-bin-prot)
-        ("ocaml-ppx-here" ,ocaml-ppx-here)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-bin-prot" ,ocaml4.07-bin-prot)
+        ("ocaml-ppx-here" ,ocaml4.07-ppx-here)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_bin_prot")))
     (home-page "https://github.com/janestreet/ppx_bin_prot")
     (synopsis "Generation of bin_prot readers and writers from types")
@@ -4840,9 +4991,9 @@ verification tool.")
 functions from type definitions.")
     (license license:asl2.0)))
 
-(define-public ocaml-ppx-jane
+(define-public ocaml4.07-ppx-jane
   (package
-    (name "ocaml-ppx-jane")
+    (name "ocaml4.07-ppx-jane")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4854,28 +5005,31 @@ functions from type definitions.")
                 "0lgppkw3aixrfnixihrsz2ipafv8fpvkdpy3pw8n0r615gg8x8la"))))
     (build-system dune-build-system)
     (arguments
-     `(#:test-target "."))
+     `(#:test-target "."
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-ppx-assert" ,ocaml-ppx-assert)
-        ("ocaml-ppx-base" ,ocaml-ppx-base)
-        ("ocaml-ppx-bench" ,ocaml-ppx-bench)
-        ("ocaml-ppx-bin-prot" ,ocaml-ppx-bin-prot)
-        ("ocaml-ppx-custom-printf" ,ocaml-ppx-custom-printf)
-        ("ocaml-ppx-expect" ,ocaml-ppx-expect)
-        ("ocaml-ppx-fail" ,ocaml-ppx-fail)
-        ("ocaml-ppx-fields-conv" ,ocaml-ppx-fields-conv)
-        ("ocaml-ppx-here" ,ocaml-ppx-here)
-        ("ocaml-ppx-inline-test" ,ocaml-ppx-inline-test)
-        ("ocaml-ppx-let" ,ocaml-ppx-let)
-        ("ocaml-ppx-optcomp" ,ocaml-ppx-optcomp)
-        ("ocaml-ppx-optional" ,ocaml-ppx-optional)
-        ("ocaml-ppx-pipebang" ,ocaml-ppx-pipebang)
-        ("ocaml-ppx-sexp-message" ,ocaml-ppx-sexp-message)
-        ("ocaml-ppx-sexp-value" ,ocaml-ppx-sexp-value)
-        ("ocaml-ppx-typerep-conv" ,ocaml-ppx-typerep-conv)
-        ("ocaml-ppx-variants-conv" ,ocaml-ppx-variants-conv)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-ppx-assert" ,ocaml4.07-ppx-assert)
+        ("ocaml-ppx-base" ,ocaml4.07-ppx-base)
+        ("ocaml-ppx-bench" ,ocaml4.07-ppx-bench)
+        ("ocaml-ppx-bin-prot" ,ocaml4.07-ppx-bin-prot)
+        ("ocaml-ppx-custom-printf" ,ocaml4.07-ppx-custom-printf)
+        ("ocaml-ppx-expect" ,ocaml4.07-ppx-expect)
+        ("ocaml-ppx-fail" ,ocaml4.07-ppx-fail)
+        ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv)
+        ("ocaml-ppx-here" ,ocaml4.07-ppx-here)
+        ("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test)
+        ("ocaml-ppx-let" ,ocaml4.07-ppx-let)
+        ("ocaml-ppx-optcomp" ,ocaml4.07-ppx-optcomp)
+        ("ocaml-ppx-optional" ,ocaml4.07-ppx-optional)
+        ("ocaml-ppx-pipebang" ,ocaml4.07-ppx-pipebang)
+        ("ocaml-ppx-sexp-message" ,ocaml4.07-ppx-sexp-message)
+        ("ocaml-ppx-sexp-value" ,ocaml4.07-ppx-sexp-value)
+        ("ocaml-ppx-typerep-conv" ,ocaml4.07-ppx-typerep-conv)
+        ("ocaml-ppx-variants-conv" ,ocaml4.07-ppx-variants-conv)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (properties `((upstream-name . "ppx_jane")))
     (home-page "https://github.com/janestreet/ppx_jane")
     (synopsis "Standard Jane Street ppx rewriters")
@@ -4883,9 +5037,9 @@ functions from type definitions.")
 driver including all standard Jane Street ppx rewriters.")
     (license license:asl2.0)))
 
-(define-public ocaml-splittable-random
+(define-public ocaml4.07-splittable-random
   (package
-    (name "ocaml-splittable-random")
+    (name "ocaml4.07-splittable-random")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4896,10 +5050,14 @@ driver including all standard Jane Street ppx rewriters.")
                (base32
                 "0l1wbd881mymlnpzlq5q53mmdz3g5d7qjhyc7lfaq1x0iaccn5lc"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-ppx-jane" ,ocaml-ppx-jane)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-ppx-jane" ,ocaml4.07-ppx-jane)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))))
     (properties `((upstream-name . "splittable_random")))
     (home-page "https://github.com/janestreet/splittable_random")
     (synopsis "PRNG that can be split into independent streams")
@@ -4933,9 +5091,9 @@ cryptographic-quality randomness in favor of performance.")
 various Jane Street packages.")
     (license license:asl2.0)))
 
-(define-public ocaml-configurator
+(define-public ocaml4.07-configurator
   (package
-    (name "ocaml-configurator")
+    (name "ocaml4.07-configurator")
     (version "0.11.0")
     (source (origin
               (method url-fetch)
@@ -4948,10 +5106,12 @@ various Jane Street packages.")
     (build-system dune-build-system)
     (arguments
      ;; No tests
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-stdio" ,ocaml-stdio)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-stdio" ,ocaml4.07-stdio)))
     (home-page "https://github.com/janestreet/configurator")
     (synopsis "Helper library for gathering system configuration")
     (description "Configurator is a small library that helps writing OCaml
@@ -4967,9 +5127,9 @@ Configurator allows one to:
 @end itemize")
     (license license:asl2.0)))
 
-(define-public ocaml-spawn
+(define-public ocaml4.07-spawn
   (package
-    (name "ocaml-spawn")
+    (name "ocaml4.07-spawn")
     (version "0.13.0")
     (source (origin
               (method git-fetch)
@@ -4989,9 +5149,11 @@ Configurator allows one to:
              (substitute* "test/tests.ml"
                (("/bin/pwd") (which "pwd"))
                (("/bin/echo") (which "echo")))
-             #t)))))
+             #t)))
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (native-inputs
-     `(("ocaml-ppx-expect" ,ocaml-ppx-expect)))
+     `(("ocaml-ppx-expect" ,ocaml4.07-ppx-expect)))
     (home-page "https://github.com/janestreet/spawn")
     (synopsis "Spawning sub-processes")
     (description
@@ -5013,9 +5175,9 @@ thousands of times faster than fork.
 @end itemize")
     (license license:asl2.0)))
 
-(define-public ocaml-core
+(define-public ocaml4.07-core
   (package
-    (name "ocaml-core")
+    (name "ocaml4.07-core")
     (version "0.11.3")
     (source (origin
               (method git-fetch)
@@ -5030,18 +5192,21 @@ thousands of times faster than fork.
     (arguments
      `(#:jbuild? #t
        ;; Require a cyclic dependency: core_extended
-       #:tests? #f))
+       #:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-configurator" ,ocaml-configurator)
-        ("ocaml-core-kernel" ,ocaml-core-kernel)
-        ("ocaml-ppx-assert" ,ocaml-ppx-assert)
-        ("ocaml-ppx-jane" ,ocaml-ppx-jane)
-        ("ocaml-sexplib" ,ocaml-sexplib)
-        ("ocaml-spawn" ,ocaml-spawn)
-        ("ocaml-stdio" ,ocaml-stdio)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
-        ("ocaml-ppxlib" ,ocaml-ppxlib)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-configurator" ,ocaml4.07-configurator)
+        ("ocaml-core-kernel" ,ocaml4.07-core-kernel)
+        ("ocaml-ppx-assert" ,ocaml4.07-ppx-assert)
+        ("ocaml-ppx-jane" ,ocaml4.07-ppx-jane)
+        ("ocaml-sexplib" ,ocaml4.07-sexplib)
+        ("ocaml-spawn" ,ocaml4.07-spawn)
+        ("ocaml-stdio" ,ocaml4.07-stdio)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))
+        ("ocaml-ppxlib" ,ocaml4.07-ppxlib)))
     (home-page "https://github.com/janestreet/core")
     (synopsis "Alternative to OCaml's standard library")
     (description "The Core suite of libraries is an alternative to OCaml's
@@ -5050,9 +5215,9 @@ standard library that was developed by Jane Street.")
     ;; by OCaml's license for consortium members (see THIRD-PARTY.txt).
     (license license:asl2.0)))
 
-(define-public ocaml-core-kernel
+(define-public ocaml4.07-core-kernel
   (package
-    (name "ocaml-core-kernel")
+    (name "ocaml4.07-core-kernel")
     (version "0.11.1")
     (source (origin
               (method git-fetch)
@@ -5066,26 +5231,30 @@ standard library that was developed by Jane Street.")
     (build-system dune-build-system)
     (arguments
      ;; Cyclic dependency with ocaml-core
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib))
     (propagated-inputs
-      `(("ocaml-base" ,ocaml-base)
-        ("ocaml-bin-prot" ,ocaml-bin-prot)
-        ("ocaml-configurator" ,ocaml-configurator)
-        ("ocaml-fieldslib" ,ocaml-fieldslib)
-        ("ocaml-jane-street-headers" ,ocaml-jane-street-headers)
-        ("ocaml-ppx-assert" ,ocaml-ppx-assert)
-        ("ocaml-ppx-base" ,ocaml-ppx-base)
-        ("ocaml-ppx-hash" ,ocaml-ppx-hash)
-        ("ocaml-ppx-inline-test" ,ocaml-ppx-inline-test)
-        ("ocaml-ppx-jane" ,ocaml-ppx-jane)
-        ("ocaml-ppx-sexp-conv" ,ocaml-ppx-sexp-conv)
-        ("ocaml-ppx-sexp-message" ,ocaml-ppx-sexp-message)
-        ("ocaml-sexplib" ,ocaml-sexplib)
-        ("ocaml-splittable-random" ,ocaml-splittable-random)
-        ("ocaml-stdio" ,ocaml-stdio)
-        ("ocaml-typerep" ,ocaml-typerep)
-        ("ocaml-variantslib" ,ocaml-variantslib)
-        ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)))
+      `(("ocaml-base" ,ocaml4.07-base)
+        ("ocaml-bin-prot" ,ocaml4.07-bin-prot)
+        ("ocaml-configurator" ,ocaml4.07-configurator)
+        ("ocaml-fieldslib" ,ocaml4.07-fieldslib)
+        ("ocaml-jane-street-headers"
+         ,(package-with-ocaml4.07 ocaml-jane-street-headers))
+        ("ocaml-ppx-assert" ,ocaml4.07-ppx-assert)
+        ("ocaml-ppx-base" ,ocaml4.07-ppx-base)
+        ("ocaml-ppx-hash" ,ocaml4.07-ppx-hash)
+        ("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test)
+        ("ocaml-ppx-jane" ,ocaml4.07-ppx-jane)
+        ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv)
+        ("ocaml-ppx-sexp-message" ,ocaml4.07-ppx-sexp-message)
+        ("ocaml-sexplib" ,ocaml4.07-sexplib)
+        ("ocaml-splittable-random" ,ocaml4.07-splittable-random)
+        ("ocaml-stdio" ,ocaml4.07-stdio)
+        ("ocaml-typerep" ,ocaml4.07-typerep)
+        ("ocaml-variantslib" ,ocaml4.07-variantslib)
+        ("ocaml-migrate-parsetree"
+         ,(package-with-ocaml4.07 ocaml-migrate-parsetree))))
     (properties `((upstream-name . "core_kernel")))
     (home-page "https://github.com/janestreet/core_kernel")
     (synopsis "Portable standard library for OCaml")
@@ -5225,9 +5394,9 @@ Usage is simple - add package bisect_ppx when building tests, run your tests,
 then run the Bisect_ppx report tool on the generated visitation files.")
     (license license:mpl2.0)))
 
-(define-public ocaml-odoc
+(define-public ocaml4.07-odoc
   (package
-    (name "ocaml-odoc")
+    (name "ocaml4.07-odoc")
     (version "1.4.2")
     (source
      (origin
@@ -5239,20 +5408,24 @@ then run the Bisect_ppx report tool on the generated visitation files.")
        (sha256
         (base32 "0rvhx139jx6wmlfz355mja6mk03x4swq1xxvk5ky6jzhalq3cf5i"))))
     (build-system dune-build-system)
+    (arguments
+     `(#:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib
+       #:dune ,ocaml4.07-dune))
     (inputs
-     `(("ocaml-alcotest" ,ocaml-alcotest)
-       ("ocaml-markup" ,ocaml-markup)
-       ("ocaml-sexplib" ,ocaml-sexplib)
-       ("ocaml-re" ,ocaml-re)
-       ("ocaml-uutf" ,ocaml-uutf)))
+     `(("ocaml-alcotest" ,(package-with-ocaml4.07 ocaml-alcotest))
+       ("ocaml-markup" ,(package-with-ocaml4.07 ocaml-markup))
+       ("ocaml-sexplib" ,ocaml4.07-sexplib)
+       ("ocaml-re" ,(package-with-ocaml4.07 ocaml-re))
+       ("ocaml-uutf" ,(package-with-ocaml4.07 ocaml-uutf))))
     (native-inputs
-     `(("ocaml-astring" ,ocaml-astring)
-       ("ocaml-cmdliner" ,ocaml-cmdliner)
-       ("ocaml-cppo" ,ocaml-cppo)
-       ("ocaml-fpath" ,ocaml-fpath)
-       ("ocaml-result" ,ocaml-result)
-       ("ocaml-tyxml" ,ocaml-tyxml)
-       ("ocaml-bisect-ppx" ,ocaml-bisect-ppx)))
+     `(("ocaml-astring" ,(package-with-ocaml4.07 ocaml-astring))
+       ("ocaml-cmdliner" ,(package-with-ocaml4.07 ocaml-cmdliner))
+       ("ocaml-cppo" ,(package-with-ocaml4.07 ocaml-cppo))
+       ("ocaml-fpath" ,(package-with-ocaml4.07 ocaml-fpath))
+       ("ocaml-result" ,(package-with-ocaml4.07 ocaml-result))
+       ("ocaml-tyxml" ,(package-with-ocaml4.07 ocaml-tyxml))
+       ("ocaml-bisect-ppx" ,(package-with-ocaml4.07 ocaml-bisect-ppx))))
     (home-page "https://github.com/ocaml/odoc")
     (synopsis "OCaml documentation generator")
     (description "Odoc is a documentation generator for OCaml.  It reads
@@ -5264,9 +5437,9 @@ advantage over ocamldoc is an accurate cross-referencer, which handles the
 complexity of the OCaml module system.")
     (license license:isc)))
 
-(define-public ocaml-fftw3
+(define-public ocaml4.07-fftw3
   (package
-    (name "ocaml-fftw3")
+    (name "ocaml4.07-fftw3")
     (version "0.8.4")
     (source
      (origin
@@ -5281,13 +5454,16 @@ complexity of the OCaml module system.")
     (build-system dune-build-system)
     (arguments
      `(#:tests? #t
-       #:test-target "tests"))
+       #:test-target "tests"
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib
+       #:dune ,ocaml4.07-dune))
     (propagated-inputs
      `(("fftw" ,fftw)
        ("fftwf" ,fftwf)))
     (native-inputs
-     `(("ocaml-cppo" ,ocaml-cppo)
-       ("ocaml-lacaml" ,ocaml-lacaml)))
+     `(("ocaml-cppo" ,(package-with-ocaml4.07 ocaml-cppo))
+       ("ocaml-lacaml" ,ocaml4.07-lacaml)))
     (home-page
      "https://github.com/Chris00/fftw-ocaml")
     (synopsis
@@ -5297,9 +5473,9 @@ complexity of the OCaml module system.")
 library FFTW.")
     (license license:lgpl2.1))) ; with static linking exception.
 
-(define-public ocaml-lacaml
+(define-public ocaml4.07-lacaml
   (package
-    (name "ocaml-lacaml")
+    (name "ocaml4.07-lacaml")
     (version "11.0.5")
     (source
      (origin
@@ -5313,12 +5489,15 @@ library FFTW.")
          "180yb79a3qgx067qcpm50q12hrimjygf06rgkzbish9d1zfm670c"))))
     (build-system dune-build-system)
     (arguments
-     `(#:tests? #f)) ; No test target.
+     `(#:tests? #f ; No test target.
+       #:ocaml ,ocaml-4.07
+       #:findlib ,ocaml4.07-findlib
+       #:dune ,ocaml4.07-dune))
     (native-inputs
      `(("openblas" ,openblas)
        ("lapack" ,lapack)
-       ("ocaml-base" ,ocaml-base)
-       ("ocaml-stdio" ,ocaml-stdio)))
+       ("ocaml-base" ,ocaml4.07-base)
+       ("ocaml-stdio" ,ocaml4.07-stdio)))
     (home-page "https://mmottl.github.io/lacaml/")
     (synopsis
      "OCaml-bindings to BLAS and LAPACK")

From 47ea2ad196a41a3c3de3e5fa970b6881495c0e8f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong@member.fsf.org>
Date: Mon, 27 Jan 2020 11:39:29 +0800
Subject: [PATCH 011/127] gnu: s6: Install documentation.

* gnu/packages/skarnet.scm (s6)[arguments]: Add 'install-doc' phase.
---
 gnu/packages/skarnet.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm
index 3768695a8f..2db42240af 100644
--- a/gnu/packages/skarnet.scm
+++ b/gnu/packages/skarnet.scm
@@ -116,7 +116,7 @@ complexity.")))
    (inputs `(("skalibs" ,skalibs)
              ("execline" ,execline)))
    (arguments
-    '(#:configure-flags (list
+    `(#:configure-flags (list
                         (string-append "--with-lib="
                                        (assoc-ref %build-inputs "skalibs")
                                        "/lib/skalibs")
@@ -126,7 +126,15 @@ complexity.")))
                         (string-append "--with-sysdeps="
                                        (assoc-ref %build-inputs "skalibs")
                                        "/lib/skalibs/sysdeps"))
-      #:tests? #f))                    ; no tests exist
+      #:tests? #f                       ; no tests exist
+      #:phases
+      (modify-phases %standard-phases
+        (add-after 'install 'install-doc
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let* ((out (assoc-ref outputs "out"))
+                   (doc (string-append out "/share/doc/s6-" ,version)))
+              (copy-recursively "doc" doc)
+              #t))))))
    (home-page "https://skarnet.org/software/s6")
    (license isc)
    (synopsis "Small suite of programs for process supervision")

From 71ffa528ef712c69d89981a7fc591b33b8f33c6d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 27 Jan 2020 10:37:35 +0200
Subject: [PATCH 012/127] gnu: keepassxc: Update to 2.5.3.

* gnu/packages/password-utils.scm (keepassxc): Update to 2.5.3.
---
 gnu/packages/password-utils.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index eed0989452..5f297e117a 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -114,7 +114,7 @@ human.")
 (define-public keepassxc
   (package
     (name "keepassxc")
-    (version "2.5.2")
+    (version "2.5.3")
     (source
      (origin
        (method url-fetch)
@@ -122,7 +122,7 @@ human.")
                            "/releases/download/" version "/keepassxc-"
                            version "-src.tar.xz"))
        (sha256
-        (base32 "0lvwc3nxyz7d7vymb6cmgwxylb9g6gsjnq247vbh4lk1ifjir58j"))))
+        (base32 "1sx647mp1xikig50p9bb6vxv18ymdfj3wkxj6qfdr1zfcv7gn005"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags '("-DWITH_XC_ALL=YES"

From 4a0e49279ddc53655f593796b0b1e170369d2a08 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong@member.fsf.org>
Date: Mon, 27 Jan 2020 17:37:34 +0800
Subject: [PATCH 013/127] gnu: public-inbox: Enable support for background
 HTTP/NNTP daemons.

