From 8a587c89af55d7fa858a65fe717cfbfbe84b0e1e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 16:45:21 +0100
Subject: [PATCH 001/181] gnu: Add r-savr.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bab6b2b64d..bc13460299 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -969,3 +969,29 @@ using pre-clustering with the k-means algorithm.  Functions are also provided
 to search for all neighbors within a given distance.  Parallelization is
 achieved for all methods using the BiocParallel framework.")
     (license license:gpl3)))
+
+(define-public r-savr
+  (package
+    (name "r-savr")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "savR" version))
+       (sha256
+        (base32
+         "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
+    (properties `((upstream-name . "savR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-reshape2" ,r-reshape2)
+       ("r-scales" ,r-scales)
+       ("r-xml" ,r-xml)))
+    (home-page "https://github.com/bcalder/savR")
+    (synopsis "Parse and analyze Illumina SAV files")
+    (description
+     "This package provides tools to parse Illumina Sequence Analysis
+Viewer (SAV) files, access data, and generate QC plots.")
+    (license license:agpl3+)))

From 3a4c6288c81d91ce48200a310ad0d83bddfb7a5a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 16:53:15 +0100
Subject: [PATCH 002/181] gnu: Add r-aggregation.

* gnu/packages/cran.scm (r-aggregation): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ec950ce0ac..33dda347b5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3071,6 +3071,26 @@ Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
 Cambridge University Press, 1993.")
     (license license:gpl2)))
 
+(define-public r-aggregation
+  (package
+    (name "r-aggregation")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "aggregation" version))
+       (sha256
+        (base32
+         "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/aggregation/")
+    (synopsis "Methods for p-value aggregation")
+    (description
+     "This package contains functionality for performing the following methods
+of p-value aggregation: Fisher's method, the Lancaster method (weighted
+Fisher's method), and Sidak correction.")
+    (license license:gpl3)))
+
 (define-public r-quantmod
   (package
     (name "r-quantmod")

From ff939ef4d53af151683fbbae389cf60d76aef6ae Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 16:55:06 +0100
Subject: [PATCH 003/181] gnu: Add r-h5.

* gnu/packages/cran.scm (r-h5): New variable.
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 33dda347b5..e22c5010d9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -32,6 +32,7 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system r)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gnome)
@@ -3472,6 +3473,36 @@ dendrograms.")
     ;; Either version of the license.
     (license (list license:gpl2 license:gpl3))))
 
+(define-public r-h5
+  (package
+    (name "r-h5")
+    (version "0.9.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "h5" version))
+       (sha256
+        (base32
+         "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)
+       ("hdf5" ,hdf5)))
+    (native-inputs
+     `(("which" ,which)))
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/mannau/h5")
+    (synopsis "Interface to the HDF5 Library")
+    (description
+     "This package provides an S4 interface to the HDF5 library supporting
+fast storage and retrieval of R-objects like vectors, matrices and arrays to
+binary files in a language independent format.  The HDF5 format can therefore
+be used as an alternative to R's save/load mechanism.  Since h5 is able to
+access only subsets of stored data it can also handle data sets which do not
+fit into memory.")
+    (license license:bsd-2)))
+
 (define-public r-cgdsr
   (package
     (name "r-cgdsr")

From a961ae469cf81797df34f22eef0f0f5ca1a21e07 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 17:09:14 +0100
Subject: [PATCH 004/181] gnu: Add r-destiny.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bc13460299..95c722ac40 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -970,6 +970,41 @@ to search for all neighbors within a given distance.  Parallelization is
 achieved for all methods using the BiocParallel framework.")
     (license license:gpl3)))
 
+(define-public r-destiny
+  (package
+    (name "r-destiny")
+    (version "2.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "destiny" version))
+       (sha256
+        (base32
+         "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-fnn" ,r-fnn)
+       ("r-ggthemes" ,r-ggthemes)
+       ("r-hmisc" ,r-hmisc)
+       ("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)
+       ("r-proxy" ,r-proxy)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
+       ("r-scales" ,r-scales)
+       ("r-scatterplot3d" ,r-scatterplot3d)
+       ("r-smoother" ,r-smoother)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-vim" ,r-vim)))
+    (home-page "https://bioconductor.org/packages/destiny/")
+    (synopsis "Create and plot diffusion maps")
+    (description "This package provides tools to create and plot diffusion
+maps.")
+    ;; Any version of the GPL
+    (license license:gpl3+)))
+
 (define-public r-savr
   (package
     (name "r-savr")

From f338e4807f71503071da1af54b887e7f08a078da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 9 Nov 2018 16:46:29 +0100
Subject: [PATCH 005/181] gnu: Add r-rgl.

* gnu/packages/cran.scm (r-rgl): New variable.
---
 gnu/packages/cran.scm | 48 ++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 47 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e22c5010d9..6840a2fc66 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -34,10 +34,13 @@
   #:use-module (guix build-system r)
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages gl)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages haskell)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
@@ -46,7 +49,8 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tls)
-  #:use-module (gnu packages web))
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xorg))
 
 (define-public r-clipr
   (package
@@ -7376,3 +7380,45 @@ netCDF files.")
      "This package provides a convenient tool to install and update
 Bioconductor packages.")
     (license license:artistic2.0)))
+
+(define-public r-rgl
+  (package
+    (name "r-rgl")
+    (version "0.99.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rgl" version))
+       (sha256
+        (base32
+         "0q8sg8fr0140ilssqhscaxkjc29w1rpp6f4k50amw3zzs9g58ak9"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("freetype" ,freetype)
+       ("libpng" ,libpng)
+       ("glu" ,glu)
+       ("libx11" ,libx11)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-crosstalk" ,r-crosstalk)
+       ("r-htmltools" ,r-htmltools)
+       ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-knitr" ,r-knitr)
+       ("r-magrittr" ,r-magrittr)
+       ("r-manipulatewidget" ,r-manipulatewidget)
+       ("r-shiny" ,r-shiny)))
+    (home-page "https://r-forge.r-project.org/projects/rgl/")
+    (synopsis "3D visualization using OpenGL")
+    (description
+     "This package provides medium to high level functions for 3D interactive graphics,
+including functions modelled on base graphics (@code{plot3d()}, etc.) as well
+as functions for constructing representations of geometric
+objects (@code{cube3d()}, etc.).  Output may be on screen using OpenGL, or to
+various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
+image formats, including PNG, Postscript, SVG, PGF.")
+    ;; Any version of the GPL.
+    (license (list license:gpl2+ license:gpl3+))))

From 213e72a18dc20ba4ae1275e1f48104737c2a7526 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 9 Nov 2018 16:46:41 +0100
Subject: [PATCH 006/181] gnu: Add r-multicool.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6840a2fc66..06bdaa8d61 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7422,3 +7422,24 @@ various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
 image formats, including PNG, Postscript, SVG, PGF.")
     ;; Any version of the GPL.
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-multicool
+  (package
+    (name "r-multicool")
+    (version "0.1-10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "multicool" version))
+       (sha256
+        (base32
+         "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://cran.r-project.org/web/packages/multicool/")
+    (synopsis "Permutations of multisets in cool-lex order")
+    (description
+     "This package provides a set of tools to permute multisets without loops
+or hash tables and to generate integer partitions.  Cool-lex order is similar
+to colexicographical order.")
+    (license license:gpl2)))

From 4106e6ad87cb9b4bd571bc1a91cb026719770095 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 9 Nov 2018 16:46:51 +0100
Subject: [PATCH 007/181] gnu: Add r-misc3d.

* gnu/packages/cran.scm (r-misc3d): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 06bdaa8d61..604ba951c6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7443,3 +7443,23 @@ image formats, including PNG, Postscript, SVG, PGF.")
 or hash tables and to generate integer partitions.  Cool-lex order is similar
 to colexicographical order.")
     (license license:gpl2)))
+
+(define-public r-misc3d
+  (package
+    (name "r-misc3d")
+    (version "0.8-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "misc3d" version))
+       (sha256
+        (base32
+         "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/misc3d/")
+    (synopsis "Miscellaneous 3D Plots")
+    (description
+     "This package provides a collection of miscellaneous 3d plots, including
+isosurfaces.")
+    ;; Any version of the GPL.
+    (license (list license:gpl2+ license:gpl3+))))

From da256afb9ed35bb15e7cab01a3aab76f1ec5639d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 9 Nov 2018 16:47:03 +0100
Subject: [PATCH 008/181] gnu: Add r-ks.

* gnu/packages/cran.scm (r-ks): New variable.
---
 gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 604ba951c6..8c5c9258a9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7463,3 +7463,35 @@ to colexicographical order.")
 isosurfaces.")
     ;; Any version of the GPL.
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-ks
+  (package
+    (name "r-ks")
+    (version "1.11.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ks" version))
+       (sha256
+        (base32
+         "0z749c3xzpf6n0g7xcfplrhap1di8k7kcfr7vigh95ywnigyhs8d"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fnn" ,r-fnn)
+       ("r-kernlab" ,r-kernlab)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-matrix" ,r-matrix)
+       ("r-mclust" ,r-mclust)
+       ("r-mgcv" ,r-mgcv)
+       ("r-misc3d" ,r-misc3d)
+       ("r-multicool" ,r-multicool)
+       ("r-mvtnorm" ,r-mvtnorm)))
+    (home-page "http://www.mvstat.net/tduong/")
+    (synopsis "Kernel smoothing")
+    (description
+     "This package provides kernel smoothers for univariate and multivariate
+data, including density functions, density derivatives, cumulative
+distributions, modal clustering, discriminant analysis, and two-sample
+hypothesis testing.")
+    ;; Either version of the GPL.
+    (license (list license:gpl2 license:gpl3))))

From cf383cf08ff1b68a9610cddf66c1851b2aeddaab Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 9 Nov 2018 16:47:12 +0100
Subject: [PATCH 009/181] gnu: Add r-feature.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8c5c9258a9..ef3c148da1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7495,3 +7495,29 @@ distributions, modal clustering, discriminant analysis, and two-sample
 hypothesis testing.")
     ;; Either version of the GPL.
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-feature
+  (package
+    (name "r-feature")
+    (version "1.2.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "feature" version))
+       (sha256
+        (base32
+         "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ks" ,r-ks)
+       ("r-misc3d" ,r-misc3d)
+       ("r-rgl" ,r-rgl)))
+    (home-page "http://www.mvstat.net/tduong/")
+    (synopsis "Inferential feature significance for kernel density estimation")
+    (description
+     "The feature package contains functions to display and compute kernel
+density estimates, significant gradient and significant curvature regions.
+Significant gradient and/or curvature regions often correspond to significant
+features (e.g. local modes).")
+    ;; Either version of the GPL.
+    (license (list license:gpl2 license:gpl3))))