* gnu/packages/mail.scm (public-inbox)[inputs]: Add perl-net-server.
---
 gnu/packages/mail.scm | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index c503b631dc..baae1d29f4 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3169,6 +3169,10 @@ related tools to process winmail.dat files.")
               (substitute* "t/ds-leak.t"
                 (("/bin/sh") (which "sh")))
               (invoke "./certs/create-certs.perl")
+              ;; XXX: This test fails due to zombie process is not reaped by
+              ;; the builder.
+              (substitute* "t/httpd-unix.t"
+                (("^SKIP: \\{") "SKIP: { skip('Guix');"))
               #t))
           (add-after 'install 'wrap-programs
             (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -3199,6 +3203,7 @@ related tools to process winmail.dat files.")
         ("perl-email-mime-contenttype" ,perl-email-mime-contenttype)
         ("perl-email-mime" ,perl-email-mime)
         ("perl-email-simple" ,perl-email-simple)
+        ("perl-net-server" ,perl-net-server)
         ("perl-filesys-notify-simple" ,perl-filesys-notify-simple)
         ("perl-plack-middleware-deflater" ,perl-plack-middleware-deflater)
         ("perl-plack-middleware-reverseproxy" ,perl-plack-middleware-reverseproxy)

From 1f7f16dcedb9703981acc47e5677d7817b39740f Mon Sep 17 00:00:00 2001
From: David Wilson <david@daviwil.com>
Date: Mon, 27 Jan 2020 04:42:14 -0800
Subject: [PATCH 014/127] gnu: emacs-org-make-toc: Update to 0.4.

* gnu/packages/emacs-xyz.scm (emacs-org-make-toc): Update to 0.4
---
 gnu/packages/emacs-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index a528f373ad..c5214405d0 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -12356,7 +12356,7 @@ into sections while preserving the structure imposed by any timestamps.")
 (define-public emacs-org-make-toc
   (package
     (name "emacs-org-make-toc")
-    (version "0.3")
+    (version "0.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -12365,7 +12365,7 @@ into sections while preserving the structure imposed by any timestamps.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0syhj8q4pv33xgl5qa6x27yhwqvfhffw5xqp819hj4qs1ddlc7j5"))))
+                "0348iq3bc3rxs5bqdvskyly4agqxiapamqkfm0323620kxl70agw"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-org" ,emacs-org)

From 5e61de242156cdb3314abac168d9682ca7a4c28f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 27 Jan 2020 14:00:10 +0100
Subject: [PATCH 015/127] gnu: python-testpath: Remove incorrect
 #:imported-modules.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes <https://bugs.gnu.org/39298>.
Reported by Clément Lassieur <clement@lassieur.org>
and Ricardo Wurmus <rekado@elephly.net>.

This pacakge would import (srfi srfi-1) from the host Guile, leading to
build failures when the host Guile is 3.0.

* gnu/packages/check.scm (python-testpath)[arguments]: Remove incorrect
 #:imported-modules.
---
 gnu/packages/check.scm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index e10e684d32..eb2e2d62e2 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -26,7 +26,7 @@
 ;;; Copyright © 2017 ng0 <ng0@n0.is>
 ;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017, 2018, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Chris Marusich <cmmarusich@gmail.com>
@@ -1441,8 +1441,6 @@ C/C++, R, and more, and uploads it to the @code{codecov.io} service.")
        #:modules ((guix build python-build-system)
                   (guix build utils)
                   (srfi srfi-1))
-       #:imported-modules (,@%python-build-system-modules
-                           (srfi srfi-1))
        #:phases
        (modify-phases %standard-phases
          (delete 'install)

From fd6412cd2c28c5b0d863428bbfcf998be1b1a4b0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:23:38 +0100
Subject: [PATCH 016/127] gnu: r-metap: Update to 1.3.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 562e151fef..3fb47884ae 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3165,14 +3165,14 @@ are standardized and usable by the accompanying mutossGUI package.")
 (define-public r-metap
   (package
     (name "r-metap")
-    (version "1.2")
+    (version "1.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "metap" version))
        (sha256
         (base32
-         "0pfbcixjrzx81l9wqhlp55khg9k63zf8pvg2n39c19akr4ppzhvf"))))
+         "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)

From c6b4b4e7198afe5a9747a00ed9df870dc753931d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:23:57 +0100
Subject: [PATCH 017/127] gnu: r-diversitree: Update to 0.9-13.

* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
---
 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 c71adbe98c..82a286b591 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12937,14 +12937,14 @@ analyses in addition to large-scale sequence-level searches.")
 (define-public r-diversitree
   (package
     (name "r-diversitree")
-    (version "0.9-11")
+    (version "0.9-13")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "diversitree" version))
         (sha256
          (base32
-          "1jqfjmmaigq581l4zxysmkhld0xv6izlbr1hihf9zplkix36majc"))))
+          "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))

From f0eecc6be97e3e8eeb879c81d96180aba3609f78 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:24:10 +0100
Subject: [PATCH 018/127] gnu: r-callr: Update to 3.4.1.

* gnu/packages/cran.scm (r-callr): Update to 3.4.1.
---
 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 ff2490bc31..51211f3ff8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -423,14 +423,14 @@ such as copy/paste from an R session.")
 (define-public r-callr
   (package
     (name "r-callr")
-    (version "3.4.0")
+    (version "3.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "callr" version))
        (sha256
         (base32
-         "1hvxw2glizq8g0qnxakcxh8jc5scn0hp1x8i70fdpqwwbgx49slr"))))
+         "0nyba0knzd44zz2xmr7zd9qh3rny0q8msysxf49843d9rlyv6y70"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-r6" ,r-r6)

From 6e27edda2c9987eeacf4782e6468f99dd1e58e63 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:24:23 +0100
Subject: [PATCH 019/127] gnu: r-rgooglemaps: Update to 1.4.5.2.

* gnu/packages/cran.scm (r-rgooglemaps): Update to 1.4.5.2.
---
 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 51211f3ff8..3e22832323 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1293,14 +1293,14 @@ coordinates.")
 (define-public r-rgooglemaps
   (package
     (name "r-rgooglemaps")
-    (version "1.4.5.1")
+    (version "1.4.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RgoogleMaps" version))
        (sha256
         (base32
-         "1lrbl0nax7rzk460mh6rq9hydahdi3ckxk4kxx3xij29jl3lmijh"))))
+         "1y2dinxmzx6mg6ynpk2q7f4k4rxjm66my185gafdcvpc4rl7svs7"))))
     (properties `((upstream-name . "RgoogleMaps")))
     (build-system r-build-system)
     (propagated-inputs `(("r-png" ,r-png)))

From 0be161720c3141f0faa705b03b4a6c585b5cd0bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:24:32 +0100
Subject: [PATCH 020/127] gnu: r-prettyunits: Update to 1.1.1.

* gnu/packages/cran.scm (r-prettyunits): Update to 1.1.1.
---
 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 3e22832323..20836af8d2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2034,14 +2034,14 @@ statistical functions and other utilities to ease their usage.")
 (define-public r-prettyunits
   (package
     (name "r-prettyunits")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "prettyunits" version))
        (sha256
         (base32
-         "0453vvslpkj1ysyv0cy9hw98q5wlnj7bvvz7vzl5ld8ij82lwy5c"))))
+         "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
     (build-system r-build-system)
     (home-page "https://github.com/gaborcsardi/prettyunits")
     (synopsis "Pretty, human readable formatting of quantities")

From fde9fc487153e0051e69bcb2d26e6cdf29de42a8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:24:40 +0100
Subject: [PATCH 021/127] gnu: r-lpsolve: Update to 5.6.15.

* gnu/packages/cran.scm (r-lpsolve): Update to 5.6.15.
---
 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 20836af8d2..6e9e3d0adb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2438,14 +2438,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
 (define-public r-lpsolve
   (package
     (name "r-lpsolve")
-    (version "5.6.13.3")
+    (version "5.6.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lpSolve" version))
        (sha256
         (base32
-         "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
+         "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
     (properties `((upstream-name . "lpSolve")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/lpSolve")

From e5b38da1ccd0212326f663532d694cbe6c955383 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:24:48 +0100
Subject: [PATCH 022/127] gnu: r-broom: Update to 0.5.4.

* gnu/packages/cran.scm (r-broom): Update to 0.5.4.
---
 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 6e9e3d0adb..2efe6bf92a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3065,14 +3065,14 @@ by base R methods related to model fitting.")
 (define-public r-broom
   (package
     (name "r-broom")
-    (version "0.5.3")
+    (version "0.5.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "broom" version))
        (sha256
         (base32
-         "177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d"))))
+         "1w35v1qrg8d0bm7a4gsdqkmrl9nmymsvmamy48vc046a1axzgzq1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)

From 485b9cea5a54c9f21dd1107be8ef6cd93bc642b1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:24:55 +0100
Subject: [PATCH 023/127] gnu: r-xts: Update to 0.12-0.

* gnu/packages/cran.scm (r-xts): Update to 0.12-0.
---
 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 2efe6bf92a..36f5037620 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3563,14 +3563,14 @@ training models for classification or ranking.")
 (define-public r-xts
   (package
     (name "r-xts")
-    (version "0.11-2")
+    (version "0.12-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xts" version))
        (sha256
         (base32
-         "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
+         "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-zoo" ,r-zoo)))
     (home-page "https://github.com/joshuaulrich/xts")

From 8a8e296406fd6254d9199f6612943b827584c43e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:25:03 +0100
Subject: [PATCH 024/127] gnu: r-tsp: Update to 1.1-8.

* gnu/packages/cran.scm (r-tsp): Update to 1.1-8.
---
 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 36f5037620..23b52f5af9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3887,14 +3887,14 @@ timeout.  It can also poll several processes at once.")
 (define-public r-tsp
   (package
     (name "r-tsp")
-    (version "1.1-7")
+    (version "1.1-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TSP" version))
        (sha256
         (base32
-         "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
+         "0g44f2a4m7rfx6y51cdbr6vcmmpbwgyzpvfjksq3lb7gcpbr7xrx"))))
     (properties `((upstream-name . "TSP")))
     (build-system r-build-system)
     (propagated-inputs `(("r-foreach" ,r-foreach)))

From c23b40335d0800da54e73911e5734e58eff11cef Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:25:10 +0100
Subject: [PATCH 025/127] gnu: r-vctrs: Update to 0.2.2.

* gnu/packages/cran.scm (r-vctrs): Update to 0.2.2.
[propagated-inputs]: Remove r-backports and r-zeallot.
---
 gnu/packages/cran.scm | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 23b52f5af9..1437c79a5e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4067,22 +4067,20 @@ to variables on the left-hand side of the assignment.")
 (define-public r-vctrs
   (package
     (name "r-vctrs")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vctrs" version))
        (sha256
         (base32
-         "0rlwjfvvhv3s5mj4lqhwlqwddpizyp46i1qbcvw0mzb5q8b0nkz0"))))
+         "008xjmlj5a5vm303wxac7bliamqwaj7mcj0jv6n9ibc8p8h93aqd"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-backports" ,r-backports)
-       ("r-digest" ,r-digest)
+     `(("r-digest" ,r-digest)
        ("r-ellipsis" ,r-ellipsis)
        ("r-glue" ,r-glue)
-       ("r-rlang" ,r-rlang)
-       ("r-zeallot" ,r-zeallot)))
+       ("r-rlang" ,r-rlang)))
     (home-page "https://github.com/r-lib/vctrs")
     (synopsis "Vector helpers")
     (description

From addf7bc2b1af88f8640250bdd6bb34af16cdaed6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:25:37 +0100
Subject: [PATCH 026/127] gnu: r-leaps: Update to 3.1.

* gnu/packages/cran.scm (r-leaps): Update to 3.1.
---
 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 1437c79a5e..7a5410cc45 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4320,14 +4320,14 @@ rules with R.")
 (define-public r-leaps
   (package
     (name "r-leaps")
-    (version "3.0")
+    (version "3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "leaps" version))
        (sha256
         (base32
-         "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
+         "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/web/packages/leaps/")

From 8958b37eb8f8f443ac68e9b715f1d557dfdd7e5b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:25:43 +0100
Subject: [PATCH 027/127] gnu: r-factominer: Update to 2.1.

* gnu/packages/cran.scm (r-factominer): Update to 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 7a5410cc45..904200a566 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5938,14 +5938,14 @@ clustering.")
 (define-public r-factominer
   (package
     (name "r-factominer")
-    (version "2.0")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "FactoMineR" version))
        (sha256
         (base32
-         "0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8"))))
+         "1b2jsv8vlaynknd7nlra6fdmr56n7678q5s28rqmagbadiqwvj4h"))))
     (properties `((upstream-name . "FactoMineR")))
     (build-system r-build-system)
     (propagated-inputs

From a82e617bf8726cf8ecee4271bfdf0c79b8ad7453 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:25:52 +0100
Subject: [PATCH 028/127] gnu: r-sjlabelled: Update to 1.1.2.

* gnu/packages/cran.scm (r-sjlabelled): Update to 1.1.2.
[propagated-inputs]: Remove r-magrittr, r-purrr, r-rlang, and r-tidyselect.
---
 gnu/packages/cran.scm | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 904200a566..d0e8ccce93 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6407,22 +6407,18 @@ information are missing.")
 (define-public r-sjlabelled
   (package
     (name "r-sjlabelled")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjlabelled" version))
        (sha256
         (base32
-         "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
+         "1vnx067mxnvz4jzhmpiarda8ln6habzj02qikvkix5piiy85sqcw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-haven" ,r-haven)
-       ("r-insight" ,r-insight)
-       ("r-magrittr" ,r-magrittr)
-       ("r-purrr" ,r-purrr)
-       ("r-rlang" ,r-rlang)
-       ("r-tidyselect" ,r-tidyselect)))
+       ("r-insight" ,r-insight)))
     (home-page "https://github.com/strengejacke/sjlabelled")
     (synopsis "Labelled data utility functions")
     (description

From a6494403b3455e88d935a9017cdec78a5aa10be3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:26:22 +0100
Subject: [PATCH 029/127] gnu: r-magick: Update to 2.3.

* gnu/packages/cran.scm (r-magick): Update to 2.3.
---
 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 d0e8ccce93..7566e0dd1c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7802,14 +7802,14 @@ multiple-imputation datasets.")
 (define-public r-magick
   (package
     (name "r-magick")
-    (version "2.2")
+    (version "2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "magick" version))
        (sha256
         (base32
-         "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
+         "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
     (build-system r-build-system)
     (inputs
      `(("imagemagick" ,imagemagick)

From 6cdd12542a19585f68474078bbbbc8314beb4008 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:26:28 +0100
Subject: [PATCH 030/127] gnu: r-survey: Update to 3.37.

* gnu/packages/cran.scm (r-survey): Update to 3.37.
---
 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 7566e0dd1c..4cf42c8408 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7835,14 +7835,14 @@ console, resulting in an interactive editing environment.")
 (define-public r-survey
   (package
     (name "r-survey")
-    (version "3.36")
+    (version "3.37")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "survey" version))
        (sha256
         (base32
-         "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
+         "1f31dvh48gzzan13pdrwh84ls35x9116095i7mdrcbrhz809r8dy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)

From 3575a16b7f485d708a9322a3fd4895666b3168e9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:26:36 +0100
Subject: [PATCH 031/127] gnu: r-sjstats: Update to 0.17.8.

* gnu/packages/cran.scm (r-sjstats): Update to 0.17.8.
[propagated-inputs]: Add r-effectsize.
---
 gnu/packages/cran.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4cf42c8408..f8e3f977fb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8401,18 +8401,19 @@ detection, parallelism through BLAS and parallel user templates.")
 (define-public r-sjstats
   (package
     (name "r-sjstats")
-    (version "0.17.7")
+    (version "0.17.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjstats" version))
        (sha256
-        (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
+        (base32 "0gagqbcmimlvxhpjkmd3s17mbrz5n937qksca1hvm6kj4rk37hzb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
        ("r-broom" ,r-broom)
        ("r-dplyr" ,r-dplyr)
+       ("r-effectsize" ,r-effectsize)
        ("r-emmeans" ,r-emmeans)
        ("r-insight" ,r-insight)
        ("r-lme4" ,r-lme4)

From 5c61d3e5b50a88ff507579b1de32610eec3f22c0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:26:51 +0100
Subject: [PATCH 032/127] gnu: r-bayestestr: Update to 0.5.1.

* gnu/packages/cran.scm (r-bayestestr): Update to 0.5.1.
---
 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 f8e3f977fb..cab9566336 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8476,14 +8476,14 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.4.0")
+    (version "0.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc"))))
+         "01kqvky1ndd1q64rzmqh5yfzz36ci8yhy4w16gjnw4c257ikhvd8"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs

From d56026a85f9c1de47b178bbe4c827ca9a488f6f8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:27:02 +0100
Subject: [PATCH 033/127] gnu: r-performance: Update to 0.4.3.

* gnu/packages/cran.scm (r-performance): Update to 0.4.3.
---
 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 cab9566336..8be5c63a99 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8501,14 +8501,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.4.2")
+    (version "0.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p"))))
+         "1164585ywbnrcy7an57kifh2gdb6g08z9pxw75ywqdcfyd51i3dz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)

From a4bc993f7bd7a15b693b2efd7dc950dd7af8be54 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:27:08 +0100
Subject: [PATCH 034/127] gnu: r-effectsize: Update to 0.1.1.

* gnu/packages/cran.scm (r-effectsize): Update to 0.1.1.
---
 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 8be5c63a99..86ac973476 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8559,14 +8559,14 @@ results using @code{ggplot2}.")
 (define-public r-effectsize
   (package
     (name "r-effectsize")
-    (version "0.0.1")
+    (version "0.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "effectsize" version))
        (sha256
         (base32
-         "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
+         "0dd7nbkg8kmash9zh2gg08m7hbpsqwpkvkdhinfqkbg5d0jinhq8"))))
     (properties `((upstream-name . "effectsize")))
     (build-system r-build-system)
     (propagated-inputs

From 4a7e857617b5009db546371278f7dcaf4905f3fc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:27:18 +0100
Subject: [PATCH 035/127] gnu: r-sjplot: Update to 2.8.2.

* gnu/packages/cran.scm (r-sjplot): Update to 2.8.2.
[propagated-inputs]: Remove r-ggrepel, r-glmmtmb, r-lme4, r-magrittr,
r-modelr, and r-psych.
---
 gnu/packages/cran.scm | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 86ac973476..5ceb42e41a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8584,13 +8584,13 @@ conversion of indices such as Cohen's d, r, odds, etc.")
 (define-public r-sjplot
   (package
     (name "r-sjplot")
-    (version "2.8.1")
+    (version "2.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjPlot" version))
        (sha256
-        (base32 "0rmfc2pq80w0kxh6icljhqm31q580s0czvllsfxk6crmpyfgxkp7"))))
+        (base32 "16721a5006q0gv45zjcwnkykxhjkzpq5n35vhik0g0ixgm3a2vci"))))
     (properties `((upstream-name . "sjPlot")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8600,17 +8600,11 @@ conversion of indices such as Cohen's d, r, odds, etc.")
        ("r-forcats" ,r-forcats)
        ("r-ggeffects" ,r-ggeffects)
        ("r-ggplot2" ,r-ggplot2)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-glmmtmb" ,r-glmmtmb)
        ("r-insight" ,r-insight)
        ("r-knitr" ,r-knitr)
-       ("r-lme4" ,r-lme4)
-       ("r-magrittr" ,r-magrittr)
        ("r-mass" ,r-mass)
-       ("r-modelr" ,r-modelr)
        ("r-parameters" ,r-parameters)
        ("r-performance" ,r-performance)
-       ("r-psych" ,r-psych)
        ("r-purrr" ,r-purrr)
        ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)

From 5b959414e0f8da3ea988ae90ef10a3007982c571 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:27:58 +0100
Subject: [PATCH 036/127] gnu: r-gh: Update to 1.1.0.

* gnu/packages/cran.scm (r-gh): Update to 1.1.0.
[propagated-inputs]: Add r-cli.
---
 gnu/packages/cran.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5ceb42e41a..d01d784314 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8649,17 +8649,18 @@ back to file after modifications.")
 (define-public r-gh
   (package
     (name "r-gh")
-    (version "1.0.1")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gh" version))
        (sha256
         (base32
-         "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
+         "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-httr" ,r-httr)
+     `(("r-cli" ,r-cli)
+       ("r-httr" ,r-httr)
        ("r-ini" ,r-ini)
        ("r-jsonlite" ,r-jsonlite)))
     (home-page "https://github.com/r-lib/gh#readme")

From e99caf8a4c9d4d2ab6e0db568b915161d8a98d61 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:28:13 +0100
Subject: [PATCH 037/127] gnu: r-afex: Update to 0.26-0.

* gnu/packages/cran.scm (r-afex): Update to 0.26-0.
---
 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 d01d784314..3ea83d1a55 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9077,14 +9077,14 @@ analysing multivariate abundance data in community ecology.")
 (define-public r-afex
   (package
     (name "r-afex")
-    (version "0.25-1")
+    (version "0.26-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "afex" version))
        (sha256
         (base32
-         "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
+         "0h3p1svgk1ap3lj08fi8nzdb3710h99bv150krf1x8wci1a0r1if"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-car" ,r-car)

From 6378827a719c13d04ae57c702b8b4c60027b3ad5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:28:21 +0100
Subject: [PATCH 038/127] gnu: r-gmp: Update to 0.5-13.6.

* gnu/packages/cran.scm (r-gmp): Update to 0.5-13.6.
---
 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 3ea83d1a55..69e2b61894 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10653,14 +10653,14 @@ preparing, executing, and processing HTTP requests.")
 (define-public r-gmp
   (package
     (name "r-gmp")
-    (version "0.5-13.5")
+    (version "0.5-13.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gmp" version))
        (sha256
         (base32
-         "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
+         "0j2sz2nw41y9306rl1b8hbn0spz7453z5iawcq0bvslyrhc1d9ir"))))
     (build-system r-build-system)
     (arguments
      '(#:phases

From 6c6d051322b4a89c4c539f156f4480c5c8e83bd7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:28:28 +0100
Subject: [PATCH 039/127] gnu: r-rmpfr: Update to 0.8-1.

* gnu/packages/cran.scm (r-rmpfr): Update to 0.8-1.
[inputs]: Add gmp.
[native-inputs]: Add pkg-config.
---
 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 69e2b61894..f1efbb9af0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10680,20 +10680,23 @@ limitations\" using the GNU Multiple Precision library.")
 (define-public r-rmpfr
   (package
     (name "r-rmpfr")
-    (version "0.7-2")
+    (version "0.8-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rmpfr" version))
        (sha256
         (base32
-         "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
+         "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
     (properties `((upstream-name . "Rmpfr")))
     (build-system r-build-system)
     (inputs
-     `(("mpfr" ,mpfr)))
+     `(("mpfr" ,mpfr)
+       ("gmp" ,gmp)))
     (propagated-inputs
      `(("r-gmp" ,r-gmp)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (home-page "http://rmpfr.r-forge.r-project.org/")
     (synopsis "R bindings to the MPFR library")
     (description

From 9073c464e50867a53657af66513840eff1cf06e1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:28:49 +0100
Subject: [PATCH 040/127] gnu: r-future: Update to 1.16.0.

* gnu/packages/cran.scm (r-future): Update to 1.16.0.
---
 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 f1efbb9af0..8cef99e5de 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11649,14 +11649,14 @@ them in distributed compute environments.")
 (define-public r-future
   (package
     (name "r-future")
-    (version "1.15.1")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future" version))
        (sha256
         (base32
-         "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
+         "1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)

From 88bdfd704b720abcc186c1a5b9609bc8defabbcb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:28:57 +0100
Subject: [PATCH 041/127] gnu: r-dorng: Update to 1.8.2.

* gnu/packages/cran.scm (r-dorng): Update to 1.8.2.
[propagated-inputs]: Remove r-pkgmaker.
---
 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 8cef99e5de..816b93d56d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11788,20 +11788,19 @@ heuristics.")
 (define-public r-dorng
   (package
     (name "r-dorng")
-    (version "1.7.1")
+    (version "1.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doRNG" version))
        (sha256
         (base32
-         "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
+         "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
     (properties `((upstream-name . "doRNG")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreach" ,r-foreach)
        ("r-iterators" ,r-iterators)
-       ("r-pkgmaker" ,r-pkgmaker)
        ("r-rngtools" ,r-rngtools)))
     (home-page "https://renozao.github.io/doRNG/")
     (synopsis "Generic reproducible parallel backend for foreach loops")

From 107c14ba847d801373495a53692c19e25e7fee6a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:29:12 +0100
Subject: [PATCH 042/127] gnu: r-cobs: Update to 1.3-4.

* gnu/packages/cran.scm (r-cobs): Update to 1.3-4.
---
 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 816b93d56d..f4f6d17e94 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -12021,14 +12021,14 @@ numbers (e.g. concentrations).")
 (define-public r-cobs
   (package
     (name "r-cobs")
-    (version "1.3-3")
+    (version "1.3-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cobs" version))
        (sha256
         (base32
-         "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
+         "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-quantreg" ,r-quantreg)

From 105639ce339a40b6da800b2f3e6494ca673ce1ee Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:29:19 +0100
Subject: [PATCH 043/127] gnu: r-adegenet: Update to 2.1.2.

* gnu/packages/cran.scm (r-adegenet): Update to 2.1.2.
---
 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 f4f6d17e94..b8639df8a9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -13207,14 +13207,14 @@ spanning tree.")
 (define-public r-adegenet
   (package
     (name "r-adegenet")
-    (version "2.1.1")
+    (version "2.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "adegenet" version))
        (sha256
         (base32
-         "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
+         "01fgrgbiddz2q4l3mx637hhwbs7r0c43yw7vpwl8p8pwbm3nykz0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ade4" ,r-ade4)

From 93e63562fb51afe0ba81042ebc6cf4b6c81b03d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:29:25 +0100
Subject: [PATCH 044/127] gnu: r-farver: Update to 2.0.3.

* gnu/packages/cran.scm (r-farver): Update to 2.0.3.
---
 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 b8639df8a9..1a77ec263e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14055,14 +14055,14 @@ consists of @code{grid} grobs and viewports that can then be manipulated with
 (define-public r-farver
   (package
     (name "r-farver")
-    (version "2.0.1")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "farver" version))
        (sha256
         (base32
-         "0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn"))))
+         "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
     (build-system r-build-system)
     (home-page "https://github.com/thomasp85/farver")
     (synopsis "Vectorized color conversion and comparison")

From d3f58abbec286d20e0de5d7c30e69bf613f5d18d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:29:39 +0100
Subject: [PATCH 045/127] gnu: r-threejs: Update to 0.3.3.

* gnu/packages/cran.scm (r-threejs): Update to 0.3.3.
[native-inputs]: Use jquery 1.12.4 and threejs version r111.
[arguments]: Adjust.
---
 gnu/packages/cran.scm | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1a77ec263e..6c90280c33 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14436,14 +14436,14 @@ and Learning to Rank measures (LambdaMart).")
 (define-public r-threejs
   (package
     (name "r-threejs")
-    (version "0.3.1")
+    (version "0.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "threejs" version))
        (sha256
         (base32
-         "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
+         "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
     (build-system r-build-system)
     (arguments
      `(#:modules ((guix build utils)
@@ -14460,8 +14460,8 @@ and Learning to Rank measures (LambdaMart).")
                      (unzip2
                       `((,(assoc-ref inputs "js-jquery")
                          "htmlwidgets/lib/jquery/jquery.min.js")
-                        (,(assoc-ref inputs "js-threejs-85")
-                         "htmlwidgets/lib/threejs-85/three.min.js"))))
+                        (,(assoc-ref inputs "js-threejs-111")
+                         "htmlwidgets/lib/threejs-111/three.min.js"))))
                  (lambda (sources targets)
                    (for-each (lambda (source target)
                                (format #t "Processing ~a --> ~a~%"
@@ -14483,17 +14483,17 @@ and Learning to Rank measures (LambdaMart).")
        ("js-jquery"
         ,(origin
            (method url-fetch)
-           (uri "https://code.jquery.com/jquery-3.3.1.js")
+           (uri "https://code.jquery.com/jquery-1.12.4.js")
            (sha256
             (base32
-             "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
-       ("js-threejs-85"
+             "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
+       ("js-threejs-111"
         ,(origin
            (method url-fetch)
-           (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
+           (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
            (sha256
             (base32
-             "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
+             "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
     (home-page "https://bwlewis.github.io/rthreejs")
     (synopsis "Interactive 3D scatter plots, networks and globes")
     (description

From 725086177a98c963a0641336576961c7553aa51b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:30:21 +0100
Subject: [PATCH 046/127] gnu: r-rhpcblasctl: Update to 0.20-17.

* gnu/packages/cran.scm (r-rhpcblasctl): Update to 0.20-17.
---
 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 6c90280c33..b425792ecf 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15454,14 +15454,14 @@ path of values for the regularization parameter.")
 (define-public r-rhpcblasctl
   (package
     (name "r-rhpcblasctl")
-    (version "0.18-205")
+    (version "0.20-17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RhpcBLASctl" version))
        (sha256
         (base32
-         "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
+         "0iwc06blr5sx7rylwczi2jrha8sk8qs0jklflwpidl0zj1jxdggp"))))
     (properties `((upstream-name . "RhpcBLASctl")))
     (build-system r-build-system)
     (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")

From 394fb5f38e12ecf6a46631f52a46d48169a9e325 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:30:29 +0100
Subject: [PATCH 047/127] gnu: r-leiden: Update to 0.3.2.

* gnu/packages/cran.scm (r-leiden): Update to 0.3.2.
---
 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 b425792ecf..f153295343 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15522,14 +15522,14 @@ computed using the L1 (Manhattan, taxicab) metric.")
 (define-public r-leiden
   (package
     (name "r-leiden")
-    (version "0.3.1")
+    (version "0.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "leiden" version))
        (sha256
         (base32
-         "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
+         "0kf6fxqf5l5vilm9g7vspc18daw84cwhpafs5szb1skwd6vrfdzw"))))
     (properties `((upstream-name . "leiden")))
     (build-system r-build-system)
     (propagated-inputs

From 5cda9ff27af34a0ebfc0d4d83d5526027a057e1b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:30:36 +0100
Subject: [PATCH 048/127] gnu: r-parameters: Update to 0.4.1.

* gnu/packages/cran.scm (r-parameters): Update to 0.4.1.
---
 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 f153295343..89e91278c7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15869,14 +15869,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "0z1hdxgippchij28h8xbbz6l29kkyakwxxj5vxnpic40cpkqqdd6"))))
+         "0xkdn1079sr6kgyhc1zmn9imca4bghnxs3f91h0z7vkzjj73qdbi"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs

From 328b5dde4bb6f37ddf5202a7cfd2c37c1e40307b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:30:43 +0100
Subject: [PATCH 049/127] gnu: r-bio3d: Update to 2.4-1.

* gnu/packages/cran.scm (r-bio3d): Update to 2.4-1.
---
 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 89e91278c7..a01e3a3434 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16116,14 +16116,14 @@ as a boxplot function.")
 (define-public r-bio3d
   (package
     (name "r-bio3d")
-    (version "2.4-0")
+    (version "2.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bio3d" version))
        (sha256
         (base32
-         "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s"))))
+         "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
     (properties `((upstream-name . "bio3d")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))

From 05e2ed8b4ff680635dc67e468db8de0ba7b2f4c0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:30:52 +0100
Subject: [PATCH 050/127] gnu: r-rngwell: Update to 0.10-6.

* gnu/packages/cran.scm (r-rngwell): Update to 0.10-6.
---
 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 a01e3a3434..aba8f70180 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16959,14 +16959,14 @@ facilitates insertion into pipelines, and content inspection.")
 (define-public r-rngwell
   (package
     (name "r-rngwell")
-    (version "0.10-5")
+    (version "0.10-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rngWELL" version))
        (sha256
         (base32
-         "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb"))))
+         "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
     (properties `((upstream-name . "rngWELL")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/rngWELL/")

From ba6d9fdcf3a6bed23c784bda1a02149f2e6ebd5e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:30:59 +0100
Subject: [PATCH 051/127] gnu: r-idpmisc: Update to 1.1.20.

* gnu/packages/cran.scm (r-idpmisc): Update to 1.1.20.
---
 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 aba8f70180..ea72719d4d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18758,14 +18758,14 @@ these algorithms also allow to detect anomalies (outliers).")
 (define-public r-idpmisc
   (package
     (name "r-idpmisc")
-    (version "1.1.19")
+    (version "1.1.20")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "IDPmisc" version))
        (sha256
         (base32
-         "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd"))))
+         "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
     (properties `((upstream-name . "IDPmisc")))
     (build-system r-build-system)
     (propagated-inputs

From 7dd0af28f7cb9e364eb19edf969ec04fab2eb854 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:31:06 +0100
Subject: [PATCH 052/127] gnu: r-shinycssloaders: Update to 0.3.

* gnu/packages/cran.scm (r-shinycssloaders): Update to 0.3.
---
 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 ea72719d4d..58ceed06d0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18936,14 +18936,14 @@ problems (food web problems, linear programming problems).")
 (define-public r-shinycssloaders
   (package
     (name "r-shinycssloaders")
-    (version "0.2.0")
+    (version "0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinycssloaders" version))
        (sha256
         (base32
-         "1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4"))))
+         "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
     (properties
      `((upstream-name . "shinycssloaders")))
     (build-system r-build-system)

From 6748b6b4582bb043ff62592d2321445ae3bfacff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:31:13 +0100
Subject: [PATCH 053/127] gnu: r-foreign: Update to 0.8-75.

* gnu/packages/statistics.scm (r-foreign): Update to 0.8-75.
---
 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 ec2994dc33..61fd51f484 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -504,14 +504,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-74")
+    (version "0.8-75")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "047w772msiki85rxxhqkxya37gmw4331l32651rr09dl2vq02pgj"))))
+         "0g4mi101srjbl17ydb2hl3854m3xj0llj6861lfr30sp08nkqavl"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")

From 545ebafe839a3ff7b2b2ccab1b20fbf2f08dca77 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:31:19 +0100
Subject: [PATCH 054/127] gnu: r-knitr: Update to 1.27.

* gnu/packages/statistics.scm (r-knitr): Update to 1.27.
---
 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 61fd51f484..138a3507d8 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1400,13 +1400,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
 (define-public r-knitr
   (package
     (name "r-knitr")
-    (version "1.26")
+    (version "1.27")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "knitr" version))
               (sha256
                (base32
-                "08f3bdd5cnnbigybr9vmkhq12n64pbmn4layl3w5rwk8xi5kbnrq"))))
+                "02nysgnx6xv0kd351s1d59yx4g0drsd9lmcgxs0rsw5f1jiycgdg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-evaluate" ,r-evaluate)

From c6d1b5dafbd45b8fb78c6a669b2fb7cfc7f9a0e0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:31:30 +0100
Subject: [PATCH 055/127] gnu: r-rlang: Update to 0.4.3.

* gnu/packages/statistics.scm (r-rlang): Update to 0.4.3.
---
 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 138a3507d8..756affdb5d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1607,13 +1607,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
     (name "r-rlang")
-    (version "0.4.2")
+    (version "0.4.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rlang" version))
               (sha256
                (base32
-                "0fczcp17kaz3s4p0nd4126bppwl20vpxfybhsndpcky9h75wklgv"))))
+                "0qsqfikbsj55x5brghnkzzp7pz0japr4xnzm993f668mlls3f6i4"))))
     (build-system r-build-system)
     (home-page "http://rlang.tidyverse.org")
     (synopsis "Functions for base types, core R and Tidyverse features")

From 564c3330ed5bfa63ffd15318f51d31779e654893 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:31:37 +0100
Subject: [PATCH 056/127] gnu: r-rcpparmadillo: Update to 0.9.800.4.0.

* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.800.4.0.
---
 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 756affdb5d..1020b30e85 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2565,13 +2565,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.800.3.0")
+    (version "0.9.800.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "0kpcspg3mafi5kncjfhnbcwimvlf19jvrxilvhbpd20sap473mh3"))))
+                "1csh54v4d0ccwmk4bqj4rca1d5rqpafvb4459x3q6k9sys0charx"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     ;; All needed for vignettes

From 8d9e85221f010a2e73025edfd9528650299cc53a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:31:44 +0100
Subject: [PATCH 057/127] gnu: r-catools: Update to 1.18.0.

* gnu/packages/statistics.scm (r-catools): Update to 1.18.0.
---
 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 1020b30e85..6e3544ed22 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2617,13 +2617,13 @@ vectors.")
 (define-public r-catools
   (package
     (name "r-catools")
-    (version "1.17.1.4")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "caTools" version))
               (sha256
                (base32
-                "151vsfakg32jn9msfdjcizhizm8k8yxlfpnsbagns9ihr59s3w49"))))
+                "0y1kgyiy322yhb0phzwvf2zgjz9awp13lhzhk9v1ddg88656jhq3"))))
     (properties `((upstream-name . "caTools")))
     (build-system r-build-system)
     (propagated-inputs

From af837b99642ddaf20f011821345ad6fc0c1c9137 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:31:51 +0100
Subject: [PATCH 058/127] gnu: r-rmarkdown: Update to 2.1.

* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.1.
---
 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 6e3544ed22..2ecd590757 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2663,13 +2663,13 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "2.0")
+    (version "2.1")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
-          (base32 "1bm3n17wa0pf1cq7qmwhbnn02x2pld7zzmmzjcvwy6apanch9fl7"))))
+          (base32 "0pa5xs0vzwn9vsgysjqbks9v5lbqphxh5agciskllibc40hhwigg"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs

From 1cc17e37ae3c1a9a8dda3249ce17cf78498da4be Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:31:56 +0100
Subject: [PATCH 059/127] gnu: r-blob: Update to 1.2.1.

* gnu/packages/statistics.scm (r-blob): Update to 1.2.1.
[propagated-inputs]: Remove r-prettyunits.
---
 gnu/packages/statistics.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 2ecd590757..7328629440 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2755,17 +2755,16 @@ that package, other packages are unaffected.")
 (define-public r-blob
   (package
     (name "r-blob")
-    (version "1.2.0")
+    (version "1.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "blob" version))
               (sha256
                (base32
-                "08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s"))))
+                "1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-prettyunits" ,r-prettyunits)
-       ("r-rlang" ,r-rlang)
+     `(("r-rlang" ,r-rlang)
        ("r-vctrs" ,r-vctrs)))
     (home-page "https://github.com/hadley/blob")
     (synopsis "Simple S3 Class for representing vectors of binary data")

From b4a374ec99d37e6c151771b09d6fa7fd170ca2b8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:32:11 +0100
Subject: [PATCH 060/127] gnu: r-xml: Update to 3.99-0.3.

* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.3.
---
 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 7328629440..3846e98c12 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2849,13 +2849,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
 (define-public r-xml
   (package
     (name "r-xml")
-    (version "3.98-1.20")
+    (version "3.99-0.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "XML" version))
               (sha256
                (base32
-                "0n28m8iz1wfgixr7fjswl238c5w9kggsrw0c8hdzp859dqvqdbs6"))))
+                "0lzpqwajs5xaqdna50vl24qkp9xvh00zypjjzy6kgdzk11isgdw1"))))
     (properties
      `((upstream-name . "XML")))
     (build-system r-build-system)

From 0d3d1934763bb5c1b0576b8121e0b954e4799b64 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:32:16 +0100
Subject: [PATCH 061/127] gnu: r-pkgmaker: Update to 0.31.