From 06bc7b82f7c6cb623911867f55b58b3316d3ddfc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 9 Nov 2018 16:47:19 +0100
Subject: [PATCH 010/181] gnu: Add r-arm.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ef3c148da1..83d8f510a1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7521,3 +7521,30 @@ Significant gradient and/or curvature regions often correspond to significant
 features (e.g. local modes).")
     ;; Either version of the GPL.
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-arm
+  (package
+    (name "r-arm")
+    (version "1.10-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "arm" version))
+       (sha256
+        (base32
+         "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abind" ,r-abind)
+       ("r-coda" ,r-coda)
+       ("r-lme4" ,r-lme4)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-nlme" ,r-nlme)))
+    (home-page "https://cran.r-project.org/web/packages/arm/")
+    (synopsis "Data analysis using regression and multilevel/hierarchical models")
+    (description
+     "This package provides functions to accompany A. Gelman and J. Hill,
+Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
+University Press, 2007.")
+    (license license:gpl3+)))

From f87a18e66079a540beea99fe6475fccb49a9ff68 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 18:58:47 +0100
Subject: [PATCH 011/181] gnu: r-rcpp: Update to 1.0.0.

* gnu/packages/cran.scm (r-rcpp): Update to 1.0.0.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 83d8f510a1..4ecd1c6a21 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -571,14 +571,16 @@ you to rapidly iterate while developing a package.")
 (define-public r-rcpp
   (package
     (name "r-rcpp")
-    (version "0.12.19")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rcpp" version))
        (sha256
-        (base32 "10mmiaawv9iwglc6z4y51mdpsfb1sivqmwr6xnfqkllcnpabdbk3"))))
+        (base32 "1hlbw4k79q9ich4w27b01gsvwrsnrflii8zjlcmgfzm1vpq8ndxp"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
     (home-page "http://www.rcpp.org")
     (synopsis "Seamless R and C++ integration")
     (description

From fccb24501a88d10352a106d160bcf11c284144c1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 18:59:32 +0100
Subject: [PATCH 012/181] gnu: r-jomo: Update to 2.6-5.

* gnu/packages/cran.scm (r-jomo): Update to 2.6-5.
[propagated-inputs]: Add r-mass.
---
 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 4ecd1c6a21..ecead0c5a4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2049,17 +2049,18 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
 (define-public r-jomo
   (package
     (name "r-jomo")
-    (version "2.6-4")
+    (version "2.6-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "jomo" version))
        (sha256
         (base32
-         "05g2rj9g7rgyb22b0gybw042nydyqsqsb31v05hifzavri8ij01x"))))
+         "109q5m69clrvvialxdxznd0wdb54ajhx84nj8slx8bf909a427mj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lme4" ,r-lme4)
+       ("r-mass" ,r-mass)
        ("r-ordinal" ,r-ordinal)
        ("r-survival" ,r-survival)))
     (home-page "https://cran.r-project.org/web/packages/jomo/")

From 492ec49890f020c1d4ad4eaf3e21e235b79e989d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 18:59:50 +0100
Subject: [PATCH 013/181] gnu: r-tmb: Update to 1.7.15.

* gnu/packages/cran.scm (r-tmb): Update to 1.7.15.
---
 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 ecead0c5a4..45526c7072 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6565,14 +6565,14 @@ Bayesian modeling.")
 (define-public r-tmb
   (package
     (name "r-tmb")
-    (version "1.7.14")
+    (version "1.7.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TMB" version))
        (sha256
         (base32
-         "0bpc504nz8xfwr8ack52dj4hpjcykn6zyf8n228z32dw9d5n96dl"))))
+         "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
     (properties `((upstream-name . "TMB")))
     (build-system r-build-system)
     (propagated-inputs

From 5174f06b0c3bf96dda4ed2b1d85c4e70fbce7ab2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 19:00:05 +0100
Subject: [PATCH 014/181] gnu: r-rgooglemaps: Update to 1.4.3.

* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.3.
---
 gnu/packages/geo.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 4481e21ddf..fa2b259d7c 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -549,14 +549,14 @@ coordinates.")
 (define-public r-rgooglemaps
   (package
    (name "r-rgooglemaps")
-   (version "1.4.2")
+   (version "1.4.3")
    (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RgoogleMaps" version))
        (sha256
         (base32
-         "112mdm53qx92n2m4ms02sbppckp44l1z19vy99j6gw3jrdprjydl"))))
+         "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4"))))
    (properties `((upstream-name . "RgoogleMaps")))
    (build-system r-build-system)
    (propagated-inputs `(("r-png" ,r-png)))

From 317f5a5a9113f0e04622f75b66db432b3b0b0c04 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 19:00:14 +0100
Subject: [PATCH 015/181] gnu: r-sn: Update to 1.5-3.

* gnu/packages/statistics.scm (r-sn): Update to 1.5-3.
---
 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 5b494c4829..f363d9a473 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5325,14 +5325,14 @@ first and second order derivatives.")
 (define-public r-sn
   (package
     (name "r-sn")
-    (version "1.5-2")
+    (version "1.5-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sn" version))
        (sha256
         (base32
-         "16gwr68zzj5v83bqfmzxnzwig3dnjrkxdhs6clri1caqkvrq6aig"))))
+         "10via4lg0vx9pzq350vwhz5wv1dhzxr2l3r6jq99nk37vmyvj8fc"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mnormt" ,r-mnormt)

From 77bea84ba128ac2c7d55530d2c581021e8d16884 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 19:00:23 +0100
Subject: [PATCH 016/181] gnu: r-biocviews: Update to 1.50.5.

* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
---
 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 8820ba0d8e..9147a9866b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7099,13 +7099,13 @@ Bioconductor, CRAN, and Github.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.50.1")
+    (version "1.50.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "0hjm3r58i0r9qhyar9pk250cx7sfijg0lnvi12a9s6brmmbip1a3"))))
+                "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)

From 88514b912427691272650195ad1941f7ead1ac36 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 19:00:33 +0100
Subject: [PATCH 017/181] gnu: r-biostrings: Update to 2.50.1.

* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
---
 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 9147a9866b..3b1b9c2c96 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7657,13 +7657,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.50.0")
+    (version "2.50.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "0zw0dj67fnpbz4iqnam5fxs92c1c8w8d7mzl0rkq4ksx0xl8vgg7"))))
+                "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)

From 03a415365a1cfcc263f56d309f33a1a581790ca7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Nov 2018 19:00:42 +0100
Subject: [PATCH 018/181] gnu: r-ensembldb: Update to 2.6.1.

* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
---
 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 3b1b9c2c96..55631530ca 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10215,14 +10215,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.6.0")
+    (version "2.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "12jqz9h6w4mxyfr43w5qbwmacn512aw0mnl0zvhsg5i7p4qj45ks"))))
+         "1js05dcv1dj4g2vj7lzlg0rgjcjlk2irdr9rxqpwxmivm8nbvf36"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)

From 005ec8d09c6b8f22457fad330c30ff0ccf495e34 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 10 Nov 2018 19:26:09 +0200
Subject: [PATCH 019/181] gnu: f2fs-tools: Update to 1.11.0.

* gnu/packages/linux.scm (f2fs-tools): Update to 1.11.0.
---
 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 e52c35fdb9..9bf995bdfc 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3402,7 +3402,7 @@ disks and SD cards.  This package provides the userland utilities.")
   (package
     (inherit f2fs-tools-1.7)
     (name "f2fs-tools")
-    (version "1.10.0")
+    (version "1.11.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3410,7 +3410,7 @@ disks and SD cards.  This package provides the userland utilities.")
                     "/f2fs-tools.git/snapshot/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "05ikaim0qq3dx9x3sp43ralwz43r3b0viv62n99kabp0vf3b0hg8"))))
+                "1qvr3hcic1vzfmyl7c0gnjxfsw8zjaadm66y337h49chv9yaq5mr"))))
     (inputs
      `(("libuuid" ,util-linux)))))
 

From 8d9bb4b4d05a20bef1cf7b1da2b1c5fb05f9b071 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Sat, 10 Nov 2018 15:14:28 +0100
Subject: [PATCH 020/181] services: dovecot: Allow to set 'client-limit'.

* doc/guix.texi (Mail Services): Update accordingly.
* gnu/services/mail.scm (service-configuration)[client-limit]: New field.
(dovecot-configuration)[services]: Set 'client-limit' to its correct default
value.
---
 doc/guix.texi         | 10 ++++++++++
 gnu/services/mail.scm | 27 ++++++++++++++++++++++-----
 2 files changed, 32 insertions(+), 5 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 441b65bcaf..d4178ce9ea 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -14349,6 +14349,16 @@ Defaults to @samp{#t}.
 