* gnu/packages/statistics.scm (r-pkgmaker): Update to 0.31.
[propagated-inputs]: Add r-assertthat.
---
 gnu/packages/statistics.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 3846e98c12..a536496523 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3234,17 +3234,18 @@ path-wise fashion.")
 (define-public r-pkgmaker
   (package
     (name "r-pkgmaker")
-    (version "0.27")
+    (version "0.31")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgmaker" version))
        (sha256
         (base32
-         "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
+         "0cc6v6kpwxwwh7k7zyw13wqdp0f9qzzr1a7vv02lskgii54aa4nb"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bibtex" ,r-bibtex)
+     `(("r-assertthat" ,r-assertthat)
+       ("r-bibtex" ,r-bibtex)
        ("r-codetools" ,r-codetools)
        ("r-digest" ,r-digest)
        ("r-magrittr" ,r-magrittr)

From 68146b96053a6c6d88287683fc8a63d456c43649 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:32:32 +0100
Subject: [PATCH 062/127] gnu: r-rngtools: Update to 1.5.

* gnu/packages/statistics.scm (r-rngtools): Update to 1.5.
[propagated-inputs]: Remove r-pkgmaker and r-stringr.
---
 gnu/packages/statistics.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index a536496523..8df6533804 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3284,19 +3284,17 @@ package registries.")
 (define-public r-rngtools
   (package
     (name "r-rngtools")
-    (version "1.4")
+    (version "1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rngtools" version))
        (sha256
         (base32
-         "1kivj594bn774lbn29ws2rmzy2km99sza0j3jqvhal6hwmk27a9s"))))
+         "0xgmg3qb6insc157as47mcm9sdjdpy9jirh7w06bxb7pfcxqfx42"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-digest" ,r-digest)
-       ("r-pkgmaker" ,r-pkgmaker)
-       ("r-stringr" ,r-stringr)))
+     `(("r-digest" ,r-digest)))
     (home-page "https://renozao.github.io/rngtools")
     (synopsis "Utility functions for working with random number generators")
     (description

From 1003fd5142560258b765f25564e9a96928d8b92b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:32:48 +0100
Subject: [PATCH 063/127] gnu: r-tidyr: Update to 1.0.2.

* gnu/packages/statistics.scm (r-tidyr): Update to 1.0.2.
---
 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 8df6533804..5fbf1f074d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3712,14 +3712,14 @@ selection.")
 (define-public r-tidyr
   (package
     (name "r-tidyr")
-    (version "1.0.0")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyr" version))
        (sha256
         (base32
-         "1403j0xd93l0r7qj738ryd5zc79hbcghrzybib3c3hrnaq5s78cj"))))
+         "0safj8bcf8libwr0jx4059bmarngvhfddrcv8k5iw39m9lpxs0r4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)

From 2c676da719b015e17666107720aa73363f37dcb5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:32:54 +0100
Subject: [PATCH 064/127] gnu: r-rrcov: Update to 1.5-2.

* gnu/packages/statistics.scm (r-rrcov): Update to 1.5-2.
[propagated-inputs]: Remove r-cluster.
---
 gnu/packages/statistics.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5fbf1f074d..0d140710bf 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4833,18 +4833,17 @@ analysis} (PCA) by projection pursuit.")
 (define-public r-rrcov
   (package
     (name "r-rrcov")
-    (version "1.4-9")
+    (version "1.5-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rrcov" version))
        (sha256
         (base32
-         "11zvxidlb1pr2j5dzvmbjqdgsmmicsq8ppjf5wcfykfyf2fkcmz7"))))
+         "0m62k58nabw7hjz1qyyf9a0d6lvcz5vcvpksjnq93zcfra9inr57"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-cluster" ,r-cluster)
-       ("r-lattice" ,r-lattice)
+     `(("r-lattice" ,r-lattice)
        ("r-mvtnorm" ,r-mvtnorm)
        ("r-pcapp" ,r-pcapp)
        ("r-robustbase" ,r-robustbase)))

From 2afae7fc9ae4ed29e798aabda83dcc4608c13240 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 16:33:11 +0100
Subject: [PATCH 065/127] gnu: r-fpc: Update to 2.2-4.

* gnu/packages/statistics.scm (r-fpc): Update to 2.2-4.
---
 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 0d140710bf..172779035e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4936,14 +4936,14 @@ of the points.")
 (define-public r-fpc
   (package
     (name "r-fpc")
-    (version "2.2-3")
+    (version "2.2-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fpc" version))
        (sha256
         (base32
-         "1dy3pla4jjgs46izqg2kxajlxr80sbr9896jbzb1qszrdx7af041"))))
+         "1gsnl5sbdg86b2wdrsy6wq83xj6mrziiq7rxa8cqksgljc7gp6yf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)

From a13db7e2ab05ee3ab9a42dd6a101130b8896fee0 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 25 Jan 2020 21:39:04 +0200
Subject: [PATCH 066/127] build: cargo-build-system: Allow patched crates.

* guix/build/cargo-build-system.scm (crate-src?): Don't check for a
gzipped tarball, just make sure it's not a directory.
---
 guix/build/cargo-build-system.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/guix/build/cargo-build-system.scm b/guix/build/cargo-build-system.scm
index 8a8d74ee1b..78c27a29e4 100644
--- a/guix/build/cargo-build-system.scm
+++ b/guix/build/cargo-build-system.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019 Ivan Petkov <ivanppetkov@gmail.com>
-;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -58,7 +58,7 @@
 (define (crate-src? path)
   "Check if PATH refers to a crate source, namely a gzipped tarball with a
 Cargo.toml file present at its root."
-    (and (gzip-file? path)
+    (and (not (directory-exists? path)) ; not a tarball
          ;; First we print out all file names within the tarball to see if it
          ;; looks like the source of a crate. However, the tarball will include
          ;; an extra path component which we would like to ignore (since we're

From 0173e69f5268f92fedade03c7265f65e51fcb937 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 25 Jan 2020 21:41:44 +0200
Subject: [PATCH 067/127] gnu: rust-libgit2-sys-0.10: Remove vendored code.

* gnu/packages/crates-io.scm (rust-libgit2-sys-0.10)[source]: Remove
vendored code.
[arguments]: Don't remove missing vendored code.
* gnu/packages/rust-apps.scm (tokei)[arguments]: Same.
---
 gnu/packages/crates-io.scm | 12 +++++-------
 gnu/packages/rust-apps.scm |  4 ----
 2 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 8155bd7a94..82267687f9 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -5603,10 +5603,13 @@ values of all the exported APIs match the platform that libc is compiled for.")
       (origin
         (method url-fetch)
         (uri (crate-uri "libgit2-sys" version))
-        (file-name (string-append name "-" version ".crate"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "0l9fvki7qxsl97vgzqwlv75nl213a5vxw7b1jaik97ala356pv6r"))))
+          "0l9fvki7qxsl97vgzqwlv75nl213a5vxw7b1jaik97ala356pv6r"))
+        (modules '((guix build utils)))
+        (snippet
+         '(begin (delete-file-recursively "libgit2") #t))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -5623,11 +5626,6 @@ values of all the exported APIs match the platform that libc is compiled for.")
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((openssl (assoc-ref inputs "openssl")))
                (setenv "OPENSSL_DIR" openssl))
-             (delete-file-recursively "libgit2")
-             (delete-file-recursively
-               (string-append "guix-vendor/rust-libgit2-sys-"
-                              ,(package-version rust-libgit2-sys-0.10)
-                              ".crate/libgit2"))
              (delete-file-recursively
                (string-append "guix-vendor/rust-libz-sys-"
                               ,(package-version rust-libz-sys-1.0)
diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm
index 8ad3c0ced4..1b0721f546 100644
--- a/gnu/packages/rust-apps.scm
+++ b/gnu/packages/rust-apps.scm
@@ -146,10 +146,6 @@ gitignore rules.")
                (setenv "OPENSSL_DIR" openssl)
                (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
                (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
-               (delete-file-recursively
-                 (string-append "guix-vendor/rust-libgit2-sys-"
-                                ,(package-version rust-libgit2-sys-0.10)
-                                ".crate/libgit2"))
                (delete-file-recursively
                  (string-append "guix-vendor/rust-libssh2-sys-"
                                 ,(package-version rust-libssh2-sys-0.2)

From e2302953d55f598e6c2d9224e3377d7116e31608 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 25 Jan 2020 21:44:18 +0200
Subject: [PATCH 068/127] gnu: rust-jemalloc-sys-0.3: Remove vendored code.

* gnu/packages/crates-io.scm (rust-jemalloc-sys-0.3)[source]: Remove
vendored code.
[arguments]: Don't remove missing vendored code.
---
 gnu/packages/crates-io.scm | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 82267687f9..ea4a3f3e28 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -5328,10 +5328,13 @@ wasm-bindgen crate.")
       (origin
         (method url-fetch)
         (uri (crate-uri "jemalloc-sys" version))
-        (file-name (string-append name "-" version ".crate"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "0ify9vlql01qhfxlj7d4p9jvcp90mj2h69nkbq7slccvbhzryfqd"))))
+          "0ify9vlql01qhfxlj7d4p9jvcp90mj2h69nkbq7slccvbhzryfqd"))
+        (modules '((guix build utils)))
+        (snippet
+         '(begin (delete-file-recursively "jemalloc") #t))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -5344,11 +5347,6 @@ wasm-bindgen crate.")
          (add-after 'configure 'override-jemalloc
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((jemalloc (assoc-ref inputs "jemalloc")))
-               (delete-file-recursively "jemalloc")
-               (delete-file-recursively
-                 (string-append "guix-vendor/rust-jemalloc-sys-"
-                                ,(package-version rust-jemalloc-sys-0.3)
-                                ".crate/jemalloc"))
                (setenv "JEMALLOC_OVERRIDE"
                        (string-append jemalloc "/lib/libjemalloc_pic.a")))
              #t)))))

From ad03f50fa80c0a5306de6b3efbd152bcf281164d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 25 Jan 2020 21:48:37 +0200
Subject: [PATCH 069/127] gnu: rust-libssh2-sys-0.2: Remove vendored code.

* gnu/packages/crates-io.scm (rust-libssh2-sys-0.2)[source]: Remove
vendored code.
[arguments]: Don't remove missing vendored code.
(rust-libgit2-sys-0.10)[arguments]: Same.
* gnu/packages/rust-apps.scm (tokei)[arguments]: Same.
---
 gnu/packages/crates-io.scm | 16 +++++-----------
 gnu/packages/rust-apps.scm |  4 ----
 2 files changed, 5 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index ea4a3f3e28..8ba8cde99a 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -5628,10 +5628,6 @@ values of all the exported APIs match the platform that libc is compiled for.")
                (string-append "guix-vendor/rust-libz-sys-"
                               ,(package-version rust-libz-sys-1.0)
                               ".crate/src/zlib"))
-             (delete-file-recursively
-               (string-append "guix-vendor/rust-libssh2-sys-"
-                              ,(package-version rust-libssh2-sys-0.2)
-                              ".crate/libssh2"))
              (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
              (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
              #t)))))
@@ -5716,10 +5712,13 @@ functions and static variables these libraries contain.")
       (origin
         (method url-fetch)
         (uri (crate-uri "libssh2-sys" version))
-        (file-name (string-append name "-" version ".crate"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "042gsgbvxgm5by4mk906j3zm4qdvzcfhjxrb55is1lrr6f0nxain"))))
+          "042gsgbvxgm5by4mk906j3zm4qdvzcfhjxrb55is1lrr6f0nxain"))
+        (modules '((guix build utils)))
+        (snippet
+         '(begin (delete-file-recursively "libssh2") #t))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t ; it wants rust-openssl-src
@@ -5737,11 +5736,6 @@ functions and static variables these libraries contain.")
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((openssl (assoc-ref inputs "openssl")))
                (setenv "OPENSSL_DIR" openssl))
-             (delete-file-recursively "libssh2")
-             (delete-file-recursively
-               (string-append "guix-vendor/rust-libssh2-sys-"
-                              ,(package-version rust-libssh2-sys-0.2)
-                              ".crate/libssh2"))
              (delete-file-recursively
                (string-append "guix-vendor/rust-libz-sys-"
                               ,(package-version rust-libz-sys-1.0)
diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm
index 1b0721f546..2099e38fff 100644
--- a/gnu/packages/rust-apps.scm
+++ b/gnu/packages/rust-apps.scm
@@ -146,10 +146,6 @@ gitignore rules.")
                (setenv "OPENSSL_DIR" openssl)
                (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
                (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
-               (delete-file-recursively
-                 (string-append "guix-vendor/rust-libssh2-sys-"
-                                ,(package-version rust-libssh2-sys-0.2)
-                                ".crate/libssh2"))
                (delete-file-recursively
                  (string-append "guix-vendor/rust-libz-sys-"
                                 ,(package-version rust-libz-sys-1.0)

From bba73d473afc8299b9e4006617264e90a46cd375 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 25 Jan 2020 21:51:48 +0200
Subject: [PATCH 070/127] gnu: rust-lzma-sys-0.1: Remove vendored code.

* gnu/packages/crates-io.scm (rust-lzma-sys-0.1)[source]: Remove
vendored code.
[arguments]: Remove custom phase.
---
 gnu/packages/crates-io.scm | 19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 8ba8cde99a..144ada8081 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -5893,26 +5893,19 @@ functions and static variables these libraries contain.")
       (origin
         (method url-fetch)
         (uri (crate-uri "lzma-sys" version))
-        (file-name (string-append name "-" version ".crate"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "14gyj256yh0wm77jbvmlc39v7lfn0navpfrja4alczarzlc8ir2k"))))
+          "14gyj256yh0wm77jbvmlc39v7lfn0navpfrja4alczarzlc8ir2k"))
+        (modules '((guix build utils)))
+        (snippet
+         '(begin (delete-file-recursively "xz-5.2") #t))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
         ("rust-cc" ,rust-cc-1.0)
-        ("rust-pkg-config" ,rust-pkg-config-0.3))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'configure 'unbundle-xz
-           (lambda _
-             (delete-file-recursively "xz-5.2")
-             (delete-file-recursively
-               (string-append "guix-vendor/rust-lzma-sys-"
-                              ,(package-version rust-lzma-sys-0.1)
-                              ".crate/xz-5.2"))
-             #t)))))
+        ("rust-pkg-config" ,rust-pkg-config-0.3))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("xz" ,xz)))

From d6dde77d7ff2aeb63b8b4ddbca6b518d84aa87ed Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 25 Jan 2020 21:53:44 +0200
Subject: [PATCH 071/127] gnu: rust-libz-sys-1.0: Remove vendored code.

* gnu/packages/crates-io.scm (rust-libz-sys-1.0)[source]: Remove
vendored code.
[arguments]: Remove custom phase.
(rust-libgit2-sys-0.10)[arguments]: Don't unvendor missing code.
(rust-libssh2-sys-0.2)[arguments]: Same.
* gnu/packages/rust-apps.scm (tokei)[arguments]: Same.
---
 gnu/packages/crates-io.scm | 27 ++++++---------------------
 gnu/packages/rust-apps.scm |  6 +-----
 2 files changed, 7 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 144ada8081..278b14e6f1 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -5624,10 +5624,6 @@ values of all the exported APIs match the platform that libc is compiled for.")
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((openssl (assoc-ref inputs "openssl")))
                (setenv "OPENSSL_DIR" openssl))
-             (delete-file-recursively
-               (string-append "guix-vendor/rust-libz-sys-"
-                              ,(package-version rust-libz-sys-1.0)
-                              ".crate/src/zlib"))
              (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
              (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
              #t)))))
@@ -5736,10 +5732,6 @@ functions and static variables these libraries contain.")
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((openssl (assoc-ref inputs "openssl")))
                (setenv "OPENSSL_DIR" openssl))
-             (delete-file-recursively
-               (string-append "guix-vendor/rust-libz-sys-"
-                              ,(package-version rust-libz-sys-1.0)
-                              ".crate/src/zlib"))
              (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
              #t)))))
     (native-inputs
@@ -6574,10 +6566,13 @@ types as proposed in RFC 1158.")
       (origin
         (method url-fetch)
         (uri (crate-uri "libz-sys" version))
-        (file-name (string-append name "-" version ".crate"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "1gjycyl2283525abks98bhxa4r259m617xfm5z52p3p3c8ry9d9f"))))
+          "1gjycyl2283525abks98bhxa4r259m617xfm5z52p3p3c8ry9d9f"))
+        (modules '((guix build utils)))
+        (snippet
+         '(begin (delete-file-recursively "src/zlib") #t))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -6585,17 +6580,7 @@ types as proposed in RFC 1158.")
         ;; Build dependencies:
         ("rust-cc" ,rust-cc-1.0)
         ("rust-pkg-config" ,rust-pkg-config-0.3)
-        ("rust-vcpkg" ,rust-vcpkg-0.2))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'configure 'delete-vendored-zlib
-           (lambda _
-             (delete-file-recursively "src/zlib")
-             (delete-file-recursively
-               (string-append "guix-vendor/rust-libz-sys-"
-                              ,(package-version rust-libz-sys-1.0)
-                              ".crate/src/zlib"))
-             #t)))))
+        ("rust-vcpkg" ,rust-vcpkg-0.2))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("zlib" ,zlib)))
diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm
index 2099e38fff..d9a672f777 100644
--- a/gnu/packages/rust-apps.scm
+++ b/gnu/packages/rust-apps.scm
@@ -145,11 +145,7 @@ gitignore rules.")
              (let ((openssl (assoc-ref inputs "openssl")))
                (setenv "OPENSSL_DIR" openssl)
                (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
-               (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
-               (delete-file-recursively
-                 (string-append "guix-vendor/rust-libz-sys-"
-                                ,(package-version rust-libz-sys-1.0)
-                                ".crate/src/zlib")))
+               (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1"))
              #t)))))
     (native-inputs
      `(("libgit2" ,libgit2)

From d0c4d1abfe54c12a0dfa467267859802f65c3bbc Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 25 Jan 2020 21:57:31 +0200
Subject: [PATCH 072/127] gnu: rust-pcre2-sys-0.2: Delete vendored code.

* gnu/packages/crates-io.scm (rust-pcre2-sys-0.2)[source]: Delete
vendored code.
[arguments]: Remove custom phase.
(rust-pcre2-0.2, rust-grep-pcre2-0.1)[arguments]: Enable build.
[native-inputs]: Add pkg-config, pcre2.
---
 gnu/packages/crates-io.scm | 29 +++++++++++++----------------
 1 file changed, 13 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 278b14e6f1..1099a25d87 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -4408,10 +4408,12 @@ the regex engine it uses pluggable.")
          "1wjc3gsan20gapga8nji6jcrmwn9n85q5zf2yfq6g50c7abkc2ql"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
+     `(#:cargo-inputs
        (("rust-grep-matcher" ,rust-grep-matcher-0.1)
         ("rust-pcre2" ,rust-pcre2-0.2))))
+    (native-inputs
+     `(("pcre2" ,pcre2)
+       ("pkg-config" ,pkg-config)))
     (home-page
      "https://github.com/BurntSushi/ripgrep")
     (synopsis "Use PCRE2 with the grep crate")
@@ -7490,12 +7492,14 @@ deserialization, and interpreter in Rust.")
          "103i66a998g1fjrqf9sdyvi8qi83hwglz3pjdcq9n2r207hsagb0"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
+     `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
         ("rust-log" ,rust-log-0.4)
         ("rust-pcre2-sys" ,rust-pcre2-sys-0.2)
         ("rust-thread-local" ,rust-thread-local-0.3))))
+    (native-inputs
+     `(("pcre2" ,pcre2)
+       ("pkg-config" ,pkg-config)))
     (home-page "https://github.com/BurntSushi/rust-pcre2")
     (synopsis "High level wrapper library for PCRE2")
     (description
@@ -7514,23 +7518,16 @@ deserialization, and interpreter in Rust.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0nwdvc43dkb89qmm5q8gw1zyll0wsfqw7kczpn23mljra3874v47"))))
+         "0nwdvc43dkb89qmm5q8gw1zyll0wsfqw7kczpn23mljra3874v47"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin (delete-file-recursively "pcre2") #t))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
         ("rust-pkg-config" ,rust-pkg-config-0.3)
-        ("rust-cc" ,rust-cc-1.0))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'configure 'unbundle-sources
-           (lambda _
-             (delete-file-recursively "pcre2")
-             (delete-file-recursively
-               (string-append "guix-vendor/rust-pcre2-sys-"
-                              ,(package-version rust-pcre2-sys-0.2)
-                              ".tar.gz/pcre2"))
-             #t)))))
+        ("rust-cc" ,rust-cc-1.0))))
     (native-inputs
      `(("pcre2" ,pcre2)
        ("pkg-config" ,pkg-config)))

From 61b95c15cfb2c9b0d02cf09f93c0df76be0972b5 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 27 Jan 2020 09:17:32 +0200
Subject: [PATCH 073/127] build: cargo-build-system: Add pkg-config environment
 variables.

* guix/build/cargo-build-system.scm (configure): Add environment
variables to use system libgit2 and libssh2.
* gnu/packages/crates-io.scm (rust-libgit2-sys-0.10,
rust-libssh2-sys-0.2)[arguments]: Remove LIBGIT2 and LIBSSH2 environment
variable settings.
* gnu/packages/rust-apps.scm (tokei)[arguments]: Same.
---
 gnu/packages/crates-io.scm        | 3 ---
 gnu/packages/rust-apps.scm        | 4 +---
 guix/build/cargo-build-system.scm | 2 ++
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 1099a25d87..a5f224f99e 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -5626,8 +5626,6 @@ values of all the exported APIs match the platform that libc is compiled for.")
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((openssl (assoc-ref inputs "openssl")))
                (setenv "OPENSSL_DIR" openssl))
-             (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
-             (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
              #t)))))
     (native-inputs
      `(("libgit2" ,libgit2)
@@ -5734,7 +5732,6 @@ functions and static variables these libraries contain.")
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((openssl (assoc-ref inputs "openssl")))
                (setenv "OPENSSL_DIR" openssl))
-             (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
              #t)))))
     (native-inputs
      `(("libssh2" ,libssh2)
diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm
index d9a672f777..90bd146442 100644
--- a/gnu/packages/rust-apps.scm
+++ b/gnu/packages/rust-apps.scm
@@ -143,9 +143,7 @@ gitignore rules.")
          (add-after 'configure 'unvendor-libraries-from-crates
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((openssl (assoc-ref inputs "openssl")))
-               (setenv "OPENSSL_DIR" openssl)
-               (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
-               (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1"))
+               (setenv "OPENSSL_DIR" openssl))
              #t)))))
     (native-inputs
      `(("libgit2" ,libgit2)
diff --git a/guix/build/cargo-build-system.scm b/guix/build/cargo-build-system.scm
index 78c27a29e4..0721989589 100644
--- a/guix/build/cargo-build-system.scm
+++ b/guix/build/cargo-build-system.scm
@@ -119,6 +119,8 @@ directory = '" port)
   ;; upgrading the compiler for example.
   (setenv "RUSTFLAGS" "--cap-lints allow")
   (setenv "CC" (string-append (assoc-ref inputs "gcc") "/bin/gcc"))
+  (setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
+  (setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
 
   ;; We don't use the Cargo.lock file to determine the package versions we use
   ;; during building, and in any case if one is not present it is created

From fcb510c541e83291ea6682cba87020a913c64914 Mon Sep 17 00:00:00 2001
From: Amin Bandali <mab@gnu.org>
Date: Mon, 27 Jan 2020 09:33:37 -0500
Subject: [PATCH 074/127] gnu: light: Install udev rules to allow sudo-less
 invocations.

* gnu/packages/linux.scm (light)[arguments]: Substitute the absolute paths
of chgrp and chmod in 90-backlight.rules and install the rules file to the
special lib/udev/rules.d/ directory of the out output.  This allows for
any member of the video group to set brightness using light without sudo.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/linux.scm | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 9b0dfd8eb7..5162dfff18 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -5042,6 +5042,21 @@ monitoring tools for Linux.  These include @code{mpstat}, @code{iostat},
         (base32 "0zrjipd392bzjvxx0rjrb0cgi0ix1d83fwgw1mcy8kc4d16cgyjg"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-udev-rules-absolute-path-bins
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "90-backlight.rules"
+               (("/bin/chgrp") (which "chgrp"))
+               (("/bin/chmod") (which "chmod")))
+             #t))
+         (add-after 'install 'install-udev-rules
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (install-file
+                "90-backlight.rules" (string-append out "/lib/udev/rules.d"))
+               #t))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)))

From 11f46dc9de9ac4513349baf56670a0939e2015f9 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 27 Jan 2020 20:28:55 +0100
Subject: [PATCH 075/127] gnu: emacs-gif-screencast: Update to 1.1.

* gnu/packages/emacs-xyz.scm (emacs-gif-screencast): Update to 1.1.
---
 gnu/packages/emacs-xyz.scm | 92 +++++++++++++++++++-------------------
 1 file changed, 45 insertions(+), 47 deletions(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index c5214405d0..f36d9feda3 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -15377,56 +15377,54 @@ try completing.  See @code{fish-completion-fallback-on-bash-p}.")
     (license license:gpl3+)))
 
 (define-public emacs-gif-screencast
-  (let ((commit "248d1e158405e6cba2c65ecaed40e2c59b089cd8")
-        (revision "2"))
-    (package
-      (name "emacs-gif-screencast")
-      (version (git-version "1.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://gitlab.com/Ambrevar/emacs-gif-screencast.git")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "19xqi5mgalnnhb4hw0fh7py2s2dllldx1xxbhwhknkdpifai8hl8"))))
-      (build-system emacs-build-system)
-      (inputs
-       `(("scrot" ,scrot)
-         ("imagemagick" ,imagemagick)
-         ("gifsicle" ,gifsicle)))
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'configure
-             (lambda* (#:key inputs outputs #:allow-other-keys)
-               (let ((scrot (assoc-ref inputs "scrot"))
-                     (imagemagick (assoc-ref inputs "imagemagick"))
-                     (gifsicle (assoc-ref inputs "gifsicle")))
-                 (make-file-writable "gif-screencast.el")
-                 ;; Specify the absolute file names of the various
-                 ;; programs so that everything works out-of-the-box.
-                 (emacs-substitute-variables
-                     "gif-screencast.el"
-                   ("gif-screencast-program"
-                    (string-append scrot "/bin/scrot"))
-                   ("gif-screencast-convert-program"
-                    (string-append imagemagick "/bin/convert"))
-                   ("gif-screencast-cropping-program"
-                    (string-append imagemagick "/bin/mogrify"))
-                   ("gif-screencast-optimize-program"
-                    (string-append gifsicle "/bin/gifsicle")))))))))
-      (home-page
-       "https://gitlab.com/Ambrevar/emacs-gif-screencast")
-      (synopsis "One-frame-per-action GIF recording")
-      (description
-       "Call @code{gif-screencast} to start a recording.
+  (package
+    (name "emacs-gif-screencast")
+    (version "1.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/Ambrevar/emacs-gif-screencast.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1g1by8lvf8c9vzm4wwsi5kp285kaj0ahsl54048ympin4pi0njw9"))))
+    (build-system emacs-build-system)
+    (inputs
+     `(("scrot" ,scrot)
+       ("imagemagick" ,imagemagick)
+       ("gifsicle" ,gifsicle)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((scrot (assoc-ref inputs "scrot"))
+                   (imagemagick (assoc-ref inputs "imagemagick"))
+                   (gifsicle (assoc-ref inputs "gifsicle")))
+               (make-file-writable "gif-screencast.el")
+               ;; Specify the absolute file names of the various
+               ;; programs so that everything works out-of-the-box.
+               (emacs-substitute-variables
+                   "gif-screencast.el"
+                 ("gif-screencast-program"
+                  (string-append scrot "/bin/scrot"))
+                 ("gif-screencast-convert-program"
+                  (string-append imagemagick "/bin/convert"))
+                 ("gif-screencast-cropping-program"
+                  (string-append imagemagick "/bin/mogrify"))
+                 ("gif-screencast-optimize-program"
+                  (string-append gifsicle "/bin/gifsicle")))))))))
+    (home-page
+     "https://gitlab.com/Ambrevar/emacs-gif-screencast")
+    (synopsis "One-frame-per-action GIF recording")
+    (description
+     "Call @code{gif-screencast} to start a recording.
 A screenshot is taken for every user action.  Call
 @code{gif-screencast-stop} (<f9> by default) to finish recording and create
 the GIF result.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public emacs-google-translate
   (package

From 3c6332128af7ca4610e0513f0577771e16e91955 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 27 Jan 2020 14:37:16 -0500
Subject: [PATCH 076/127] gnu: linux-libre@4.14: Update to 4.14.168.

* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.168.
(linux-libre-4.14-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 5162dfff18..ebc27dccc6 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -373,10 +373,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.167")
+(define-public linux-libre-4.14-version "4.14.168")
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "0hzyb5k6adhg4vkhix21kg7z6gdzyk1dnzylvbsz9yh2m73qzdrb")))
+        (hash (base32 "1ziixdg4jsr17kgfa9dpckczk0r2mc5jayqb2f6br19al79pfmyv")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))

From 678f651e8d3800826a2e1bf7ddfa5dac587a149d Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 27 Jan 2020 14:38:13 -0500
Subject: [PATCH 077/127] gnu: linux-libre@4.19: Update to 4.19.99.

* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.99.
(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 ebc27dccc6..8a3972c786 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -365,10 +365,10 @@ 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 "4.19.98")
+(define-public linux-libre-4.19-version "4.19.99")
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "0dr9vnaaycq77r49mj001zvkxhdyxkgh27dbjsaxcq1dq8xv3zli")))
+        (hash (base32 "1axmspnqir2zz7lail95y5yaamxl86k39sd4im3c77dgjkwj3g4d")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))

From 062cbc4f2b746f5b7fb1766107b5fd183628ed17 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 20:47:46 +0100
Subject: [PATCH 078/127] gnu: r-destiny: Update to 3.0.1.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3fb47884ae..0b8598a737 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2160,14 +2160,14 @@ possible, parallelization is achieved using the BiocParallel framework.")
 (define-public r-destiny
   (package
     (name "r-destiny")
-    (version "3.0.0")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "destiny" version))
        (sha256
         (base32
-         "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz"))))
+         "1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)

From c5d75df36693d677c268b2141fdaa5fb3d767561 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 20:47:57 +0100
Subject: [PATCH 079/127] gnu: r-ropls: Update to 1.18.8.

* gnu/packages/bioconductor.scm (r-ropls): Update to 1.18.8.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0b8598a737..b0f224fd5c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5164,14 +5164,14 @@ packages.")
 (define-public r-ropls
   (package
     (name "r-ropls")
-    (version "1.18.6")
+    (version "1.18.8")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
-         "1sm2fmygrra9gdcs90lmk5y1ag6arga6159kggx4ij8bkhyc66vb"))))
+         "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)

From 0dfaebfa2e90fa044bec102da3704451e57b2d7d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 20:48:04 +0100
Subject: [PATCH 080/127] gnu: r-multiassayexperiment: Update to 1.12.2.

* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b0f224fd5c..469f2897ae 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7177,14 +7177,14 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.12.1")
+    (version "1.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "0xpi5qpffg9pn8szkvicpc43a0r534wngyqwvsip8w66zi8c9kpc"))))
+         "0722f3jl1xq8k8w7vrv986jd16bgysqp3n07pgmdn0hh1zh2mcqc"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)

From caf4290bd8ab4cedde72a7ec74aaf6b42ce39469 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 20:48:10 +0100
Subject: [PATCH 081/127] gnu: r-s4vectors: Update to 0.24.3.

* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 82a286b591..46086cb8ec 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7349,13 +7349,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.24.2")
+    (version "0.24.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "1s1h00k2ki7sd0hz4l8n41xr6ixszag7lm0ryrbb08idgcy16ipn"))))
+                "01f7dms4kw9ajwqlvh5s47riv748xrrs41na03byhjvn4fbdc44y"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)

From c7b98a84d90d918b044f403886e93cf418ed2f3a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 20:48:16 +0100
Subject: [PATCH 082/127] gnu: r-genomicfeatures: Update to 1.38.1.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46086cb8ec..87c950df3b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7930,13 +7930,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.38.0")
+    (version "1.38.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0xd9rlsicycbanbcfhc97cj8b8vk94g7lkbmhk37w1511bq35wz5"))))
+                "1c1x29f447dv0i1wi88paji645lfsgmg4ckn19hyhlra72smhzqc"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)

From 94600c3960d7e2f12a3a9b6d2ed0d98ddacdd055 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Jan 2020 20:48:22 +0100
Subject: [PATCH 083/127] gnu: r-gviz: Update to 1.30.1.

* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87c950df3b..b7b80cec02 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10317,14 +10317,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.30.0")
+    (version "1.30.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "1p7n4yc77272rd8ybsim3rcg6kf6wmc95pwwav40b754imxn263z"))))
+         "03jj193fzmhvkjw8f5zk6wgflkvm3phny0q38scawcplfsyb8z64"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs

From 4fc4e5fdd9da6320aa94eeec61cbb84a7dc9460e Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Mon, 27 Jan 2020 21:26:10 +0100
Subject: [PATCH 084/127] gnu: gnome: Remove gnome-initial-setup.

Fixes <https://bugs.gnu.org/39281>
Reported by Jack Hill <jackhill@jackhill.us>.

* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Remove
gnome-initial-setup.
---
 gnu/packages/gnome.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index e843bdfe08..d4264d8925 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -7865,7 +7865,9 @@ world.")
        ("gnome-control-center" ,gnome-control-center)
        ("gnome-desktop" ,gnome-desktop)
        ("gnome-getting-started-docs" ,gnome-getting-started-docs)
-       ("gnome-initial-setup" ,gnome-initial-setup)
+       ;; Adding gnome-initial-setup causes GDM startup failure.
+       ;; See <https://issues.guix.gnu.org/issue/39281>.
+       ; ("gnome-initial-setup" ,gnome-initial-setup)
        ("gnome-keyring" ,gnome-keyring)
        ("gnome-menus" ,gnome-menus)
        ("gnome-session" ,gnome-session)

From a38bf7c843c75a6ed55495c75c26ccc7afc44a00 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 20 Jan 2020 20:21:09 +0100
Subject: [PATCH 085/127] gnu: Add r-deconstructsigs.

* gnu/packages/bioconductor.scm (r-deconstructsigs): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 469f2897ae..c1da8ac106 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -694,6 +694,34 @@ annotations.")
      "This is a manifest package for Illumina's EPIC methylation arrays.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
+;; from Bioconductor.
+(define-public r-deconstructsigs
+  (package
+    (name "r-deconstructsigs")
+    (version "1.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "deconstructSigs" version))
+              (sha256
+               (base32
+                "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
+    (properties
+     `((upstream-name . "deconstructSigs")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-reshape2" ,r-reshape2)))
+    (home-page "https://github.com/raerose01/deconstructSigs")
+    (synopsis "Identifies signatures present in a tumor sample")
+    (description "This package takes sample information in the form of the
+fraction of mutations in each of 96 trinucleotide contexts and identifies
+the weighted combination of published signatures that, when summed, most
+closely reconstructs the mutational profile.")
+    (license license:gpl2+)))
+
 (define-public r-do-db
   (package
     (name "r-do-db")

From 150c38c2eda13537a01f481276a0750bb1c49678 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 27 Jan 2020 15:04:28 +0100
Subject: [PATCH 086/127] gnu: sicp: Do not import module from the host Guile.

This is a followup to 4144eb195c28cbfd1ca2a131cf4b64afcad713ae
and 5e61de242156cdb3314abac168d9682ca7a4c28f.

* gnu/packages/scheme.scm (sicp)[arguments]: Remove (srfi srfi-26) from
 #:modules.
---
 gnu/packages/scheme.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm
index c765125b85..1009896a70 100644
--- a/gnu/packages/scheme.scm
+++ b/gnu/packages/scheme.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2018, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
@@ -637,8 +637,7 @@ threads.")
                        ("source" ,source)
                        ("texinfo" ,texinfo)))
       (arguments
-       `(#:modules ((guix build utils)
-                    (srfi srfi-26))
+       `(#:modules ((guix build utils))
          #:builder
          (begin
            (use-modules (guix build utils)

From cd903b04430588d668f0e601cbc05e1117727558 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 27 Jan 2020 18:19:38 +0100
Subject: [PATCH 087/127] git-authenticate: Add roptat's new key.

This is a followup to 2cbede5935eb6a40173bbdf30a9ad22bf7574c22.

* build-aux/git-authenticate.scm (%committers): Add roptat's new key.
---
 build-aux/git-authenticate.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/build-aux/git-authenticate.scm b/build-aux/git-authenticate.scm
index 980a6d8e9f..d92da90758 100644
--- a/build-aux/git-authenticate.scm
+++ b/build-aux/git-authenticate.scm
@@ -166,8 +166,12 @@
      "0154 E1B9 1CC9 D9EF 7764  8DE7 F3A7 27DB 44FC CA36")
     ("roelj"
      "17CB 2812 EB63 3DFF 2C7F  0452 C3EC 1DCA 8430 72E1")
-    ("roptat"
+    ("roptat (old)"
      "B5FA E628 5B41 3728 B2A0  FAED 4311 1F45 2008 6A0C")
+    ("roptat"
+     ;; From commit 2cbede5935eb6a40173bbdf30a9ad22bf7574c22 (Jan. 2020).  See
+     ;; <https://lists.gnu.org/archive/html/guix-devel/2020-01/msg00499.html>.
+     "1EFB 0909 1F17 D28C CBF9  B13A 53D4 57B2 D636 EE82")
     ("samplet"
      ;; primary: "D6B0 C593 DA8C 5EDC A44C  7A58 C336 91F7 1188 B004"
      "A02C 2D82 0EF4 B25B A6B5  1D90 2AC6 A5EC 1C35 7C59")

From 2d3a622d04de7b7f58192dc868b846ec416f95bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 27 Jan 2020 23:01:59 +0100
Subject: [PATCH 088/127] gnu: guile-charting: Add "guile3.0-charting" variant.