 @end deftypevr
 
+@deftypevr {@code{service-configuration} parameter} non-negative-integer client-limit
+Maximum number of simultaneous client connections per process.  Once
+this number of connections is received, the next incoming connection
+will prompt Dovecot to spawn another process.  If set to 0,
+@code{default-client-limit} is used instead.
+
+Defaults to @samp{0}.
+
+@end deftypevr
+
 @deftypevr {@code{service-configuration} parameter} non-negative-integer service-count
 Number of connections to handle before starting a new process.
 Typically the only useful values are 0 (unlimited) or 1.  1 is more
diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm
index 573efa0433..abc1c15cfe 100644
--- a/gnu/services/mail.scm
+++ b/gnu/services/mail.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Andy Wingo <wingo@igalia.com>
-;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
@@ -290,6 +290,12 @@ the section name.")
    "Listeners for the service.  A listener is either an
 @code{unix-listener-configuration}, a @code{fifo-listener-configuration}, or
 an @code{inet-listener-configuration}.")
+  (client-limit
+   (non-negative-integer 0)
+   "Maximum number of simultaneous client connections per process.  Once this
+number of connections is received, the next incoming connection will prompt
+Dovecot to spawn another process.  If set to 0, @code{default-client-limit} is
+used instead.")
   (service-count
    (non-negative-integer 1)
    "Number of connections to handle before starting a new process.
@@ -475,6 +481,7 @@ complex, customize the address and port fields of the
     (list
      (service-configuration
       (kind "imap-login")
+      (client-limit 0)
       (listeners
        (list
         (inet-listener-configuration (protocol "imap") (port 143) (ssl? #f))
@@ -487,10 +494,15 @@ complex, customize the address and port fields of the
         (inet-listener-configuration (protocol "pop3s") (port 995) (ssl? #t)))))
      (service-configuration
       (kind "lmtp")
+      (client-limit 1)
       (listeners
        (list (unix-listener-configuration (path "lmtp") (mode "0666")))))
-     (service-configuration (kind "imap"))
-     (service-configuration (kind "pop3"))
+     (service-configuration
+      (kind "imap")
+      (client-limit 1))
+     (service-configuration
+      (kind "pop3")
+      (client-limit 1))
      (service-configuration (kind "auth")
       ;; In what could be taken to be a bug, the default value of 1 for
       ;; service-count makes it so that a PAM auth worker can't fork off
@@ -501,10 +513,15 @@ complex, customize the address and port fields of the
       ;; is the default for all other services.  As a hack, bump this value to
       ;; 30.
       (service-count 30)
+      (client-limit 0)
       (listeners
        (list (unix-listener-configuration (path "auth-userdb")))))
-     (service-configuration (kind "auth-worker"))
-     (service-configuration (kind "dict")
+     (service-configuration
+      (kind "auth-worker")
+      (client-limit 1))
+     (service-configuration
+      (kind "dict")
+      (client-limit 1)
       (listeners (list (unix-listener-configuration (path "dict")))))))
    "List of services to enable.  Available services include @samp{imap},
 @samp{imap-login}, @samp{pop3}, @samp{pop3-login}, @samp{auth}, and

From be8dd4a5fec804f2f004dd3a87c2872af44dc88d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Sat, 10 Nov 2018 18:45:27 +0100
Subject: [PATCH 021/181] services: dovecot: Allow to set 'process-limit'.

* doc/guix.texi (Mail Services): Update accordingly.
* gnu/services/mail.scm (service-configuration)[process-limit]: New field.
(dovecot-configuration)[services]: Set 'process-limit' to its correct default
value.
---
 doc/guix.texi         |  9 +++++++++
 gnu/services/mail.scm | 17 ++++++++++++++---
 2 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index d4178ce9ea..c74351dd87 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -14364,6 +14364,15 @@ Number of connections to handle before starting a new process.
 Typically the only useful values are 0 (unlimited) or 1.  1 is more
 secure, but 0 is faster.  <doc/wiki/LoginProcess.txt>.
 Defaults to @samp{1}.
+
+@end deftypevr
+
+@deftypevr {@code{service-configuration} parameter} non-negative-integer process-limit
+Maximum number of processes that can exist for this service.  If set to
+0, @code{default-process-limit} is used instead.
+
+Defaults to @samp{0}.
+
 @end deftypevr
 
 @deftypevr {@code{service-configuration} parameter} non-negative-integer process-min-avail
diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm
index abc1c15cfe..dfbdf6d6cc 100644
--- a/gnu/services/mail.scm
+++ b/gnu/services/mail.scm
@@ -301,6 +301,10 @@ used instead.")
    "Number of connections to handle before starting a new process.
 Typically the only useful values are 0 (unlimited) or 1.  1 is more
 secure, but 0 is faster.  <doc/wiki/LoginProcess.txt>.")
+  (process-limit
+   (non-negative-integer 0)
+   "Maximum number of processes that can exist for this service.  If set to 0,
+@code{default-process-limit} is used instead.")
   (process-min-avail
    (non-negative-integer 0)
    "Number of processes to always keep waiting for more connections.")
@@ -482,6 +486,7 @@ complex, customize the address and port fields of the
      (service-configuration
       (kind "imap-login")
       (client-limit 0)
+      (process-limit 0)
       (listeners
        (list
         (inet-listener-configuration (protocol "imap") (port 143) (ssl? #f))
@@ -495,14 +500,17 @@ complex, customize the address and port fields of the
      (service-configuration
       (kind "lmtp")
       (client-limit 1)
+      (process-limit 0)
       (listeners
        (list (unix-listener-configuration (path "lmtp") (mode "0666")))))
      (service-configuration
       (kind "imap")
-      (client-limit 1))
+      (client-limit 1)
+      (process-limit 1024))
      (service-configuration
       (kind "pop3")
-      (client-limit 1))
+      (client-limit 1)
+      (process-limit 1024))
      (service-configuration (kind "auth")
       ;; In what could be taken to be a bug, the default value of 1 for
       ;; service-count makes it so that a PAM auth worker can't fork off
@@ -514,14 +522,17 @@ complex, customize the address and port fields of the
       ;; 30.
       (service-count 30)
       (client-limit 0)
+      (process-limit 1)
       (listeners
        (list (unix-listener-configuration (path "auth-userdb")))))
      (service-configuration
       (kind "auth-worker")
-      (client-limit 1))
+      (client-limit 1)
+      (process-limit 0))
      (service-configuration
       (kind "dict")
       (client-limit 1)
+      (process-limit 0)
       (listeners (list (unix-listener-configuration (path "dict")))))))
    "List of services to enable.  Available services include @samp{imap},
 @samp{imap-login}, @samp{pop3}, @samp{pop3-login}, @samp{auth}, and

From a7553a7360ac07ff114b807fc3026f08158d34c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Sat, 10 Nov 2018 18:37:55 +0100
Subject: [PATCH 022/181] services: dovecot: Set correct default value for the
 "auth" service.

* gnu/services/mail.scm (dovecot-configuration): Set 'service-count' to 0 for
the "auth" service.
---
 gnu/services/mail.scm | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm
index dfbdf6d6cc..fcaedd038b 100644
--- a/gnu/services/mail.scm
+++ b/gnu/services/mail.scm
@@ -511,16 +511,9 @@ complex, customize the address and port fields of the
       (kind "pop3")
       (client-limit 1)
       (process-limit 1024))
-     (service-configuration (kind "auth")
-      ;; In what could be taken to be a bug, the default value of 1 for
-      ;; service-count makes it so that a PAM auth worker can't fork off
-      ;; subprocesses for making blocking queries.  The result is that nobody
-      ;; can log in -- very secure, but not very useful!  If we simply omit
-      ;; the service-count, it will default to the value of
-      ;; auth-worker-max-count, which is 30, instead of defaulting to 1, which
-      ;; is the default for all other services.  As a hack, bump this value to
-      ;; 30.
-      (service-count 30)
+     (service-configuration
+      (kind "auth")
+      (service-count 0)
       (client-limit 0)
       (process-limit 1)
       (listeners

From e8b9aaf0b167812dee6be26772837ef2a271a843 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 10 Nov 2018 20:54:00 +0200
Subject: [PATCH 023/181] mtd-utils: Update to 2.0.2.

* gnu/packages/linux.scm (mtd-utils): Update to 2.0.2.
[arguments]: Remove 'test-target, 'make-flags. Re-enable 'configure
phase. Add 'configure-flag for the unit-tests.
[native-inputs]: Add cmocka, pkg-config.
---
 gnu/packages/linux.scm | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 9bf995bdfc..7d1987b0d7 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3949,7 +3949,7 @@ are exceeded.")
 (define-public mtd-utils
   (package
     (name "mtd-utils")
-    (version "1.5.2")
+    (version "2.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3957,18 +3957,18 @@ are exceeded.")
                     "mtd-utils-" version ".tar.bz2"))
               (sha256
                (base32
-                "007lhsd8yb34l899r4m37whhzdw815cz4fnjbpnblfha524p7dax"))))
+                "1f30jszknc5v6ykmil8ajxgksmcg54q3rsp84jsancp9x0dycggv"))))
+    (arguments
+     '(#:configure-flags '("--enable-unit-tests")))
+    (native-inputs
+     `(("cmocka" ,cmocka)
+       ("pkg-config" ,pkg-config)))
     (inputs
-     `(("acl" ,acl)
+     `(("acl" ,acl) ; for XATTR
        ("libuuid" ,util-linux)
        ("lzo" ,lzo)
        ("zlib" ,zlib)))
     (build-system gnu-build-system)
-    (arguments
-     `(#:test-target "tests"
-       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
-       #:phases (modify-phases %standard-phases
-                  (delete 'configure))))
     (synopsis "MTD Flash Storage Utilities")
     (description "This package provides utilities for testing, partitioning, etc
 of flash storage.")

From 95906eee1813058e83b44f9f0f893481f8e34b33 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 20:33:02 +0100
Subject: [PATCH 024/181] gnu: guile-ics: Remove custom bootstrap phase.

* gnu/packages/guile.scm (guile-ics)[arguments]: Remove.
---
 gnu/packages/guile.scm | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 8c55c749d8..133a338c6e 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2017 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016 Alex Sassmannshausen <alex@pompo.co>
-;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Erik Edrosa <erik.edrosa@gmail.com>
 ;;; Copyright © 2016 Eraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Alex Kost <alezost@gmail.com>
@@ -860,14 +860,6 @@ provides tight coupling to Guix.")
                (base32
                 "0qjjvadr7gibdq9jvwkmlkb4afsw9n2shfj9phpiadinxk3p4m2g"))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'autoreconf
-                    (lambda _
-                      ;; Repository comes with a broken symlink
-                      (delete-file "README")
-                      (symlink "README.org" "README")
-                      (zero? (system* "autoreconf" "-fi")))))))
     (native-inputs
      `(("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)

From 745378562488c051f7f20cb2722c3a61b81d0189 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:35:01 +0100
Subject: [PATCH 025/181] gnu: Add guile-email.