* gnu/packages/plotutils.scm (guile-charting)[source]: In 'snippet',
have 'configure' look for 3.0.
(guile3.0-charting): New variable.
---
 gnu/packages/plotutils.scm | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm
index 237baa932c..ac8a6f46fc 100644
--- a/gnu/packages/plotutils.scm
+++ b/gnu/packages/plotutils.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 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016, 2017, 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -99,6 +99,11 @@ scientific data.")
               (modules '((guix build utils)))
               (snippet
                '(begin
+                  ;; Allow builds with Guile 3.0.
+                  (substitute* "configure"
+                    (("2\\.2 2\\.0")
+                     "3.0 2.2 2.0"))
+
                   ;; By default, .go files would be installed to
                   ;; $libdir/…/ccache instead of $libdir/…/site-ccache.  Fix
                   ;; that.
@@ -116,6 +121,13 @@ scientific data.")
 using the Cairo drawing library.")
     (license license:lgpl2.1+)))
 
+(define-public guile3.0-charting
+  (package
+    (inherit guile-charting)
+    (name "guile3.0-charting")
+    (inputs `(("guile" ,guile-3.0)))
+    (propagated-inputs `(("guile-cairo" ,guile3.0-cairo)))))
+
 (define-public ploticus
   (package
     (name "ploticus")

From 5d703da3f7475a5f3912361edf5217d29578d9a6 Mon Sep 17 00:00:00 2001
From: Alexandros Theodotou <alex@zrythm.org>
Date: Wed, 8 Jan 2020 14:26:45 +0000
Subject: [PATCH 089/127] gnu: Add libaudec.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/audio.scm (libaudec): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/audio.scm | 33 ++++++++++++++++++++++++++++++++-
 1 file changed, 32 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 95222a5d81..c0fb800193 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -23,7 +23,7 @@
 ;;; Copyright © 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2019 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
-;;; Copyright © 2019 Alexandros Theodotou <alex@zrythm.org>
+;;; Copyright © 2019, 2020 Alexandros Theodotou <alex@zrythm.org>
 ;;; Copyright © 2019 Christopher Lemmer Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;; Copyright © 2019 Hartmt Goebel <h.goebel@crazy-compilers.com>
@@ -54,6 +54,7 @@
   #:use-module (guix build-system waf)
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system meson)
   #:use-module (guix build-system python)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (gnu packages)
@@ -4009,3 +4010,33 @@ in the package.")
     ;; (see the file 'COPYING.LGPL'). This allows writing ECI applications
     ;; that are not licensed under GPL.
     (license (list license:gpl2 license:lgpl2.1))))
+
+(define-public libaudec
+  (package
+    (name "libaudec")
+    (version "0.2")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://git.zrythm.org/git/libaudec")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32
+            "0lfydvs92b0hr72z71ci3yi356rjzi162pgms8dphgg18bz8dazv"))))
+   (build-system meson-build-system)
+   (arguments
+    `(#:configure-flags `("-Denable_tests=true -Denable_ffmpeg=true")))
+   (inputs
+    `(("libsamplerate" ,libsamplerate)
+      ("libsndfile" ,libsndfile)
+      ("ffmpeg" ,ffmpeg)))
+   (native-inputs
+     `(("pkg-config", pkg-config)))
+   (synopsis "Library for reading and resampling audio files")
+   (description "libaudec is a wrapper library over ffmpeg, sndfile and
+libsamplerate for reading and resampling audio files, based on Robin Gareus'
+@code{audio_decoder} code.")
+   (home-page "https://git.zrythm.org/cgit/libaudec")
+   (license license:agpl3+)))

From 93f4511eb0c9b33f5083c2a04f4148e0a494059c Mon Sep 17 00:00:00 2001
From: Alexandros Theodotou <alex@zrythm.org>
Date: Wed, 8 Jan 2020 14:31:05 +0000
Subject: [PATCH 090/127] gnu: Add zrythm.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/music.scm (zrythm): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/music.scm | 49 +++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 48 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 63e2686617..e378e9880b 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -24,7 +24,7 @@
 ;;; Copyright © 2019 Jakob L. Kreuze <zerodaysfordays@sdf.lonestar.org>
 ;;; Copyright © 2019 raingloom <raingloom@protonmail.com>
 ;;; Copyright © 2019 David Wilson <david@daviwil.com>
-;;; Copyright © 2019 Alexandros Theodotou <alex@zrythm.org>
+;;; Copyright © 2019, 2020 Alexandros Theodotou <alex@zrythm.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -5138,3 +5138,50 @@ MIDI drums and comes as two separate drumkits: Black Pearl and Red Zeppelin.")
     (description "Helm is a cross-platform polyphonic synthesizer available standalone
 and as an LV2 plugin.")
     (license license:gpl3+)))
+
+(define-public zrythm
+  (package
+    (name "zrythm")
+    (version "0.7.345")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://www.zrythm.org/releases/zrythm-"
+                            version ".tar.xz"))
+        (sha256
+          (base32
+            "1csiwq38a1ckx23lairfpl7qjkz71wsa7a9vsxl3k58f9ybibiil"))))
+   (build-system meson-build-system)
+   (arguments
+    `(#:glib-or-gtk? #t
+      #:configure-flags
+      `("-Denable_tests=true" "-Dmanpage=true"
+        "-Dinstall_dseg_font=false" "-Denable_ffmpeg=true")))
+   (inputs
+    `(("alsa-lib" ,alsa-lib)
+      ("jack" ,jack-1)
+      ("font-dseg", font-dseg)
+      ("ffmpeg", ffmpeg)
+      ("fftw", fftw)
+      ("fftwf", fftwf)
+      ("gettext", gettext-minimal)
+      ("glibc", glibc)
+      ("gtk+", gtk+)
+      ("libsamplerate" ,libsamplerate)
+      ("libsndfile" ,libsndfile)
+      ("libyaml" ,libyaml)
+      ("lilv", lilv)
+      ("xdg-utils", xdg-utils)
+      ("rubberband", rubberband)))
+   (native-inputs
+     `(("pkg-config", pkg-config)
+       ("help2man", help2man)
+       ("libaudec" ,libaudec)
+       ("lv2", lv2)
+       ("glib" ,glib "bin"))) ;for 'glib-compile-resources'
+   (synopsis "Digital audio workstation focusing on usability")
+   (description "Zrythm is a digital audio workstation designed to be
+featureful and easy to use.  It offers unlimited automation options, LV2
+plugin support, JACK support and chord assistance.")
+   (home-page "https://www.zrythm.org")
+   (license license:agpl3+)))

From 412622ad661bb1d60cd520fba1d4c6a0280551d0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= <boskovits@gmail.com>
Date: Tue, 28 Jan 2020 00:32:06 +0100
Subject: [PATCH 091/127] gnu: go-github-com-prometheus-node-exporter: Update
 to 0.18.1.

* gnu/packages/monitoring.scm
(go-github-com-prometheus-node-exporter): Update to 0.18.1.
---
 gnu/packages/monitoring.scm | 40 ++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 21 deletions(-)

diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm
index 78f94bbe4b..1eb095ce50 100644
--- a/gnu/packages/monitoring.scm
+++ b/gnu/packages/monitoring.scm
@@ -401,28 +401,26 @@ WSGI and the node exporter textfile collector.")
   (package-with-python2 python-prometheus-client))
 
 (define-public go-github-com-prometheus-node-exporter
-  (let ((commit "55c32fcf02492fe4946f7ab563547cc5df7fc61e")
-        (revision "0"))
-    (package
-      (name "go-github-com-prometheus-node-exporter")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/prometheus/node_exporter.git")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "041b87a0sid23c29swqmi5hw6cxbxvkfj3415jg73cm2pi8wh5s6"))))
-      (build-system go-build-system)
-      (arguments
-       '(#:import-path "github.com/prometheus/node_exporter"))
-      (synopsis "Prometheus exporter for hardware and OS metrics")
-      (description "Prometheus exporter for metrics exposed by *NIX kernels,
+  (package
+    (name "go-github-com-prometheus-node-exporter")
+    (version "0.18.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/prometheus/node_exporter.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0s3sp1gj86p7npxl38hkgs6ymd3wjjmc5hydyg1b5wh0x3yvpx07"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/prometheus/node_exporter"))
+    (synopsis "Prometheus exporter for hardware and OS metrics")
+    (description "Prometheus exporter for metrics exposed by *NIX kernels,
 written in Go with pluggable metric collectors.")
-      (home-page "https://github.com/prometheus/node_exporter")
-      (license license:asl2.0))))
+    (home-page "https://github.com/prometheus/node_exporter")
+    (license license:asl2.0)))
 
 (define-public fswatch
   (package

From e53829be49901ac05127ebc73d33f9d6206606e9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jakub=20K=C4=85dzio=C5=82ka?= <kuba@kadziolka.net>
Date: Tue, 14 Jan 2020 00:50:37 +0100
Subject: [PATCH 092/127] gnu: termite: Open links properly without xdg-utils
 in profile

* gnu/packages/terminals.scm (termite)[inputs]: Add XDG-UTILS.
  [arguments](patch-xdg-open): New phase.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/terminals.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index b5c3b69f53..dae14aee8f 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -17,6 +17,7 @@
 ;;; Copyright © 2019 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -138,6 +139,11 @@ configurable through a graphical wizard.")
     (arguments
       `(#:phases
         (modify-phases %standard-phases
+          (add-after 'unpack 'patch-xdg-open
+            (lambda _
+              (substitute* "termite.cc"
+                (("xdg-open") (which "xdg-open")))
+              #t))
           (delete 'configure))
         #:tests? #f
         ;; This sets the destination when installing the necessary terminal
@@ -150,6 +156,7 @@ configurable through a graphical wizard.")
     (inputs
      `(("vte" ,vte-ng)
        ("gtk+" ,gtk+)
+       ("xdg-utils" ,xdg-utils)
        ("ncurses" ,ncurses)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))

From 7ee8acbb76bd440a8985a4b2a20b75521c6853ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jakub=20K=C4=85dzio=C5=82ka?= <kuba@kadziolka.net>
Date: Sun, 19 Jan 2020 13:44:10 +0100
Subject: [PATCH 093/127] gnu: Add bvi.

* gnu/packages/hexedit.scm (bvi): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/hexedit.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/hexedit.scm b/gnu/packages/hexedit.scm
index 9aea8e8700..365b6dab08 100644
--- a/gnu/packages/hexedit.scm
+++ b/gnu/packages/hexedit.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -80,3 +81,25 @@ low-level functionality of a debugger with the usability of an @dfn{Integrated
 Development Environment} (IDE).")
     (home-page "http://hte.sourceforge.net/")
     (license license:gpl2)))
+
+(define-public bvi
+  (package
+    (name "bvi")
+    (version "1.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/bvi/bvi/" version
+                    "/bvi-" version ".src.tar.gz"))
+              (sha256
+               (base32
+                "0a0yl0dcyff31k3dr4dpgqmlwygp8iaslnr5gmb6814ylxf2ad9h"))))
+    (build-system gnu-build-system)
+    (arguments '(#:tests? #f))          ; no check target
+    (inputs
+     `(("ncurses" ,ncurses)))
+    (synopsis "Binary file editor")
+    (description "@command{bvi} is a display-oriented editor for binary files,
+based on the @command{vi} text editor.")
+    (home-page "http://bvi.sourceforge.net/")
+    (license license:gpl3+)))

From a947ade67d02a3fcb4bfe4f0dcb1d4c575cd6368 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 27 Jan 2020 19:07:10 +0200
Subject: [PATCH 094/127] gnu: Add vim-guix-vim.

* gnu/packages/vim.scm (vim-guix-vim): New variable.
---
 gnu/packages/vim.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm
index b5952e3e21..f130ae4392 100644
--- a/gnu/packages/vim.scm
+++ b/gnu/packages/vim.scm
@@ -938,3 +938,37 @@ through its msgpack-rpc API.")
 
 (define-public python2-pynvim
   (package-with-python2 python-pynvim))
+
+(define-public vim-guix-vim
+  (package
+    (name "vim-guix-vim")
+    (version "0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://gitlab.com/Efraim/guix.vim")
+                     (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1f8h8m96fqh3f9hy87spgh9kdqzyxl11n9s3rywvyq5xhn489bnk"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (vimfiles (string-append out "/share/vim/vimfiles")))
+               (for-each
+                 (lambda (dir)
+                   (copy-recursively dir (string-append vimfiles "/" dir)))
+                 '("compiler" "doc" "indent" "ftdetect" "ftplugin" "syntax"))
+               #t))))))
+    (home-page "https://gitlab.com/Efraim/guix.vim")
+    (synopsis "Guix integration in Vim")
+    (description "This package provides support for GNU Guix in Vim.")
+    (license license:vim)))

From 26d361b5cfc252b3a43ec8f63bf418ed654e2bc0 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Tue, 28 Jan 2020 08:44:50 +0100
Subject: [PATCH 095/127] gnu: Add emacs-company-ebdb.

* gnu/packages/emacs-xyz.scm (emacs-company-ebdb): 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 f36d9feda3..d1969845dc 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -21123,3 +21123,24 @@ pattern guessed from thing under current cursor position.
 mercury-mode provided by Emacs as a wrapper around prolog-mode.")
       (home-page "https://github.com/ahungry/metal-mercury-mode")
       (license license:gpl3+))))
+
+(define-public emacs-company-ebdb
+  (package
+    (name "emacs-company-ebdb")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://elpa.gnu.org/packages/"
+                           "company-ebdb-" version ".el"))
+       (sha256
+        (base32 "146qpiigz12zp1823ggxfrx090g0mxs7gz1ba7sa0iq6ibgzwwm9"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-company" ,emacs-company)))
+    (home-page "https://elpa.gnu.org/packages/company-ebdb.html")
+    (synopsis "Company completion backend for EBDB in Message mode")
+    (description "@code{company-ebdb} provides Company mode integration for
+EBDB.  It is copied more or less intact from @code{company-bbdb}, originally
+by Jan Tatarik.")
+    (license license:gpl3+)))

From a3cad594c01eb5b6ce239c9be197cc42088fb18f Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Tue, 28 Jan 2020 08:46:40 +0100
Subject: [PATCH 096/127] gnu: emacs-xyz: Update copyright header.

---
 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 d1969845dc..ed03c2bddd 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -51,7 +51,7 @@
 ;;; Copyright © 2019 Baptiste Strazzulla <bstrazzull@hotmail.fr>
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
-;;; Copyright © 2019 Amin Bandali <mab@gnu.org>
+;;; Copyright © 2019, 2020 Amin Bandali <mab@gnu.org>
 ;;; Copyright © 2019 Jelle Licht <jlicht@fsfe.org>
 ;;; Copyright © 2019 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2019 Stephen Webber <montokapro@gmail.com>

From d5a08205ebd0ba44b113cde6369e8f3c890eb4fd Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Tue, 28 Jan 2020 09:18:01 +0100
Subject: [PATCH 097/127] gnu: manuskript: Update to 0.11.0.

* gnu/packages/text-editors.scm (manuskript): Update to 0.11.0.
---
 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 922de86eb1..7806a4c8b2 100644
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@ -468,7 +468,7 @@ environment with Markdown markup.")
 (define-public manuskript
   (package
     (name "manuskript")
-    (version "0.10.0")
+    (version "0.11.0")
     (source
      (origin
        (method git-fetch)
@@ -477,7 +477,7 @@ environment with Markdown markup.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0q413vym7hzjpyg3krj5y63hwpncdifjkyswqmr76zg5yqnklnh3"))))
+        (base32 "1l6l9k6k69yv8xqpll0zv9cwdqqg4zvxy90l6sx5nv2yywh5crla"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f                      ;no test

From 2545ab2a0c6841c47e04d3ef874da311dc213213 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Jan 2020 10:14:45 +0200
Subject: [PATCH 098/127] gnu: gourmet: Don't use unstable tarball.

* gnu/packages/nutrition.scm (gourmet)[source]: Download using git-fetch.
---
 gnu/packages/nutrition.scm | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/nutrition.scm b/gnu/packages/nutrition.scm
index bae166de3f..ebab2c44fc 100644
--- a/gnu/packages/nutrition.scm
+++ b/gnu/packages/nutrition.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,7 +22,7 @@
 (define-module (gnu packages nutrition)
   #:use-module (guix packages)
   #:use-module (guix licenses)
-  #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages databases)
@@ -38,13 +39,14 @@
     (version "0.17.4")
     (source
      (origin
-      (method url-fetch)
-      (uri (string-append "https://github.com/thinkle/gourmet/archive/"
-                          version ".tar.gz"))
-      (file-name (string-append name "-" version ".tar.gz"))
+      (method git-fetch)
+      (uri (git-reference
+             (url "https://github.com/thinkle/gourmet")
+             (commit version)))
+      (file-name (git-file-name name version))
       (sha256
        (base32
-        "1qvz175arzqm10lpfx8ffadrgirs3240zzqcp0h7sl53qfwx7v8k"))))
+        "09a2zk140l4babwdj8pwcgl9v7rvwff9cn7h3ppfhm3yvsgkrx07"))))
     (build-system python-build-system)
     (native-inputs
      `(("distutils-extra"   ,python2-distutils-extra)

From 84c10c3b22314f93ecd25fc25662391be9e0814d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Jan 2020 10:15:43 +0200
Subject: [PATCH 099/127] gnu: gourmet: Adjust install phase.

* gnu/packages/nutrition.scm (gourmet)[arguments]: Adjust custom
'install phase.
---
 gnu/packages/nutrition.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/nutrition.scm b/gnu/packages/nutrition.scm
index ebab2c44fc..f936c2651b 100644
--- a/gnu/packages/nutrition.scm
+++ b/gnu/packages/nutrition.scm
@@ -66,9 +66,9 @@
        #:phases
        (modify-phases %standard-phases
          (replace 'install
-           (lambda* (#:key make-flags #:allow-other-keys)
+           (lambda* (#:key outputs #:allow-other-keys)
              (invoke "python" "setup.py" "install" "--prefix"
-                     (assoc-ref %outputs "out")))))))
+                     (assoc-ref outputs "out")))))))
     (home-page "https://thinkle.github.io/gourmet/")
     (synopsis "Recipe organizer")
     (description

From cfb065fcb936fe773f25f1797564320baa3990f3 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Tue, 28 Jan 2020 09:23:56 +0100
Subject: [PATCH 100/127] gnu: Add emacs-boxquote.

* gnu/packages/emacs-xyz.scm (emacs-boxquote): 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 ed03c2bddd..e6c4bfc459 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -21124,6 +21124,31 @@ mercury-mode provided by Emacs as a wrapper around prolog-mode.")
       (home-page "https://github.com/ahungry/metal-mercury-mode")
       (license license:gpl3+))))
 
+(define-public emacs-boxquote
+  ;; The following commit is 2.1 release with a switch to GPL3+ license.
+  (let ((commit "7e47e0e2853bc1215739b2e28f260e9eed93b2c5")
+        (revision "0"))
+    (package
+      (name "emacs-boxquote")
+      (version (git-version "2.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/davep/boxquote.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1aqhg24gajvllbqxb0zxrnx6sddas37k2ldfinqyszd856sjhsg3"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/davep/boxquote.el")
+      (synopsis "Quote text with different kinds of boxes")
+      (description "@code{boxquote} provides a set of functions for using
+a text quoting style that partially boxes in the left hand side of an area of
+text, such a marking style might be used to show externally included text or
+example code.")
+      (license license:gpl3+))))
+
 (define-public emacs-company-ebdb
   (package
     (name "emacs-company-ebdb")

From 479f401361a5f7dc54c7fefdca211bd2452dea5a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jakub=20K=C4=85dzio=C5=82ka?= <kuba@kadziolka.net>
Date: Mon, 27 Jan 2020 22:08:48 +0100
Subject: [PATCH 101/127] gnu: Add python-pypng.

* gnu/packages/python-xyz.scm (python-pypng): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/python-xyz.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2af2b2011c..31aeffa161 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -68,6 +68,7 @@
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org>
 ;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -17436,3 +17437,32 @@ Project, or not such a gitlab instance when your upstream doesn't use any
 dedicated platform.  The tool proposes a unified interface for any format and
 an upload option to send your work back to the platform.")
     (license license:gpl3+)))
+
+(define-public python-pypng
+  (package
+    (name "python-pypng")
+    (version "0.0.20")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pypng" version))
+       (sha256
+        (base32 "02qpa22ls41vwsrzw9r9qhj1nhq05p03hb5473pay6y980s86chh"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/drj11/pypng")
+    (synopsis "Pure Python PNG image encoder/decoder")
+    (description
+     "The PyPNG module implements support for PNG images.  It reads and writes
+PNG files with all allowable bit depths (1/2/4/8/16/24/32/48/64 bits per
+pixel) and colour combinations: greyscale (1/2/4/8/16 bit); RGB, RGBA,
+LA (greyscale with alpha) with 8/16 bits per channel; colour mapped
+images (1/2/4/8 bit).  Adam7 interlacing is supported for reading and writing.
+A number of optional chunks can be specified (when writing) and
+understood (when reading): tRNS, bKGD, gAMA.
+
+PyPNG is not a high level toolkit for image processing (like PIL) and does not
+aim at being a replacement or competitor.  Its strength lies in fine-grained
+extensive support of PNG features.  It can also read and write Netpbm PAM
+files, with a focus on its use as an intermediate format for implementing
+custom PNG processing.")
+    (license license:expat)))

From 19568f9e79ed74b7100d25d3f2ea245f857ca742 Mon Sep 17 00:00:00 2001
From: Amin Bandali <mab@gnu.org>
Date: Tue, 28 Jan 2020 03:20:30 -0500
Subject: [PATCH 102/127] gnu: Add emacs-mwim.