* gnu/packages/guile.scm (guile-email): New variable.
---
 gnu/packages/guile.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 133a338c6e..747317429e 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -2279,6 +2279,35 @@ using S-expressions.")
 tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
     (license license:gpl3+)))
 
+(define-public guile-email
+  (let ((commit "fa52eac55e5946db89621a6c583d2aa357864dee")
+        (revision "1"))
+    (package
+      (name "guile-email")
+      (version (git-version "0.1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://git.systemreboot.net/guile-email")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1037mbz7qd9bzaqp8ysyhnl9ipd97fmj3b9jr8qfzx9179vvsj63"))))
+      (build-system gnu-build-system)
+      (native-inputs
+       `(("pkg-config" ,pkg-config)
+         ("autoconf" ,autoconf)
+         ("automake" ,automake)))
+      (inputs
+       `(("guile" ,guile-2.2.4)))
+      (home-page "https://git.systemreboot.net/guile-email")
+      (synopsis "Guile email parser")
+      (description "This package provides an email parser written in pure
+Guile.")
+      (license license:agpl3+))))
+
 ;; There has not been any release yet.
 (define-public guile-newt
   (let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83")

From 2d900b046487ab9805a54f9be02d08c9553367de Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:35:16 +0100
Subject: [PATCH 026/181] gnu: Add guile-debbugs-next.

* gnu/packages/guile.scm (guile-debbugs-next): New variable.
---
 gnu/packages/guile.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 747317429e..6ae0fe2e77 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -2308,6 +2308,31 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
 Guile.")
       (license license:agpl3+))))
 
+(define-public guile-debbugs-next
+  (let ((commit "75a331d561c8b6f8efcf16216dab961c17759efe")
+        (revision "1"))
+    (package (inherit guile-debbugs)
+      (name "guile-debbugs")
+      (version (git-version "0.0.3" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.savannah.gnu.org/git/guile-debbugs.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0br3mgbw41bpc9x57jlghl0i8dz9nl63r4wzs5l47aqszf84870y"))))
+      (build-system gnu-build-system)
+      (native-inputs
+       `(("pkg-config" ,pkg-config)
+         ("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("texinfo" ,texinfo)))
+      (inputs
+       `(("guile" ,guile-2.2.4)
+         ("guile-email" ,guile-email))))))
+
 ;; There has not been any release yet.
 (define-public guile-newt
   (let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83")

From e3a4703174d949181d20fb64dde6f9b9e9576df7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:35:50 +0100
Subject: [PATCH 027/181] gnu: Add mumi.

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

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 35b7d27df3..f670a63ee7 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -119,6 +119,7 @@
   #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system guile)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial))
@@ -2640,3 +2641,50 @@ replacement for the @code{urlview} program.")
      "TNEF is a tar-like program that unpacks MIME attachments of type
 @code{application/ms-tnef}.")
     (license gpl2+)))
+
+(define-public mumi
+  (let ((commit "648311b9b9d9d974fb2d76dacfe956fc7b842401")
+        (revision "1"))
+    (package
+      (name "mumi")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.elephly.net/software/mumi.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "081yvjhy8ig3xyixkdklrzf3bf2bczn92g5hpxmsl8m9cpcj77vv"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'install 'wrap-executable
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin"))
+                      (scm (string-append out "/share/guile/site/2.2"))
+                      (go  (string-append out "/lib/guile/2.2/site-ccache")))
+                 (wrap-program (string-append bin "/mumi")
+                   `("GUILE_LOAD_PATH" ":" prefix
+                     (,scm ,(getenv "GUILE_LOAD_PATH")))
+                   `("GUILE_LOAD_COMPILED_PATH" ":" prefix
+                     (,go ,(getenv "GUILE_LOAD_COMPILED_PATH"))))
+                 #t))))))
+      (inputs
+       `(("guile-debbugs" ,guile-debbugs-next)
+         ("guile-email" ,guile-email)
+         ("guile-fibers" ,guile-fibers)
+         ("guile-json" ,guile-json)
+         ("guile-syntax-highlight" ,guile-syntax-highlight)
+         ("guile" ,guile-2.2.4)))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("pkg-config" ,pkg-config)))
+      (home-page "https://git.elephly.net/software/mumi.git")
+      (synopsis "Debbugs web interface")
+      (description "Mumi is a Debbugs web interface.")
+      (license agpl3+))))

From 74c903edabdc9a654f957a1a0eb3a97ea144e1f4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:37:07 +0100
Subject: [PATCH 028/181] Add missing license import.

* gnu/packages/mail.scm: Import agpl3+.
---
 gnu/packages/mail.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index f670a63ee7..978b22333e 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -110,7 +110,9 @@
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages docbook)
   #:use-module ((guix licenses)
-                #:select (fdl1.1+ gpl2 gpl2+ gpl3 gpl3+ lgpl2.1 lgpl2.1+ lgpl3+
+                #:select (fdl1.1+
+                           agpl3+
+                           gpl2 gpl2+ gpl3 gpl3+ lgpl2.1 lgpl2.1+ lgpl3+
                            non-copyleft (expat . license:expat) bsd-3
                            public-domain bsd-4 isc (openssl . license:openssl)
                            bsd-2 x11-style agpl3 asl2.0 perl-license))

From 79b8341292de460864e56829d1ec5ed1861cbb57 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Sat, 10 Nov 2018 23:27:05 +0100
Subject: [PATCH 029/181] gnu: emacs-circe: Update to 2.10.

* gnu/packages/emacs.scm (emacs-circe): Update to 2.10.
---
 gnu/packages/emacs.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index c6008e6a94..e3808071a2 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -7688,17 +7688,17 @@ value of the access token.")
 (define-public emacs-circe
   (package
     (name "emacs-circe")
-    (version "2.6")
+    (version "2.10")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/jorgenschaefer/circe.git")
              (commit (string-append "v" version))))
-       (file-name (string-append name "-" version "-checkout"))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "19h3983zy3f15cgs86irvbdzz55qyjm48qd7gjlzcxplr7vnnh0j"))))
+         "10gi14kwxd81blddpvqh95lgmpbfgp0m955naxix3bs3r6a75n4s"))))
     (build-system emacs-build-system)
     ;; In order to securely connect to an IRC server using TLS, Circe requires
     ;; the GnuTLS binary.

From ca364e7a3caef120ce19f38aa36edd491f226a82 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:41:11 +0100
Subject: [PATCH 030/181] gnu: jalv-select: Fetch sources from git.

* gnu/packages/music.scm (jalv-select)[source]: Fetch from git.
[arguments]: Add phase make-manpages-writable.
---
 gnu/packages/music.scm | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 3f0498ee53..28a40839b6 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1254,12 +1254,14 @@ Editor.  It is compatible with Power Tab Editor 1.7 and Guitar Pro.")
     (name "jalv-select")
     (version "0.8")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/brummer10/jalv_select/"
-                                  "archive/V" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/brummer10/jalv_select.git")
+                    (commit (string-append "V" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0zraagwr681b5s3qifxf399c7q93jz23c8sr42gmff9zqnvxc75q"))))
+                "0gqh768sbvn9ffyx1vqg9i57py9x9v4l65bk6wjsvgga4d7m83k1"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
@@ -1274,6 +1276,13 @@ Editor.  It is compatible with Power Tab Editor 1.7 and Guitar Pro.")
                 (string-append "ls -1 " (assoc-ref inputs "jalv") "/bin")))
              (substitute* "jalv.select.h"
                (("gtkmm.h") "gtkmm-2.4/gtkmm.h"))
+             #t))
+         (add-before 'reset-gzip-timestamps 'make-manpages-writable
+           (lambda* (#:key outputs #:allow-other-keys)
+             (for-each make-file-writable
+                       (find-files (string-append (assoc-ref outputs "out")
+                                                  "/share/man")
+                                   ".*\\.gz$"))
              #t)))))
     (inputs
      `(("lilv" ,lilv)

From 57906fad59a8527f0eb912b293941968c77aa9f0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:43:05 +0100
Subject: [PATCH 031/181] gnu: portmidi-for-extempore: Fetch sources from git.

* gnu/packages/music.scm (portmidi-for-extempore)[source]: Fetch from git.
---
 gnu/packages/music.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 28a40839b6..5e545e20d1 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1865,13 +1865,14 @@ using a system-independent interface.")
     (name "portmidi-for-extempore")
     (version "217")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/extemporelang/portmidi/"
-                                  "archive/" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/extemporelang/portmidi.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0gjikwciyr8kk4y3qiv1pcq58xpgw38ql1m2gs6g0qc1s8sx4235"))))
+                "1inriyrjf7xx2b7r54x0vmf9ngyqgr7g5060c22bwkbsgg53apzv"))))
     (build-system cmake-build-system)
     (arguments `(#:tests? #f)) ; no tests
     (native-inputs '())

From 78eff857708b527adfaa9d5964e4a73aaf7854bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:43:55 +0100
Subject: [PATCH 032/181] gnu: ams-lv2: Fetch sources from git.

* gnu/packages/music.scm (ams-lv2)[source]: Fetch from git.
---
 gnu/packages/music.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 5e545e20d1..dffcd9441c 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -2288,13 +2288,14 @@ follows a traditional multi-track tape recorder control paradigm.")
     (version "1.2.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/blablack/ams-lv2/"
-                           "archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/blablack/ams-lv2.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1xacxyzqcj83g9c1gwfn36gg1c6yi15v7km4vidfidrjzb4x27fq"))))
+         "1n1dnqnj24xhiy9323lj52nswr5120cj56fpckg802miss05sr6x"))))
     (build-system waf-build-system)
     (arguments
      `(#:phases

From b255365cd162920ff51c62f319370283218bfcb3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:44:57 +0100
Subject: [PATCH 033/181] gnu: lvtk: Fetch sources from git.

* gnu/packages/audio.scm (lvtk)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index ee18b00226..5e02291502 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1879,14 +1879,14 @@ software.")
     (name "lvtk")
     (version "1.2.0")
     (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/lvtk/lvtk/archive/"
-                                 version
-                                 ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/lvtk/lvtk.git")
+                   (commit version)))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "03nbj2cqcklqwh50zj2gwm07crh5iwqbpxbpzwbg5hvgl4k4rnjd"))))
+               "1b01zvzl70ana6l1kn8fgyr7msnn3c7x61cgw7fdpp50322352p8"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f  ; no check target

From 917dc89672b09c969297b36a2e2ce637d3358785 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:47:17 +0100
Subject: [PATCH 034/181] gnu: csound: Fetch sources from git.

* gnu/packages/audio.scm (csound)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 5e02291502..56a8a4b541 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -654,14 +654,14 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
     (name "csound")
     (version "6.11.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/csound/csound/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/csound/csound.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "072pk5h9w0vhw0ncc9dn90haw1yv18v04iwwjn8nsp6930w7dvxd"))))
+                "1hlkrnv3gghx4v382nl6v6k2k1dzm5ddk35m5g3q6pzc959726s7"))))
     (build-system cmake-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)

From 2ae2395422fe2fa8046ace78e6b06e073c8f6539 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:49:57 +0100
Subject: [PATCH 035/181] gnu: swh-plugins-lv2: Fetch sources from git.