* gnu/packages/emacs-xyz.scm (emacs-mwim): 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 e6c4bfc459..a7377d8e42 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -21169,3 +21169,28 @@ example code.")
 EBDB.  It is copied more or less intact from @code{company-bbdb}, originally
 by Jan Tatarik.")
     (license license:gpl3+)))
+
+(define-public emacs-mwim
+  ;; Use the latest commit not in a release version as of yet, since it
+  ;; contains a bug fix for the cases where `comment-start-skip' is nil.
+  (let ((commit "b4f3edb4c0fb8f8b71cecbf8095c2c25a8ffbf85")
+        (revision "0"))
+    (package
+      (name "emacs-mwim")
+      (version (git-version "0.4" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/alezost/mwim.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0l3k611gp9g2x2vfmh92wnhnda81dslpwwpb8mxmzk308man77ya"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/alezost/mwim.el")
+      (synopsis "Move to the beginning/end of line, code or comment")
+      (description "@code{mwim} provides several commands to switch between
+various line positions, like moving to the beginning/end of code, line, or
+comment.")
+      (license license:gpl3+))))

From 8684575a88fc19d6b421af46d19fa64e1bf613fa Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Jan 2020 10:49:02 +0200
Subject: [PATCH 103/127] gnu: ocaml-lwt: Don't use unstable tarball.

* gnu/packages/ocaml.scm (ocaml-lwt)[source]: Download using git-fetch.
---
 gnu/packages/ocaml.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index df998af1f5..a8fdd00d8e 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -1784,12 +1784,13 @@ for mapping files in memory.  This function is the same as the
     (version "5.1.1")
     (source
       (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/ocsigen/lwt/archive/" version
-                            ".tar.gz"))
-        (file-name (string-append name "-" version ".tar.gz"))
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/ocsigen/lwt")
+               (commit version)))
+        (file-name (git-file-name name version))
         (sha256 (base32
-                  "0gwdmhn0qx03agc45dplj73ia5y1gb42aan64ywfxmll3lsnr2h7"))))
+                 "1nl7rdnwfdhwcsm5zpay1nr9y5cbapd9x1qzily7zk9ab4v52m8g"))))
     (build-system dune-build-system)
     (arguments
      `(#:package "lwt"))

From 4d85a7dd26c06b22e7fcafc0855a6a84df3a38dd Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Jan 2020 10:51:40 +0200
Subject: [PATCH 104/127] gnu: ocaml-ocplib-endian: Don't use unstable tarball.

* gnu/packages/ocaml.scm (ocaml-ocplib-endian)[source]: Download using
git-fetch.
---
 gnu/packages/ocaml.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index a8fdd00d8e..65d89bca26 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -2659,13 +2659,14 @@ standard iterator type starting from 4.07.")
     (name "ocaml-ocplib-endian")
     (version "1.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/OCamlPro/ocplib-endian/"
-                                  "archive/" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/OCamlPro/ocplib-endian/")
+                     (commit version)))
               (sha256
                (base32
-                "0hwj09rnzjs0m0kazz5h2mgs6p95j0zlga8cda5srnzqmzhniwkn"))
-              (file-name (string-append name "-" version ".tar.gz"))))
+                "0s1ld3kavz892b8awyxyg1mr98h2g61gy9ci5v6yb49bsii6wicw"))
+              (file-name (git-file-name name version))))
     (build-system ocaml-build-system)
     (native-inputs
      `(("cppo" ,ocaml-cppo)

From c8f16c7f7e043bdcfbdffdd09909778adecb9160 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Jan 2020 10:53:42 +0200
Subject: [PATCH 105/127] gnu: ocaml-ctypes: Don't use unstable tarball.

* gnu/packages/ocaml.scm (ocaml-ctypes)[source]: Download using git-fetch.
[arguments]: Add phase to make files writable.
---
 gnu/packages/ocaml.scm | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 65d89bca26..32b03359d8 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -3254,12 +3254,14 @@ long and size_t whose sizes depend on the host platform.")
    (version "0.14.0")
    (home-page "https://github.com/ocamllabs/ocaml-ctypes")
    (source (origin
-             (method url-fetch)
-             (uri (string-append home-page "/archive/" version ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (method git-fetch)
+             (uri (git-reference
+                    (url home-page)
+                    (commit version)))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "0zrsd42q2nciyg9375g2kydqax6ay299rhyfgms59qiw7d9ylyp9"))))
+               "1b2q3h63ngf4x9qp65qwapf2dg9q0mcdah6qjm2q0c7v2p5vysv9"))))
    (build-system ocaml-build-system)
    (arguments
     `(#:tests? #f; require an old lwt
@@ -3267,6 +3269,14 @@ long and size_t whose sizes depend on the host platform.")
       (list (string-append "INSTALL_HEADERS = $(wildcard $($(PROJECT).dir)/*.h)"))
       #:phases
       (modify-phases %standard-phases
+        (add-after 'unpack 'make-writable
+          (lambda _
+            (for-each
+              (lambda (file)
+                (let ((stat (stat file)))
+                  (chmod file (+ #o200 (stat:mode stat)))))
+              (find-files "." "."))
+            #t))
         (delete 'configure))))
    (native-inputs
     `(("pkg-config" ,pkg-config)))

From 2fe83ce10fcfc50d49cdafe2d6981adaf4a27d9d Mon Sep 17 00:00:00 2001
From: Amin Bandali <mab@gnu.org>
Date: Tue, 28 Jan 2020 10:28:04 +0100
Subject: [PATCH 106/127] gnu: Add emacs-delight.

* gnu/packages/emacs-xyz.scm (emacs-delight): New variable.
---
 gnu/packages/emacs-xyz.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index a7377d8e42..e5af72121a 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -21194,3 +21194,21 @@ by Jan Tatarik.")
 various line positions, like moving to the beginning/end of code, line, or
 comment.")
       (license license:gpl3+))))
+
+(define-public emacs-delight
+  (package
+    (name "emacs-delight")
+    (version "1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://elpa.gnu.org/packages/"
+                           "delight-" version ".el"))
+       (sha256
+        (base32 "0kzlvzwmn6zj0874086q2xw0pclyi7wlkq48zh2lkd2796xm8vw7"))))
+    (build-system emacs-build-system)
+    (home-page "https://elpa.gnu.org/packages/delight.html")
+    (synopsis "Dimmer switch for your mode-line lighter text")
+    (description "@code{delight} enables customizing or hiding the
+mode-line text (lighter) of major and minor modes.")
+    (license license:gpl3+)))

From 3450bb81e212187a2c65d7e884668d4fc805ef09 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Sat, 28 Dec 2019 00:28:15 +0100
Subject: [PATCH 107/127] gnu: Add omnitux.

* gnu/packages/education.scm (omnitux): New variable.
---
 gnu/packages/education.scm | 102 +++++++++++++++++++++++++++++++++++++
 1 file changed, 102 insertions(+)

diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index ecb8678b02..7d785233e1 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -485,6 +485,108 @@ letters of the alphabet, spelling, eye-hand coordination, etc.")
     (home-page "http://www.schoolsplay.org")
     (license license:gpl3+)))
 
+(define-public omnitux
+  (package
+    (name "omnitux")
+    (version "1.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/omnitux/omnitux/"
+                           "v" version "/omnitux-" version ".tar.bz2"))
+       (sha256
+        (base32 "1wmmmbzmxd0blhn00d4g91xwavnab143a31ca3i8hrqgzh6qz9w6"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Remove pre-compiled .pyc files from source.
+           (for-each delete-file (find-files "bin" "\\.pyc$"))
+           #t))))
+    (build-system python-build-system)
+    (inputs
+     `(("python2-pygame" ,python2-pygame)
+       ("python2-pygtk" ,python2-pygtk)))
+    (arguments
+     `(#:tests? #f                      ;no test
+       #:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'build)                ;no setup.py
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (share (string-append out "/share"))
+                    (data (string-append share "/omnitux")))
+               ;; Install documentation.
+               (let ((doc (string-append share "/doc/" ,name "-" ,version)))
+                 (for-each (lambda (f) (install-file f doc))
+                           '("LICENSE.txt" "README.txt")))
+               ;; Install data.
+               (install-file "omnitux.sh" data)
+               (for-each (lambda (d)
+                           (copy-recursively d (string-append data "/" d)))
+                         '("bin" "data"))
+               ;; Install the launcher.
+               (let* ((bin (string-append out "/bin"))
+                      (script (string-append bin "/omnitux"))
+                      (bash (string-append (assoc-ref %build-inputs "bash")
+                                           "/bin/bash"))
+                      (python (string-append (assoc-ref %build-inputs "python")
+                                             "/bin/python2")))
+                 (mkdir-p bin)
+                 (with-output-to-file script
+                   (lambda ()
+                     (format #t "#!~a~%" bash)
+                     (format #t
+                             "cd ~a; ~a menu.py~%"
+                             (string-append data "/bin")
+                             python)))
+                 (chmod script #o755))
+               ;; Install icon and desktop file.
+               (let ((pixmaps (string-append share "/pixmaps")))
+                 (install-file "data/default/icons/Omnitux_logo.svg" pixmaps))
+               (let ((apps (string-append out "/share/applications")))
+                 (mkdir-p apps)
+                 (with-output-to-file (string-append apps "/omnitux.desktop")
+                   (lambda _
+                     (format #t
+                             "[Desktop Entry]~@
+                              Name=Omnitux~@
+                              GenericName=Omnitux
+                              Comment=An educational game based on multimedia elements.~@
+                              Comment[fr]=Un jeu ludo-éducatif basé sur des éléments multimédias.~@
+                              Exec=~a/bin/omnitux~@
+                              Type=Application~@
+                              Categories=Game;Education;~@
+                              Terminal=false~@
+                              Icon=Omnitux_logo.svg~@"
+                             out))))
+               #t))))))
+    (home-page "http://omnitux.sourceforge.net/")
+    (synopsis "Educational activities based on multimedia elements")
+    (description "The project aims to provide various educational
+activities around multimedia elements (images, sounds, texts).  Types
+of activities include:
+@itemize
+@item associations,
+@item items to place on a map or a schema,
+@item counting activities,
+@item puzzles,
+@item card faces to remember,
+@item find differences between two pictures,
+@item ...
+@end itemize
+
+Activities are available in English, French, German, Polish,
+Portuguese, Spanish and Italian.")
+    ;; Project's license is GPL3+, but multimedia elements are
+    ;; released under various licenses.
+    (license (list license:gpl3+
+                   license:gpl2+
+                   license:cc-by-sa2.0
+                   license:cc-by-sa3.0
+                   license:public-domain))))
+
 (define-public fet
   (package
     (name "fet")

From f4167bdad7a98fd1248b8fff4d18c56d91427514 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Tue, 28 Jan 2020 10:34:24 +0100
Subject: [PATCH 108/127] gnu: education.scm: Update copyright line.

---
 gnu/packages/education.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index 7d785233e1..4f8d7582c7 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2018, 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;

From d823fd96b5a62e0d3d9bed08afc228dc52f7ba06 Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Tue, 28 Jan 2020 14:26:49 +0100
Subject: [PATCH 109/127] gnu: Add bruteforce-luks.

* gnu/packages/password-utils.scm (bruteforce-luks): New variable.
---
 gnu/packages/password-utils.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index 5f297e117a..8d74490d23 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -24,6 +24,7 @@
 ;;; Copyright © 2018, 2019 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
 ;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org>
+;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -56,6 +57,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crypto)
+  #:use-module (gnu packages cryptsetup)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages file)
   #:use-module (gnu packages freedesktop)
@@ -1066,3 +1068,30 @@ binaries.  All of these utils are designed to execute only one specific
 function.  Since they all work with @code{STDIN} and @code{STDOUT} you can
 group them into chains.")
     (license license:expat)))
+
+(define-public bruteforce-luks
+  (package
+    (name "bruteforce-luks")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/glv2/bruteforce-luks/releases/download/"
+                           version
+                           "/bruteforce-luks-"
+                           version
+                           ".tar.lz"))
+       (sha256
+        (base32 "0yawrlbbklhmvwr99wm7li3r0d5kxvpkwf33a12rji7z0ya5p340"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("lzip" ,lzip)))
+    (inputs
+     `(("cryptsetup" ,cryptsetup)))
+    (synopsis "LUKS encrypted volume cracker")
+    (description
+     "This is a cracker for LUKS encrypted volumes.  It can be used either in
+exhaustive mode to try every password given a charset or in dictionary mode to
+try every password contained in a file.")
+    (home-page "https://github.com/glv2/bruteforce-luks")
+    (license license:gpl3+)))

From 87146f31167953fb3d3c9eb69d70baa0c42aa6e1 Mon Sep 17 00:00:00 2001
From: Jonathan Brielmaier <jonathan.brielmaier@web.de>
Date: Tue, 28 Jan 2020 15:41:09 +0100
Subject: [PATCH 110/127] gnu: lxqt: Correct home page.

* gnu/packages/lxqt.scm (lxqt)[home-page]: It's lxqt not lxde.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
---
 gnu/packages/lxqt.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm
index b23d2e17dc..12c92e52d1 100644
--- a/gnu/packages/lxqt.scm
+++ b/gnu/packages/lxqt.scm
@@ -1386,5 +1386,5 @@ desktop.")
        ("qterminal" ,qterminal)))
     (synopsis "The Lightweight Qt Desktop Environment")
     (description "LXQt is a lightweight Qt desktop environment.")
-    (home-page "https://lxde.org")
+    (home-page "https://lxqt.org/")
     (license license:gpl2+)))

From cd328a7315d75ab167be4e238e0ac3c78fb86cee Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 20 Jan 2020 02:23:59 +0100
Subject: [PATCH 111/127] gnu: Add bcachefs-tools.

* gnu/packages/file-systems.scm (bcachefs-tools): New public variable.
---
 gnu/packages/file-systems.scm | 61 ++++++++++++++++++++++++++++++++++-
 1 file changed, 60 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm
index a3dc993055..d7a0d6dbac 100644
--- a/gnu/packages/file-systems.scm
+++ b/gnu/packages/file-systems.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
@@ -37,6 +37,7 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages crypto)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages documentation)
@@ -52,8 +53,66 @@
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages valgrind)
   #:use-module (gnu packages xml))
 
+(define-public bcachefs-tools
+  (let ((commit "ab2f1ec24f5307b0cf1e3c4ad19bf350d9f54d9f")
+        (revision "0"))
+    (package
+      (name "bcachefs-tools")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://evilpiepirate.org/git/bcachefs-tools.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "10pafvaxg1lvwnqjv3a4rsi96bghbpcsgh3vhqilndi334k3b0hd"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:make-flags
+         (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+               "INITRAMFS_DIR=$(PREFIX)/share/initramfs-tools"
+               "CC=gcc"
+               "PYTEST=pytest")
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure))         ; no configure script
+         #:tests? #f))                  ; XXX 6 valgrind tests fail
+      (native-inputs
+       `(("pkg-config" ,pkg-config)
+
+         ;; For tests.
+         ("python-pytest" ,python-pytest)
+         ("valgrind" ,valgrind)))
+      (inputs
+       `(("keyutils" ,keyutils)
+         ("libaio" ,libaio)
+         ("libscrypt" ,libscrypt)
+         ("libsodium" ,libsodium)
+         ("liburcu" ,liburcu)
+         ("util-linux" ,util-linux)     ; lib{blkid,uuid}
+         ("lz4" ,lz4)
+         ("zlib" ,zlib)
+         ("zstd:lib" ,zstd "lib")))
+      (home-page "https://bcachefs.org/")
+      (synopsis "Tools to create and manage bcachefs file systems")
+      (description
+       "The bcachefs-tools are command-line utilites for creating, checking,
+and otherwise managing bcachefs file systems.
+
+Bcachefs is a @acronym{CoW, copy-on-write} file system supporting native
+encryption, compression, snapshots, and (meta)data checksums.  It can use
+multiple block devices for replication and/or performance, similar to RAID.
+
+In addition, bcachefs provides all the functionality of bcache, a block-layer
+caching system, and lets you assign different roles to each device based on its
+performance and other characteristics.")
+      (license license:gpl2+))))
+
 (define-public httpfs2
   (package
     (name "httpfs2")

From e572ec3cc3b15c281dc6a5c1d850550242ea451f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 28 Jan 2020 17:16:00 +0100
Subject: [PATCH 112/127] gnu: iproute2: Update to 5.5.0.

* gnu/packages/linux.scm (iproute): Update to 5.5.0.
---
 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 8a3972c786..01f6227cc0 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -1788,7 +1788,7 @@ that the Ethernet protocol is much simpler than the IP protocol.")
 (define-public iproute
   (package
     (name "iproute2")
-    (version "5.3.0")
+    (version "5.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1796,7 +1796,7 @@ that the Ethernet protocol is much simpler than the IP protocol.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "0gvv269wjn4279hxr5zzwsk2c5qgswr47za3hm1x4frsk52iw76b"))))
+                "0ywg70f98wgfai35jl47xzpjp45a6n7crja4vc8ql85cbi1l7ids"))))
     (build-system gnu-build-system)
     (arguments
      `( ;; There is a test suite, but it wants network namespaces and sudo.

From 4968ea2c9279389d3b2f427dec29d07f1031784c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 17 Jan 2020 22:18:29 +0100
Subject: [PATCH 113/127] Use HTTPS for liballeg.org.

* gnu/packages/game-development.scm (allegro-4, allegro)[home-page]:
Use HTTPS.
* guix/licenses.scm (giftware): Likewise.
---
 gnu/packages/game-development.scm | 4 ++--
 guix/licenses.scm                 | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 13006f3509..5160bcf2ea 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -723,7 +723,7 @@ package is the Nuklear bindings for LÖVE created by Kevin Harrison.")
 multimedia programming.  It handles common, low-level tasks such as creating
 windows, accepting user input, loading data, drawing images, playing sounds,
 etc.")
-    (home-page "http://liballeg.org")
+    (home-page "https://liballeg.org")
     (license license:giftware)))
 
 (define-public allegro
@@ -764,7 +764,7 @@ etc.")
 multimedia programming.  It handles common, low-level tasks such as creating
 windows, accepting user input, loading data, drawing images, playing sounds,
 etc.")
-    (home-page "http://liballeg.org")
+    (home-page "https://liballeg.org")
     (license license:bsd-3)))
 
 (define-public allegro-5.0
diff --git a/guix/licenses.scm b/guix/licenses.scm
index 41d4fefad2..a44a5bac0d 100644
--- a/guix/licenses.scm
+++ b/guix/licenses.scm
@@ -286,7 +286,7 @@ at URI, which may be a file:// URI pointing the package's tree."
 
 (define giftware
   (license "Giftware"
-           "http://liballeg.org/license.html"
+           "https://liballeg.org/license.html"
            "The Allegro 4 license"))
 
 (define gpl1

From e7c938b2bf591819a64ea0ecb51a863d71339da2 Mon Sep 17 00:00:00 2001
From: Amin Bandali <mab@gnu.org>
Date: Tue, 28 Jan 2020 12:06:46 -0500
Subject: [PATCH 114/127] gnu: Add emacs-unkillable-scratch.