* gnu/packages/audio.scm (swh-plugins-lv2)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 56a8a4b541..cdfea7fc02 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -610,13 +610,14 @@ envelope follower, distortion effects, tape effects and more.")
     (name "swh-plugins-lv2")
     (version "1.0.16")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/swh/"
-                                  "lv2/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/swh/lv2.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0j1mih0lp4fds07knp5i32in515sh0df1qi6694pmyz2wqnm295w"))))
+                "0y7nnww864mm4k6ayy2lhcws3wlbhb2gkyjbrwk921fvc18qk9mz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no check target

From 0b8db035040dc404be966306cbd2ba321ef56d99 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:55:48 +0100
Subject: [PATCH 036/181] gnu: infamous-plugins: Fetch sources from git.

* gnu/packages/audio.scm (infamous-plugins)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index cdfea7fc02..1e6484ebf1 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -572,13 +572,14 @@ based on human speech recordings.")
     (name "infamous-plugins")
     (version "0.2.04")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/ssj71/infamousPlugins/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ssj71/infamousPlugins.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1n6rhqsmvad7692w2h01niw5gqg5yk7a09wxl5ivs77zyp93vf7z"))))
+                "0hmqk80w4qxq09iag7b7srf2g0wigkyhzq0ywxvhz2iz0hq9k0dh"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests

From eca7729301a7c10886bc6790cf499acb534286d3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 22:57:28 +0100
Subject: [PATCH 037/181] gnu: rtmidi: Fetch sources from git.

* gnu/packages/audio.scm (rtmidi)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 1e6484ebf1..b383c4785d 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2274,14 +2274,14 @@ tempo and pitch of an audio recording independently of one another.")
     (name "rtmidi")
     (version "2.1.0")
     (source (origin
-              (method url-fetch)
-              (uri
-               (string-append "https://github.com/powertab/rtmidi/archive/"
-                              version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/powertab/rtmidi.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0d49lapnmdgmjxh4vw57h6xk74nn5r0zwysv7jbd7m8kqhpq5rjj"))))
+                "106v177y3nrjv2l1yskch4phpqd8h97b67zj0jiq9pc3c69jr1ay"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target

From 458baefb4008d04d1423c654c8f7e2999a6be317 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:12:38 +0100
Subject: [PATCH 038/181] gnu: rsound: Fetch sources from git.

* gnu/packages/audio.scm (rsound)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index b383c4785d..61081521d5 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2812,12 +2812,13 @@ synthesizer written in C++.")
     (version "1.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/Themaister/RSound/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Themaister/RSound.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1wzs40c0k5zpkmm5ffl6c17xmr399sxli7ys0fbb9ib0fd334knx"))))
+        (base32 "0gspmr3klwnq98h17p5hc6ifygya4p80g4g8r7a1qavm3mv19waf"))))
     (build-system gnu-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)

From 8e5995e3979d846972dfbdf7658aa2d3b2cb2395 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:15:41 +0100
Subject: [PATCH 039/181] gnu: xjackfreak: Fetch sources from git.

* gnu/packages/audio.scm (xjackfreak)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 61081521d5..489ec4bfb7 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2851,14 +2851,14 @@ with a much different focus than most other audio daemons.")
     (name "xjackfreak")
     (version "1.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/johnhldavis/xjackfreak/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/johnhldavis/xjackfreak.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xj6gpxfnw9jbdgwgm0x23xgfvj2kwmwb1nk0drw8lxgcchkq7d9"))))
+                "18c546qidbrj0f5wfiq5llii2192xpln0ab3r4vpr7i3wybxqjfz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags

From 4289a306b7256cb4dbf3a7a193f38c5da17db788 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:21:37 +0100
Subject: [PATCH 040/181] gnu: cuetools: Fetch sources from git.

* gnu/packages/audio.scm (cuetools)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 489ec4bfb7..8486072ebf 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3026,15 +3026,16 @@ point audio data.")
     (name "cuetools")
     (version "1.4.1")
     (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/svend/cuetools/archive/"
-                                 version ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/svend/cuetools.git")
+                   (commit version)))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "01xi3rvdmil9nawsha04iagjylqr1l9v9vlzk99scs8c207l58i4"))))
+               "02ksv1ahf1v4cr2xbclsfv5x17m9ivzbssb5r8xjm97yh8a7spa3"))))
     (build-system gnu-build-system)
-    ;; The source tarball is not bootstrapped.
+    ;; The source checkout is not bootstrapped.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)

From b249ff5d37311577d73ffd4999f6e6726e098a0f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:26:18 +0100
Subject: [PATCH 041/181] gnu: dcadec: Fetch sources from git.

* gnu/packages/audio.scm (dcadec)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 8486072ebf..08e3c8b542 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3076,13 +3076,14 @@ use them split WAVE data into multiple files.")
     (name "dcadec")
     (version "0.2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/foo86/dcadec/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/foo86/dcadec.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0i0dpypgqkhhi4v1fmsp2way6w9kbcix3c7q79pmg39yvrzj17gd"))))
+                "07nd0ajizrp1w02bsyfcv18431r8m8rq8gjfmz9wmckpg7cxj2hs"))))
     (build-system gnu-build-system)
     (arguments
      ;; Test files are missing: https://github.com/foo86/dcadec/issues/53

From c2a2d364dff53daddaa036cf50bbaf9b7bd42d8c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:27:03 +0100
Subject: [PATCH 042/181] gnu: cli-visualizer: Fetch sources from git.

* gnu/packages/audio.scm (cli-visualizer)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 08e3c8b542..613e2a31b8 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3388,13 +3388,14 @@ the following features:
     (version "1.6")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/dpayne/cli-visualizer/archive/"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dpayne/cli-visualizer.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "07zkm87f2fr8kc6531zrkya7q81sdanm6813y2f54mg13g41y6hi"))))
+         "0mirp8bk398di5xyq95iprmdyvplfghxqmrfj7jdnpy554vx7ppc"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("which" ,which)))

From a7fde1a86d35d1c2542bd637b2b6eeabd7b9dde8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:27:50 +0100
Subject: [PATCH 043/181] gnu: cava: Fetch sources from git.

* gnu/packages/audio.scm (cava)[source]: Fetch from git.
---
 gnu/packages/audio.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 613e2a31b8..5848411087 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3443,14 +3443,14 @@ representations.")
     (name "cava")
     (version "0.6.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/karlstav/cava/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/karlstav/cava.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "13d72swnjs894llf0paandmhf1lf90dz6ygkcdw4bv84wzkq1f4q"))))
+                "1kvhqgijs29909w3sq9m0bslx2zxxn4b3i07kdz4hb0dqkppxpjy"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)

From bed4eb373ecfc2cb63bdecf4e18bbd7106e98fe3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:28:45 +0100
Subject: [PATCH 044/181] gnu: gxtuner: Fetch sources from git.

* gnu/packages/music.scm (gxtuner)[source]: Fetch from git.
---
 gnu/packages/music.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index dffcd9441c..c405ea8511 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -2330,13 +2330,14 @@ and hold, etc.")
     (name "gxtuner")
     (version "2.4")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/brummer10/gxtuner/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/brummer10/gxtuner.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1hn5qjac7qd00v0sp7ijhhc3sb26ks9bni06nngivva21h61xrjr"))))
+                "1fxd2akan2njlr7fpkh84830783qhh1gg7yakswqk5dd466dcn96"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags

From 37ebc19cfbfdb248e8d36cbb587a89780e2e93c1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:30:52 +0100
Subject: [PATCH 045/181] gnu: msgpack: Remove custom bootstrap phase.

* gnu/packages/serialization.scm (msgpack)[arguments]: Remove.
---
 gnu/packages/serialization.scm | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 40b3d1bae0..2df0ce1364 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -99,7 +99,6 @@ arbitrary data types and reversibly turns them into different representations,
 such as compact binary encodings, XML, or JSON.")
     (license license:bsd-3)))
 
-
 (define-public msgpack
   (package
     (name "msgpack")
@@ -132,13 +131,6 @@ such as compact binary encodings, XML, or JSON.")
     ;; zbuffer.hpp) which #include <zlib.h>.  However, 'guix gc --references'
     ;; does not detect a store reference to zlib since these headers are not
     ;; compiled.
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _
-             (invoke "autoreconf" "-vfi")
-             #t)))))
     (home-page "https://www.msgpack.org")
     (synopsis "Binary serialization library")
     (description "Msgpack is a library for C/C++ that implements binary

From bc1ff4aabafc8e1dbc8196d0eaef911806c74099 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sat, 10 Nov 2018 16:03:48 +0100
Subject: [PATCH 046/181] gnu-maintenance: ".sign" and ".asc" files no longer
 match 'release-file?'.

* guix/gnu-maintenance.scm (release-file?): Exclude ".sign" and ".asc"
file in addition to ".sig".
---
 guix/gnu-maintenance.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm
index 3634f4bb27..21cb353f50 100644
--- a/guix/gnu-maintenance.scm
+++ b/guix/gnu-maintenance.scm
@@ -247,7 +247,7 @@ network to check in GNU's database."
 (define (release-file? project file)
   "Return #f if FILE is not a release tarball of PROJECT, otherwise return
 true."
-  (and (not (string-suffix? ".sig" file))
+  (and (not (member (file-extension file) '("sig" "sign" "asc")))
        (and=> (regexp-exec %tarball-rx file)
               (lambda (match)
                 ;; Filter out unrelated files, like `guile-www-1.1.1'.

From 5230dce154a8861d806fcd667f2d424def571ed6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sat, 10 Nov 2018 16:20:25 +0100
Subject: [PATCH 047/181] gnu-maintenance: Base kernel.org updater on HTML
 directory listings.

Partially fixes <https://bugs.gnu.org/28159>.

The FTP server at ftp.free.fr had become unable to produce directory
listings, effectively making the updater dysfunctional.  Furthermore FTP
is considered obsolescent so HTTP + HTML looks more future-proof.

* guix/gnu-maintenance.scm (html->sxml, html-links)
(latest-html-release): New procedures.
(latest-kernel.org-release): Rewrite in terms of 'latest-html-release'.
---
 guix/gnu-maintenance.scm | 111 ++++++++++++++++++++++++++++++++++-----
 1 file changed, 98 insertions(+), 13 deletions(-)

diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm
index 21cb353f50..bfd47a831d 100644
--- a/guix/gnu-maintenance.scm
+++ b/guix/gnu-maintenance.scm
@@ -21,6 +21,7 @@
   #:use-module (web uri)
   #:use-module (web client)
   #:use-module (web response)
+  #:use-module (sxml simple)
   #:use-module (ice-9 regex)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1)
@@ -218,7 +219,7 @@ network to check in GNU's database."
 
 
 ;;;
-;;; Latest release.
+;;; Latest FTP release.
 ;;;
 
 (define (ftp-server/directory package)
@@ -440,6 +441,88 @@ hosted on ftp.gnu.org, or not under that name (this is the case for
                                         #:server server
                                         #:directory directory))))
 
+
+;;;
+;;; Latest HTTP release.
+;;;
+
+(define (html->sxml port)
+  "Read HTML from PORT and return the corresponding SXML tree."
+  (let ((str (get-string-all port)))
+    (catch #t
+      (lambda ()
+        ;; XXX: This is the poor developer's HTML-to-XML converter.  It's good
+        ;; enough for directory listings at <https://kernel.org/pub> but if
+        ;; needed we could resort to (htmlprag) from Guile-Lib.
+        (call-with-input-string (string-replace-substring str "<hr>" "<hr />")
+          xml->sxml))
+      (const '(html)))))                          ;parse error
+
+(define (html-links sxml)
+  "Return the list of links found in SXML, the SXML tree of an HTML page."
+  (let loop ((sxml sxml)
+             (links '()))
+    (match sxml
+      (('a ('@ attributes ...) body ...)
+       (match (assq 'href attributes)
+         (#f          (fold loop links body))
+         (('href url) (fold loop (cons url links) body))))
+      ((tag ('@ _ ...) body ...)
+       (fold loop links body))
+      ((tag body ...)
+       (fold loop links body))
+      (_
+       links))))
+
+(define* (latest-html-release package
+                              #:key
+                              (base-url "https://kernel.org/pub")
+                              (directory (string-append "/" package))
+                              (file->signature (cut string-append <> ".sig")))
+  "Return an <upstream-source> for the latest release of PACKAGE (a string) on
+SERVER under DIRECTORY, or #f.  BASE-URL should be the URL of an HTML page,
+typically a directory listing as found on 'https://kernel.org/pub'.
+
+FILE->SIGNATURE must be a procedure; it is passed a source file URL and must
+return the corresponding signature URL, or #f it signatures are unavailable."
+  (let* ((uri  (string->uri (string-append base-url directory "/")))
+         (port (http-fetch/cached uri #:ttl 3600))
+         (sxml (html->sxml port)))
+    (define (url->release url)
+      (and (string=? url (basename url))          ;relative reference?
+           (release-file? package url)
+           (let-values (((name version)
+                         (package-name->name+version (sans-extension url)
+                                                     #\-)))
+             (upstream-source
+              (package name)
+              (version version)
+              (urls (list (string-append base-url directory "/" url)))
+              (signature-urls
+               (list (string-append base-url directory "/"
+                                    (file-sans-extension url)
+                                    ".sign")))))))
+
+    (define candidates
+      (filter-map url->release (html-links sxml)))
+
+    (close-port port)
+    (match candidates
+      (() #f)
+      ((first . _)
+       ;; Select the most recent release and return it.
+       (reduce (lambda (r1 r2)
+                 (if (version>? (upstream-source-version r1)
+                                (upstream-source-version r2))
+                     r1 r2))
+               first
+               (coalesce-sources candidates))))))
+
+
+;;;
+;;; Updaters.
+;;;
+
 (define %gnu-file-list-uri
   ;; URI of the file list for ftp.gnu.org.
   (string->uri "https://ftp.gnu.org/find.txt.gz"))
@@ -555,19 +638,21 @@ releases are on gnu.org."
 
 (define (latest-kernel.org-release package)
   "Return the latest release of PACKAGE, the name of a kernel.org package."
-  (let ((uri (string->uri (origin-uri (package-source package)))))
-    (false-if-ftp-error
-     (latest-ftp-release
-      (package-name package)
-      #:server "ftp.free.fr"                      ;a mirror reachable over FTP
-      #:directory (string-append "/mirrors/ftp.kernel.org"
-                                 (dirname (uri-path uri)))
+  (define %kernel.org-base
+    ;; This URL and sub-directories thereof are nginx-generated directory
+    ;; listings suitable for 'latest-html-release'.
+    "https://mirrors.edge.kernel.org/pub")
 
-      ;; kernel.org provides "foo-x.y.tar.sign" files, which are signatures of
-      ;; the uncompressed tarball.
-      #:file->signature (lambda (tarball)
-                          (string-append (file-sans-extension tarball)
-                                         ".sign"))))))
+  (define (file->signature file)
+    (string-append (file-sans-extension file) ".sign"))
+
+  (let* ((uri       (string->uri (origin-uri (package-source package))))
+         (package   (package-upstream-name package))
+         (directory (dirname (uri-path uri))))
+    (latest-html-release package
+                         #:base-url %kernel.org-base
+                         #:directory directory
+                         #:file->signature file->signature)))
 
 (define %gnu-updater
   ;; This is for everything at ftp.gnu.org.

From 30288ae57e77cf39c90276708e4920f4f1aea2ca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sat, 10 Nov 2018 16:24:30 +0100
Subject: [PATCH 048/181] gnu: mdadm: Update to 4.1.

* gnu/packages/linux.scm (mdadm): Update to 4.1.
---
 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 7d1987b0d7..b1021d5624 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -2917,7 +2917,7 @@ MPEG-2 and audio over Linux IEEE 1394.")
 (define-public mdadm
   (package
     (name "mdadm")
-    (version "4.0")
+    (version "4.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2925,7 +2925,7 @@ MPEG-2 and audio over Linux IEEE 1394.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "1ad3mma641946wn5lsllwf0lifw9lps34fv1nnkhyfpd9krffshx"))))
+                "0jjgjgqijpdp7ijh8slzzjjw690kydb1jjadf0x5ilq85628hxmb"))))
     (build-system gnu-build-system)
     (inputs
      `(("udev" ,eudev)))

From a3b72a8f1737bbf8c4388cc230571ea5c3831d0b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sat, 10 Nov 2018 18:41:57 +0100
Subject: [PATCH 049/181] ci: Add procedures to access evaluations.

* guix/ci.scm (<checkout>, <evaluation>): New record types.
(latest-builds): Add #:evaluation and #:system and honor it.  Define
'option'.
(json->checkout, json->evaluation, latest-evaluations)
(evaluations-for-commit): New procedures.
---
 guix/ci.scm | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 71 insertions(+), 3 deletions(-)

diff --git a/guix/ci.scm b/guix/ci.scm
index 881f3d3927..1727297dd7 100644
--- a/guix/ci.scm
+++ b/guix/ci.scm
@@ -19,6 +19,7 @@
 (define-module (guix ci)
   #:use-module (guix http-client)
   #:autoload   (json parser) (json->scm)
+  #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-9)
   #:export (build?
             build-id
@@ -27,9 +28,21 @@
             build-status
             build-timestamp
 
+            checkout?
+            checkout-commit
+            checkout-input
+
+            evaluation?
+            evaluation-id
+            evaluation-spec
+            evaluation-complete?
+            evaluation-checkouts
+
             %query-limit
             queued-builds
-            latest-builds))
+            latest-builds
+            latest-evaluations
+            evaluation-for-commit))
 
 ;;; Commentary:
 ;;;
@@ -47,6 +60,20 @@
   (status      build-status)                      ;integer
   (timestamp   build-timestamp))                  ;integer
 
+(define-record-type <checkout>
+  (make-checkout commit input)
+  checkout?
+  (commit      checkout-commit)                   ;string (SHA1)
+  (input       checkout-input))                   ;string (name)
+
+(define-record-type <evaluation>
+  (make-evaluation id spec complete? checkouts)
+  evaluation?
+  (id          evaluation-id)                     ;integer
+  (spec        evaluation-spec)                   ;string
+  (complete?   evaluation-complete?)              ;Boolean
+  (checkouts   evaluation-checkouts))             ;<checkout>*
+
 (define %query-limit
   ;; Max number of builds requested in queries.
   1000)
@@ -70,9 +97,50 @@
                                           (number->string limit)))))
     (map json->build queue)))
 
-(define* (latest-builds url #:optional (limit %query-limit))
+(define* (latest-builds url #:optional (limit %query-limit)
+                        #:key evaluation system)
+  "Return the latest builds performed by the CI server at URL.  If EVALUATION
+is an integer, restrict to builds of EVALUATION.  If SYSTEM is true (a system
+string such as \"x86_64-linux\"), restrict to builds for SYSTEM."
+  (define* (option name value #:optional (->string identity))
+    (if value
+        (string-append "&" name "=" (->string value))
+        ""))
+
   (let ((latest (json-fetch (string-append url "/api/latestbuilds?nr="
-                                           (number->string limit)))))
+                                           (number->string limit)
+                                           (option "evaluation" evaluation
+                                                   number->string)
+                                           (option "system" system)))))
     ;; Note: Hydra does not provide a "derivation" field for entries in
     ;; 'latestbuilds', but Cuirass does.
     (map json->build latest)))
+
+(define (json->checkout json)
+  (make-checkout (hash-ref json "commit")
+                 (hash-ref json "input")))
+
+(define (json->evaluation json)
+  (make-evaluation (hash-ref json "id")
+                   (hash-ref json "specification")
+                   (case (hash-ref json "in-progress")
+                     ((0) #t)
+                     (else #f))
+                   (map json->checkout (hash-ref json "checkouts"))))
+
+(define* (latest-evaluations url #:optional (limit %query-limit))
+  "Return the latest evaluations performed by the CI server at URL."
+  (map json->evaluation
+       (json->scm
+        (http-fetch (string-append url "/api/evaluations?nr="
+                                   (number->string limit))))))
+
+
+(define* (evaluations-for-commit url commit #:optional (limit %query-limit))
+  "Return the evaluations among the latest LIMIT evaluations that have COMMIT
+as one of their inputs."
+  (filter (lambda (evaluation)
+            (find (lambda (checkout)
+                    (string=? (checkout-commit checkout) commit))
+                  (evaluation-checkouts evaluation)))
+          (latest-evaluations url limit)))