* gnu/packages/emacs-xyz.scm (emacs-unkillable-scratch): 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 e5af72121a..e834dfffb3 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -21212,3 +21212,28 @@ comment.")
     (description "@code{delight} enables customizing or hiding the
 mode-line text (lighter) of major and minor modes.")
     (license license:gpl3+)))
+
+(define-public emacs-unkillable-scratch
+  ;; Use the latest (unreleased) commit as of now, since it contains a handy
+  ;; `unkillable-scratch-do-not-reset-scratch-buffer' customization to not
+  ;; repopulate the scratch buffer with `initial-scratch-message'.
+  (let ((commit "b24c2a760529833f230c14cb02ff6e7ec92288ab")
+        (revision "0"))
+    (package
+      (name "emacs-unkillable-scratch")
+      (version (git-version "1.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/EricCrosson/unkillable-scratch.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "13wjbcxr3km4s96yhpavgs5acs5pvqv3ih1p84diqb3x3i6wd4pa"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/EricCrosson/unkillable-scratch")
+      (synopsis "Prevents the *scratch* buffer from being killed")
+      (description "@code{unkillable-scratch} helps prevent killing buffers
+matching a given regexp.")
+      (license license:gpl2+))))

From 07a7cccbac59dd8265fffdd4b87616cd0419a2c7 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Tue, 28 Jan 2020 20:23:41 +0100
Subject: [PATCH 115/127] gnu: ode: Properly disable tests when
 cross-compiling.

* gnu/packages/game-development.scm (ode): Properly disable tests when
using (%current-target-system).
---
 gnu/packages/game-development.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 5160bcf2ea..2498f6f39d 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1999,9 +1999,9 @@ a.k.a. XenoCollide) as described in Game Programming Gems 7.")
     (build-system cmake-build-system)
     (arguments
      ;; Tests fail on all systems but x86_64.
-     `(#:tests? ,(string=? "x86_64-linux"
-                           (or (%current-target-system)
-                               (%current-system)))
+     `(#:tests? ,(string-prefix? "x86_64-"
+                                 (or (%current-target-system)
+                                     (%current-system)))
        #:configure-flags '("-DODE_WITH_LIBCCD_SYSTEM=ON")
        #:phases
        (modify-phases %standard-phases

From 9111f9750084cbc214d36e2ee16308f8edabf11d Mon Sep 17 00:00:00 2001
From: Leo Prikler <leo.prikler@student.tugraz.at>
Date: Mon, 27 Jan 2020 23:56:57 +0100
Subject: [PATCH 116/127] services: gdm: Disable initial system setup in GDM.

* gnu/services/xorg.scm (gdm-configuration-file): Disable gnome-initial-setup.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
---
 gnu/services/xorg.scm | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/gnu/services/xorg.scm b/gnu/services/xorg.scm
index 9c84f7413f..73a32e4b02 100644
--- a/gnu/services/xorg.scm
+++ b/gnu/services/xorg.scm
@@ -862,7 +862,12 @@ the GNOME desktop environment.")
                    "#TimedLoginEnable=false\n"
                    "#TimedLogin=\n"
                    "#TimedLoginDelay=0\n"
-                   "#InitialSetupEnable=true\n"
+                   ;; Disable initial system setup inside GDM.
+                   ;; Whatever settings are set there should already be
+                   ;; taken care of through `guix system'.
+                   ;; See also
+                   ;; <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=39281>.
+                   "InitialSetupEnable=false\n"
                    ;; Enable me once X is working.
                    "WaylandEnable=false\n"
                    "\n"

From 24882d3d9a0529f34217aac2da2c8d6e2a076a63 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Tue, 28 Jan 2020 21:09:45 +0100
Subject: [PATCH 117/127] gnu: gnome: Re-add gnome-initial-setup.

* gnu/packages/gnome.scm (gnome)[propagated-inputs}: Add gnome-initial-setup.
---
 gnu/packages/gnome.scm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index d4264d8925..e843bdfe08 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -7865,9 +7865,7 @@ world.")
        ("gnome-control-center" ,gnome-control-center)
        ("gnome-desktop" ,gnome-desktop)
        ("gnome-getting-started-docs" ,gnome-getting-started-docs)
-       ;; Adding gnome-initial-setup causes GDM startup failure.
-       ;; See <https://issues.guix.gnu.org/issue/39281>.
-       ; ("gnome-initial-setup" ,gnome-initial-setup)
+       ("gnome-initial-setup" ,gnome-initial-setup)
        ("gnome-keyring" ,gnome-keyring)
        ("gnome-menus" ,gnome-menus)
        ("gnome-session" ,gnome-session)

From e19e3430cdb7c884ac6f91a618aafa6bb94554be Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 29 Jan 2020 00:52:20 +0100
Subject: [PATCH 118/127] gnu: opensmtpd-next: Update to 6.6.2p1 [security
 fixes].
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Upstream[0] says “Qualys has found a critical vulnerability leading to
a possible privilege escalation” and will provide more information
later.

[0]: https://www.opensmtpd.org

* gnu/packages/mail.scm (opensmtpd-next): Update to 6.6.2p1.
---
 gnu/packages/mail.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index baae1d29f4..aa37c4e38c 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -2367,14 +2367,14 @@ e-mails with other systems speaking the SMTP protocol.")
 (define-public opensmtpd-next
   (package
     (name "opensmtpd-next")
-    (version "6.6.1p1")
+    (version "6.6.2p1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.opensmtpd.org/archives/"
                            "opensmtpd-" version ".tar.gz"))
        (sha256
-        (base32 "1ngil8j13m2rq07g94j4yjr6zmaimzy8wbfr17shi7rxnazys6zb"))))
+        (base32 "16nz2n4s3djlasd6m6dqfwggf6igyfxzq5igny5i0qb8lnn13f33"))))
     (build-system gnu-build-system)
     (inputs
      `(("bdb" ,bdb)

From d868261533c4f315dd4812c86f174c3d1a1b08b2 Mon Sep 17 00:00:00 2001
From: Timotej Lazar <timotej.lazar@araneo.si>
Date: Tue, 28 Jan 2020 19:25:38 +0100
Subject: [PATCH 119/127] gnu: godot: Update to 3.1.2.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/game-development.scm (godot): Update to 3.1.2.
[inputs]: Remove openssl, replaced by a bundled copy of mbedtls.
[arguments](configure-flags): Remove builtin_openssl flag.
[source]: Don’t try to remove the (now nonexistent) bundled openssl directory.

Signed-off-by: Christopher Baines <mail@cbaines.net>
---
 gnu/packages/game-development.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 2498f6f39d..bbc9cbc0bd 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -18,6 +18,7 @@
 ;;; Copyright © 2019, 2020 Leo Prikler <leo.prikler@student.tugraz.at>
 ;;; Copyright © 2019 Jethro Cao <jethrocao@gmail.com>
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2020 Timotej Lazar <timotej.lazar@araneo.si>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1503,7 +1504,7 @@ games.")
 (define-public godot
   (package
     (name "godot")
-    (version "3.0.6")
+    (version "3.1.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1512,7 +1513,7 @@ games.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0g64h0x8dlv6aa9ggfcidk2mknkfl5li7z1phcav8aqp9srj8avf"))
+                "12305wj2i4067jc50l8r0wmb7zjcna24fli8vb8kiaild0jrlip6"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1527,7 +1528,6 @@ games.")
                                 "libvorbis"
                                 "libvpx"
                                 "libwebp"
-                                "openssl"
                                 "opus"
                                 "zlib"))
                     #t)))))
@@ -1550,7 +1550,6 @@ games.")
                            "builtin_libvorbis=no"
                            "builtin_libvpx=no"
                            "builtin_libwebp=no"
-                           "builtin_openssl=no"
                            "builtin_opus=no"
                            "builtin_zlib=no")
        #:tests? #f ; There are no tests
@@ -1612,7 +1611,6 @@ games.")
               ("libxinerama" ,libxinerama)
               ("libxrandr" ,libxrandr)
               ("mesa" ,mesa)
-              ("openssl" ,openssl)
               ("opusfile" ,opusfile)
               ("pulseaudio" ,pulseaudio)))
     (home-page "https://godotengine.org/")

From c1bc92c0aa02d8967107efe45dbb27fe824f17a4 Mon Sep 17 00:00:00 2001
From: Timotej Lazar <timotej.lazar@araneo.si>
Date: Tue, 28 Jan 2020 19:25:39 +0100
Subject: [PATCH 120/127] gnu: godot: Unbundle some dependencies.

* gnu/packages/game-development.scm (godot)[inputs]: Add bullet, mbedtls-apache,
pcre2 and zstd.
[arguments](configure-flags): Use system libraries for the above.
[source](snippet): Remove bundled copies.

Signed-off-by: Christopher Baines <mail@cbaines.net>
---
 gnu/packages/game-development.scm | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index bbc9cbc0bd..47fc9a72a7 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -78,6 +78,7 @@
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages music)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages pcre)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
@@ -1521,15 +1522,19 @@ games.")
                   ;; of these may be modified; see "thirdparty/README.md".
                   (with-directory-excursion "thirdparty"
                     (for-each delete-file-recursively
-                              '("freetype"
+                              '("bullet"
+                                "freetype"
                                 "libogg"
                                 "libpng"
                                 "libtheora"
                                 "libvorbis"
                                 "libvpx"
                                 "libwebp"
+                                "mbedtls"
                                 "opus"
-                                "zlib"))
+                                "pcre2"
+                                "zlib"
+                                "zstd"))
                     #t)))))
     (build-system scons-build-system)
     (arguments
@@ -1541,6 +1546,7 @@ games.")
                                '())
                            ;; Avoid using many of the bundled libs.
                            ;; Note: These options can be found in the SConstruct file.
+                           "builtin_bullet=no"
                            "builtin_freetype=no"
                            "builtin_glew=no"
                            "builtin_libmpdec=no"
@@ -1550,8 +1556,11 @@ games.")
                            "builtin_libvorbis=no"
                            "builtin_libvpx=no"
                            "builtin_libwebp=no"
+                           "builtin_mbedtls=no"
                            "builtin_opus=no"
-                           "builtin_zlib=no")
+                           "builtin_pcre2=no"
+                           "builtin_zlib=no"
+                           "builtin_zstd=no")
        #:tests? #f ; There are no tests
        #:phases
        (modify-phases %standard-phases
@@ -1598,6 +1607,7 @@ games.")
                #t))))))
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs `(("alsa-lib" ,alsa-lib)
+              ("bullet" ,bullet)
               ("freetype" ,freetype)
               ("glew" ,glew)
               ("glu" ,glu)
@@ -1610,9 +1620,12 @@ games.")
               ("libxi" ,libxi)
               ("libxinerama" ,libxinerama)
               ("libxrandr" ,libxrandr)
+              ("mbedtls" ,mbedtls-apache)
               ("mesa" ,mesa)
               ("opusfile" ,opusfile)
-              ("pulseaudio" ,pulseaudio)))
+              ("pcre2" ,pcre2)
+              ("pulseaudio" ,pulseaudio)
+              ("zstd" ,zstd "lib")))
     (home-page "https://godotengine.org/")
     (synopsis "Advanced 2D and 3D game engine")
     (description

From 18f8e935e85a99d5c284c0a6b719351a402ada21 Mon Sep 17 00:00:00 2001
From: Timotej Lazar <timotej.lazar@araneo.si>
Date: Tue, 28 Jan 2020 19:25:40 +0100
Subject: [PATCH 121/127] gnu: godot: List which third party files to keep.

Remove everything else to catch added dependencies in new versions.

* gnu/packages/game-development.scm (godot)[source](snippet): Instead of
  removing (only) the unbundled libs, remove everything except the listed files.

Signed-off-by: Christopher Baines <mail@cbaines.net>
---
 gnu/packages/game-development.scm | 51 ++++++++++++++++++++-----------
 1 file changed, 33 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 47fc9a72a7..ceec993d04 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1515,27 +1515,42 @@ games.")
               (sha256
                (base32
                 "12305wj2i4067jc50l8r0wmb7zjcna24fli8vb8kiaild0jrlip6"))
-              (modules '((guix build utils)))
+              (modules '((guix build utils)
+                         (ice-9 ftw)
+                         (srfi srfi-1)))
               (snippet
                '(begin
-                  ;; Drop libraries that we take from Guix.  Note that some
-                  ;; of these may be modified; see "thirdparty/README.md".
+                  ;; Keep only those bundled files we have not (yet) replaced
+                  ;; with Guix versions. Note that some of these may be
+                  ;; modified; see "thirdparty/README.md".
                   (with-directory-excursion "thirdparty"
-                    (for-each delete-file-recursively
-                              '("bullet"
-                                "freetype"
-                                "libogg"
-                                "libpng"
-                                "libtheora"
-                                "libvorbis"
-                                "libvpx"
-                                "libwebp"
-                                "mbedtls"
-                                "opus"
-                                "pcre2"
-                                "zlib"
-                                "zstd"))
-                    #t)))))
+                    (let* ((preserved-files
+                            '("README.md"
+                              "b2d_convexdecomp"
+                              "certs"
+                              "cvtt"
+                              "enet"
+                              "etc2comp"
+                              "fonts"
+                              "glad"
+                              "jpeg-compressor"
+                              "libsimplewebm"
+                              "libwebsockets"
+                              "miniupnpc"
+                              "minizip"
+                              "misc"
+                              "nanosvg"
+                              "pvrtccompressor"
+                              "recastnavigation"
+                              "squish"
+                              "thekla_atlas"
+                              "tinyexr"
+                              "xatlas")))
+                      (for-each delete-file-recursively
+                                (lset-difference string=?
+                                                 (scandir ".")
+                                                 (cons* "." ".." preserved-files)))))
+                  #t))))
     (build-system scons-build-system)
     (arguments
      `(#:scons ,scons-python2

From 4e8d1116ff211c74231724ff1a47c7b855063bd1 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 29 Jan 2020 10:06:43 +0100
Subject: [PATCH 122/127] gnu: mbedtls-apache: Update to 2.16.4.

* gnu/packages/tls.scm (mbedtls-apache): Update to 2.16.4.
---
 gnu/packages/tls.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 10d864348c..358445301b 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -858,7 +858,7 @@ then ported to the GNU / Linux environment.")
 (define-public mbedtls-apache
   (package
     (name "mbedtls-apache")
-    (version "2.16.3")
+    (version "2.16.4")
     (source
      (origin
        (method url-fetch)
@@ -868,7 +868,7 @@ then ported to the GNU / Linux environment.")
                            version "-apache.tgz"))
        (sha256
         (base32
-         "0qd65lnr63vmx2gxla6lcmm5gawlnaj4wy4h4vmdc3h9h9nyw6zc"))))
+         "1yxj5wahaj87xhdi89zbk78ig77b166h464yrj5gb3lwv8mz6h9l"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags

From 92ebd8ede481f5965834d3d676d661cf375b299b Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 29 Jan 2020 10:07:11 +0100
Subject: [PATCH 123/127] gnu: mbedtls-apache: Do not build the static
 libraries.

* gnu/packages/tls.scm (mbedtls-apache)[arguments]: Add
"-DUSE_STATIC_MBEDTLS_LIBRARY=OFF" in #:configure-flags.
---
 gnu/packages/tls.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 358445301b..39f33c6ddc 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -872,7 +872,8 @@ then ported to the GNU / Linux environment.")
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
-       (list "-DUSE_SHARED_MBEDTLS_LIBRARY=ON")))
+       (list "-DUSE_SHARED_MBEDTLS_LIBRARY=ON"
+             "-DUSE_STATIC_MBEDTLS_LIBRARY=OFF")))
     (native-inputs
      `(("perl" ,perl)
        ("python" ,python)))

From eae94df6125af78c26a6a4d3eceae207c6bfbc93 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 29 Jan 2020 10:07:53 +0100
Subject: [PATCH 124/127] gnu: p11-kit: Update to 0.23.19.

* gnu/packages/tls.scm (p11-kit): Update to 0.23.19.
[source](uri): Adjust tarball name.
---
 gnu/packages/tls.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 39f33c6ddc..901060eeb4 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -122,15 +122,15 @@ in intelligent transportation networks.")
 (define-public p11-kit
   (package
     (name "p11-kit")
-    (version "0.23.18.1")
+    (version "0.23.19")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "https://github.com/p11-glue/p11-kit/releases/"
-                          "download/" version "/p11-kit-" version ".tar.gz"))
+                          "download/" version "/p11-kit-" version ".tar.xz"))
       (sha256
        (base32
-        "0vrwab1082f7l5sbzpb28nrs3q4d2q7wzbi8c977rpah026bvhrl"))))
+        "1w7i4f5lc8darjkfjsm1ldvhkv0x29mvwg89klmh5kb2xqf6x4wi"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

From 1256ac1857382a6bcb309e6e614940d628b280e6 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 29 Jan 2020 10:09:27 +0100
Subject: [PATCH 125/127] gnu: whois: Update to 5.5.5.

* gnu/packages/networking.scm (whois): Update to 5.5.5.
---
 gnu/packages/networking.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 5f03c8f172..5c2c91891c 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -559,14 +559,14 @@ and up to 1 Mbit/s downstream.")
 (define-public whois
   (package
     (name "whois")
-    (version "5.5.4")
+    (version "5.5.5")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://debian/pool/main/w/whois/"
                            "whois_" version ".tar.xz"))
        (sha256
-        (base32 "0k97aiz7ngkjz3vhzvk27kqhnmqmkskdfx310c94qnh8fd7hiqfi"))))
+        (base32 "03akwma24gzfnsmwpjxmkzmcaxzg6fc68hmyaz0xmsl28i28l3n3"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no test suite

From d5037890b44a2ac0cc55ef650edf2d52851b421b Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 29 Jan 2020 10:09:43 +0100
Subject: [PATCH 126/127] gnu: OpenAL: Update to 1.20.1.

* gnu/packages/audio.scm (openal): Update to 1.20.1.
---
 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 c0fb800193..7b46e2cb6f 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2044,7 +2044,7 @@ lv2-c++-tools.")
 (define-public openal
   (package
     (name "openal")
-    (version "1.20.0")
+    (version "1.20.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2052,7 +2052,7 @@ lv2-c++-tools.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "03p6s5gap0lvig2fs0a8nib5rxsc24dbqjsydpwvlm5l49wlk2f0"))))
+                "0vax0b1lgd4212bpxa1rciz52d4mv3dkfvcbbhzw4cjp698v1kmn"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f  ; no check target

From 602059e794182a035f3919c3eb88d7d2085e24df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jakub=20K=C4=85dzio=C5=82ka?= <kuba@kadziolka.net>
Date: Sun, 19 Jan 2020 13:44:34 +0100
Subject: [PATCH 127/127] gnu: hexedit: Make F1 help more reliable.

* gnu/packages/hexedit.scm (hexedit)[arguments](patch-man-path): New
phase.
[inputs]: Add MAN-DB.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/hexedit.scm | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/hexedit.scm b/gnu/packages/hexedit.scm
index 365b6dab08..e1a029167a 100644
--- a/gnu/packages/hexedit.scm
+++ b/gnu/packages/hexedit.scm
@@ -25,6 +25,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages man)
   #:use-module (gnu packages ncurses)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -44,12 +45,26 @@
                (base32
                 "1xsxa5mip892jkvz9jshj73y6c7j3mgp8y393ciihqlyf2nmfs67"))))
     (build-system gnu-build-system)
-    (arguments '(#:tests? #f))          ; no check target
+    (arguments
+     `(#:tests? #f                      ; no check target
+       #:phases
+       (modify-phases %standard-phases
+         ;; Make F1 open the man page even if man-db is not in the profile.
+         (add-after 'unpack 'patch-man-path
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (substitute* "interact.c"
+               (("\"man\"")
+                (string-append "\"" (assoc-ref inputs "man-db") "/bin/man\""))
+               (("\"hexedit\"")
+                (string-append "\"" (assoc-ref outputs "out")
+                               "/share/man/man1/hexedit.1.gz\"")))
+             #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)))
     (inputs
-     `(("ncurses" ,ncurses)))
+     `(("man-db" ,man-db)
+       ("ncurses" ,ncurses)))
     (synopsis "View and edit files or devices in hexadecimal or ASCII")
     (description "hexedit shows a file both in ASCII and in hexadecimal.  The
 file can be a device as the file is read a piece at a time.  You can modify