From 9d466489cdbbfb2097ec3e211351d7b34fb70b60 Mon Sep 17 00:00:00 2001
From: Meiyo Peng <meiyo.peng@gmail.com>
Date: Mon, 29 Oct 2018 11:17:50 +0800
Subject: [PATCH 050/181] gnu: Add marisa.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/datastructures.scm (marisa): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/datastructures.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructures.scm
index 8517654def..4e5e59a2e3 100644
--- a/gnu/packages/datastructures.scm
+++ b/gnu/packages/datastructures.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,6 +49,29 @@ binary trees, binary search trees, red-black trees, 2D arrays, permutations
 and heaps.")
     (license license:gpl2+)))
 
+(define-public marisa
+  (package
+    (name "marisa")
+    (version "0.2.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/s-yata/marisa-trie"
+                           "/releases/download/v" version "/" name "-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "19ifrcmnbr9whaaf4ly3s9ndyiq9sjqhnfkrxbz9zsb44w2n36hf"))))
+    (build-system gnu-build-system)
+    (home-page "https://github.com/s-yata/marisa-trie")
+    (synopsis "Trie data structure C++ library")
+    (description "Matching Algorithm with Recursively Implemented
+StorAge (MARISA) is a static and space-efficient trie data structure C++
+library.")
+
+    ;; Dual-licensed, according to docs/readme.en.html (source files lack
+    ;; copyright/license headers.)
+    (license (list license:bsd-2 license:lgpl2.1+))))
+
 (define-public sparsehash
   (package
     (name "sparsehash")

From 1a0363cf0794bb7f8149800b665f80728b3635ff Mon Sep 17 00:00:00 2001
From: Meiyo Peng <meiyo.peng@gmail.com>
Date: Mon, 29 Oct 2018 11:22:55 +0800
Subject: [PATCH 051/181] gnu: Add opencc.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/textutils.scm (opencc): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/textutils.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 084017dbde..1d498b5a75 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -15,6 +15,7 @@
 ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -756,3 +757,26 @@ indentation.
 @end itemize\n")
     (home-page "http://docx2txt.sourceforge.net")
     (license license:gpl3+)))
+
+(define-public opencc
+  (package
+    (name "opencc")
+    (version "1.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/BYVoid/OpenCC"
+                           "/archive/ver." version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "01870gbkf711msirf3206k0ajaabypjhnx3fny5wikw0ladn9q8w"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("python" ,python-wrapper)))
+    (home-page "https://github.com/BYVoid/OpenCC")
+    (synopsis "Convert between Traditional Chinese and Simplified Chinese")
+    (description "Open Chinese Convert (OpenCC) converts between Traditional
+Chinese and Simplified Chinese, supporting character-level conversion,
+phrase-level conversion, variant conversion, and regional idioms among
+Mainland China, Taiwan, and Hong-Kong.")
+    (license license:asl2.0)))

From 2f968763c350ddbacfa84a96b9716e4eb5c8f942 Mon Sep 17 00:00:00 2001
From: Meiyo Peng <meiyo.peng@gmail.com>
Date: Mon, 29 Oct 2018 13:20:18 +0800
Subject: [PATCH 052/181] gnu: ibus: Indent code properly.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/ibus.scm (ibus, ibus-libpinyin): Indent code properly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/ibus.scm | 308 +++++++++++++++++++++---------------------
 1 file changed, 154 insertions(+), 154 deletions(-)

diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index 08fce5f6fb..40fa930293 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -43,166 +43,166 @@
 
 (define-public ibus
   (package
-   (name "ibus")
-   (version "1.5.19")
-   (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/ibus/ibus/"
-                                 "releases/download/"
-                                 version "/ibus-" version ".tar.gz"))
-             (sha256
-              (base32
-               "0a94bnpm24581317hdnihwr4cniriml10p4ffgxg14xhvaccfrjb"))))
-   (build-system glib-or-gtk-build-system)
-   (arguments
-    `(#:tests? #f  ; tests fail because there's no connection to dbus
-      #:configure-flags `("--disable-emoji-dict" ; cannot find emoji.json path
-                          "--disable-python2"
-                          "--enable-python-library"
-                          ,(string-append "--with-ucd-dir="
-                                          (getcwd) "/ucd")
-                          "--enable-wayland")
-      #:make-flags
-      (list "CC=gcc"
-            (string-append "pyoverridesdir="
-                           (assoc-ref %outputs "out")
-                           "/lib/python3.6/site-packages/gi/overrides/"))
-      #:phases
-      (modify-phases %standard-phases
-        (add-after 'unpack 'prepare-ucd-dir
-          (lambda* (#:key inputs #:allow-other-keys)
-            (mkdir-p "../ucd")
-            (symlink (assoc-ref inputs "unicode-blocks") "../ucd/Blocks.txt")
-            (symlink (assoc-ref inputs "unicode-nameslist") "../ucd/NamesList.txt")
-            #t))
-        (add-before 'configure 'disable-dconf-update
-          (lambda _
-            (substitute* "data/dconf/Makefile.in"
-              (("dconf update") "echo dconf update"))
-            #t))
-        (add-after 'unpack 'delete-generated-files
-          (lambda _
-            (for-each (lambda (file)
-                        (let ((c (string-append (string-drop-right file 4) "c")))
-                          (when (file-exists? c)
-                            (format #t "deleting ~a\n" c)
-                            (delete-file c))))
-                      (find-files "." "\\.vala"))
-            #t))
-        (add-after 'unpack 'fix-paths
-          (lambda* (#:key inputs #:allow-other-keys)
-            (substitute* "src/ibusenginesimple.c"
-              (("/usr/share/X11/locale")
-               (string-append (assoc-ref inputs "libx11")
-                              "/share/X11/locale")))
-            (substitute* "ui/gtk3/xkblayout.vala"
-              (("\"(setxkbmap|xmodmap)\"" _ prog)
-               (string-append "\"" (assoc-ref inputs prog) "\"")))
-            #t))
-        (add-after 'wrap-program 'wrap-with-additional-paths
-          (lambda* (#:key outputs #:allow-other-keys)
-            ;; Make sure 'ibus-setup' runs with the correct PYTHONPATH and
-            ;; GI_TYPELIB_PATH.
-            (let ((out (assoc-ref outputs "out")))
-              (wrap-program (string-append out "/bin/ibus-setup")
-                `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))
-                `("GI_TYPELIB_PATH" ":" prefix
-                  (,(getenv "GI_TYPELIB_PATH")
-                   ,(string-append out "/lib/girepository-1.0")))))
-            #t)))))
-   (inputs
-    `(("dbus" ,dbus)
-      ("dconf" ,dconf)
-      ("gconf" ,gconf)
-      ("gtk2" ,gtk+-2)
-      ("gtk+" ,gtk+)
-      ("intltool" ,intltool)
-      ("json-glib" ,json-glib)
-      ("libnotify" ,libnotify)
-      ("libx11" ,libx11)
-      ("setxkbmap" ,setxkbmap)
-      ("wayland" ,wayland)
-      ("xmodmap" ,xmodmap)
-      ("iso-codes" ,iso-codes)
-      ("pygobject2" ,python-pygobject)
-      ("python" ,python)))
-   (native-inputs
-    `(("glib" ,glib "bin") ; for glib-genmarshal
-      ("gobject-introspection" ,gobject-introspection) ; for g-ir-compiler
-      ("unicode-nameslist"
-       ,(origin
-          (method url-fetch)
-          (uri "https://www.unicode.org/Public/UNIDATA/NamesList.txt")
-          (sha256
-           (base32 "0yr2h0nfqhirfi3bxl33z6cc94qqshlpgi06c25xh9754irqsgv8"))))
-      ("unicode-blocks"
-       ,(origin
-          (method url-fetch)
-          (uri "https://www.unicode.org/Public/UNIDATA/Blocks.txt")
-          (sha256
-           (base32 "0lnh9iazikpr548bd7nkaq9r3vfljfvz0rg2462prac8qxk7ni8b"))))
-      ("vala" ,vala)
-      ("pkg-config" ,pkg-config)))
-   (native-search-paths
-    (list (search-path-specification
-           (variable "IBUS_COMPONENT_PATH")
-           (files '("share/ibus/component")))))
-   (synopsis "Input method framework")
-   (description
-    "IBus is an input framework providing a full-featured and user-friendly
+    (name "ibus")
+    (version "1.5.19")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/ibus/ibus/"
+                                  "releases/download/"
+                                  version "/ibus-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0a94bnpm24581317hdnihwr4cniriml10p4ffgxg14xhvaccfrjb"))))
+    (build-system glib-or-gtk-build-system)
+    (arguments
+     `(#:tests? #f  ; tests fail because there's no connection to dbus
+       #:configure-flags `("--disable-emoji-dict" ; cannot find emoji.json path
+                           "--disable-python2"
+                           "--enable-python-library"
+                           ,(string-append "--with-ucd-dir="
+                                           (getcwd) "/ucd")
+                           "--enable-wayland")
+       #:make-flags
+       (list "CC=gcc"
+             (string-append "pyoverridesdir="
+                            (assoc-ref %outputs "out")
+                            "/lib/python3.6/site-packages/gi/overrides/"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'prepare-ucd-dir
+           (lambda* (#:key inputs #:allow-other-keys)
+             (mkdir-p "../ucd")
+             (symlink (assoc-ref inputs "unicode-blocks") "../ucd/Blocks.txt")
+             (symlink (assoc-ref inputs "unicode-nameslist") "../ucd/NamesList.txt")
+             #t))
+         (add-before 'configure 'disable-dconf-update
+           (lambda _
+             (substitute* "data/dconf/Makefile.in"
+               (("dconf update") "echo dconf update"))
+             #t))
+         (add-after 'unpack 'delete-generated-files
+           (lambda _
+             (for-each (lambda (file)
+                         (let ((c (string-append (string-drop-right file 4) "c")))
+                           (when (file-exists? c)
+                             (format #t "deleting ~a\n" c)
+                             (delete-file c))))
+                       (find-files "." "\\.vala"))
+             #t))
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "src/ibusenginesimple.c"
+               (("/usr/share/X11/locale")
+                (string-append (assoc-ref inputs "libx11")
+                               "/share/X11/locale")))
+             (substitute* "ui/gtk3/xkblayout.vala"
+               (("\"(setxkbmap|xmodmap)\"" _ prog)
+                (string-append "\"" (assoc-ref inputs prog) "\"")))
+             #t))
+         (add-after 'wrap-program 'wrap-with-additional-paths
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Make sure 'ibus-setup' runs with the correct PYTHONPATH and
+             ;; GI_TYPELIB_PATH.
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/ibus-setup")
+                 `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))
+                 `("GI_TYPELIB_PATH" ":" prefix
+                   (,(getenv "GI_TYPELIB_PATH")
+                    ,(string-append out "/lib/girepository-1.0")))))
+             #t)))))
+    (inputs
+     `(("dbus" ,dbus)
+       ("dconf" ,dconf)
+       ("gconf" ,gconf)
+       ("gtk2" ,gtk+-2)
+       ("gtk+" ,gtk+)
+       ("intltool" ,intltool)
+       ("json-glib" ,json-glib)
+       ("libnotify" ,libnotify)
+       ("libx11" ,libx11)
+       ("setxkbmap" ,setxkbmap)
+       ("wayland" ,wayland)
+       ("xmodmap" ,xmodmap)
+       ("iso-codes" ,iso-codes)
+       ("pygobject2" ,python-pygobject)
+       ("python" ,python)))
+    (native-inputs
+     `(("glib" ,glib "bin") ; for glib-genmarshal
+       ("gobject-introspection" ,gobject-introspection) ; for g-ir-compiler
+       ("unicode-nameslist"
+        ,(origin
+           (method url-fetch)
+           (uri "https://www.unicode.org/Public/UNIDATA/NamesList.txt")
+           (sha256
+            (base32 "0yr2h0nfqhirfi3bxl33z6cc94qqshlpgi06c25xh9754irqsgv8"))))
+       ("unicode-blocks"
+        ,(origin
+           (method url-fetch)
+           (uri "https://www.unicode.org/Public/UNIDATA/Blocks.txt")
+           (sha256
+            (base32 "0lnh9iazikpr548bd7nkaq9r3vfljfvz0rg2462prac8qxk7ni8b"))))
+       ("vala" ,vala)
+       ("pkg-config" ,pkg-config)))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "IBUS_COMPONENT_PATH")
+            (files '("share/ibus/component")))))
+    (synopsis "Input method framework")
+    (description
+     "IBus is an input framework providing a full-featured and user-friendly
 input method user interface.  It comes with multilingual input support.  It
 may also simplify input method development.")
-   (home-page "https://github.com/ibus/ibus/wiki")
-   (license lgpl2.1+)))
+    (home-page "https://github.com/ibus/ibus/wiki")
+    (license lgpl2.1+)))
 
 (define-public ibus-libpinyin
   (package
-   (name "ibus-libpinyin")
-   (version "1.10.0")
-   (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/libpinyin/ibus-libpinyin/"
-                                 "releases/download/" version
-                                 "/ibus-libpinyin-" version ".tar.gz"))
-             (sha256
-              (base32
-               "0yq8aw4lddiviag8cnik6fp52vvk8lxv6bym13a3xya84c6zii3c"))))
-   (build-system glib-or-gtk-build-system)
-   (arguments
-    `(#:phases
-      (modify-phases %standard-phases
-        (add-after 'wrap-program 'wrap-with-additional-paths
-          (lambda* (#:key inputs outputs #:allow-other-keys)
-            ;; Make sure 'ibus-setup-libpinyin' runs with the correct
-            ;; PYTHONPATH and GI_TYPELIB_PATH.
-            (let ((out (assoc-ref outputs "out")))
-              (wrap-program (string-append out "/libexec/ibus-setup-libpinyin")
-                `("PYTHONPATH" ":" prefix
-                  (,(getenv "PYTHONPATH")
-                   ,(string-append (assoc-ref inputs "ibus")
-                                   "/lib/girepository-1.0")))
-                `("GI_TYPELIB_PATH" ":" prefix
-                  (,(string-append (assoc-ref inputs "ibus")
-                                   "/lib/girepository-1.0"))))
-              #t))))))
-   (inputs
-    `(("ibus" ,ibus)
-      ("libpinyin" ,libpinyin)
-      ("bdb" ,bdb)
-      ("sqlite" ,sqlite)
-      ("python" ,python)
-      ("pyxdg" ,python-pyxdg)
-      ("gtk+" ,gtk+)))
-   (native-inputs
-    `(("pkg-config" ,pkg-config)
-      ("intltool" ,intltool)
-      ("glib" ,glib "bin")))
-   (synopsis "Chinese pinyin and ZhuYin input methods for IBus")
-   (description
-    "This package includes a Chinese pinyin input method and a Chinese
+    (name "ibus-libpinyin")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/libpinyin/ibus-libpinyin/"
+                                  "releases/download/" version
+                                  "/ibus-libpinyin-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0yq8aw4lddiviag8cnik6fp52vvk8lxv6bym13a3xya84c6zii3c"))))
+    (build-system glib-or-gtk-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'wrap-program 'wrap-with-additional-paths
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Make sure 'ibus-setup-libpinyin' runs with the correct
+             ;; PYTHONPATH and GI_TYPELIB_PATH.
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/libexec/ibus-setup-libpinyin")
+                 `("PYTHONPATH" ":" prefix
+                   (,(getenv "PYTHONPATH")
+                    ,(string-append (assoc-ref inputs "ibus")
+                                    "/lib/girepository-1.0")))
+                 `("GI_TYPELIB_PATH" ":" prefix
+                   (,(string-append (assoc-ref inputs "ibus")
+                                    "/lib/girepository-1.0"))))
+               #t))))))
+    (inputs
+     `(("ibus" ,ibus)
+       ("libpinyin" ,libpinyin)
+       ("bdb" ,bdb)
+       ("sqlite" ,sqlite)
+       ("python" ,python)
+       ("pyxdg" ,python-pyxdg)
+       ("gtk+" ,gtk+)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("intltool" ,intltool)
+       ("glib" ,glib "bin")))
+    (synopsis "Chinese pinyin and ZhuYin input methods for IBus")
+    (description
+     "This package includes a Chinese pinyin input method and a Chinese
 ZhuYin (Bopomofo) input method based on libpinyin for IBus.")
-   (home-page "https://github.com/libpinyin/ibus-libpinyin")
-   (license gpl2+)))
+    (home-page "https://github.com/libpinyin/ibus-libpinyin")
+    (license gpl2+)))
 
 (define-public libpinyin
   (package

From 78209a165be9dca931a9d7828c842d9babd5ed98 Mon Sep 17 00:00:00 2001
From: Meiyo Peng <meiyo.peng@gmail.com>
Date: Mon, 29 Oct 2018 11:29:33 +0800
Subject: [PATCH 053/181] gnu: Add librime.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/ibus.scm (librime): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/ibus.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index 40fa930293..f689c02baa 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,21 +25,27 @@
   #:use-module (guix licenses)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (gnu packages)
   #:use-module (gnu packages anthy)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages datastructures)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages iso-codes)
+  #:use-module (gnu packages logging)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages serialization)
+  #:use-module (gnu packages textutils)
   #:use-module (gnu packages xorg))
 
 (define-public ibus
@@ -279,3 +286,33 @@ applications allow text input via IBus, installing this package will enable
 Japanese language input in most graphical applications.")
     (home-page "https://github.com/fujiwarat/ibus-anthy")
     (license gpl2+)))
+
+(define-public librime
+  (package
+    (name "librime")
+    (version "1.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/rime/" name
+                           "/archive/" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0qh0hy8bvj17bnzaxk0bmv4gsnbsd6jx8csr84936xmhkrysdday"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("boost" ,boost)
+       ("glog" ,glog)
+       ("leveldb" ,leveldb)
+       ("marisa" ,marisa)
+       ("opencc" ,opencc)
+       ("yaml-cpp" ,yaml-cpp)))
+    (home-page "https://rime.im/")
+    (synopsis "The core library of Rime Input Method Engine")
+    (description "@dfn{librime} is the core library of Rime Input Method
+Engine, which is a lightweight, extensible input method engine supporting
+various input schemas including glyph-based input methods, romanization-based
+input methods as well as those for Chinese dialects.  It has the ability to
+compose phrases and sentences intelligently and provide very accurate
+traditional Chinese output.")
+    (license bsd-3)))

From 1329f095bb1f79db1c9a86581bfa1e13dffc2520 Mon Sep 17 00:00:00 2001
From: Meiyo Peng <meiyo.peng@gmail.com>
Date: Mon, 29 Oct 2018 11:35:20 +0800
Subject: [PATCH 054/181] gnu: Add rime-data.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/ibus.scm (rime-data): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/ibus.scm | 277 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 277 insertions(+)

diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index f689c02baa..afb7602930 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -25,6 +25,7 @@
   #:use-module (guix licenses)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system glib-or-gtk)
@@ -316,3 +317,279 @@ input methods as well as those for Chinese dialects.  It has the ability to
 compose phrases and sentences intelligently and provide very accurate
 traditional Chinese output.")
     (license bsd-3)))
+
+(define-public rime-data
+  (package
+    (name "rime-data")
+    (version "0.38.20181029")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rime/plum.git")
+             (commit "fb4f829da2007f2dbb37d60a79bc67c25ea16568")))
+       (file-name "plum-checkout")
+       (sha256
+        (base32 "1m1wiv9j5bay4saga58c7dj4h8gqivsbyp16y245ifvxvp9czj67"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                  ; no tests
+       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+                          "no_update=1")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-source
+           (lambda _
+             ;; Set .DEFAULT_GOAL to `all'.
+             ;; Don't build binary schemas. The output is not deterministic.
+             (substitute* "Makefile"
+               (("^\\.DEFAULT_GOAL := preset")
+                ".DEFAULT_GOAL := all"))
+             #t))
+         ;; Add schema packages into "package/rime" directory.
+         (add-after 'unpack 'add-packages
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let* ((dest-dir "package/rime"))
+               (mkdir-p dest-dir)
+               (for-each (lambda (pkg)
+                           (symlink (assoc-ref inputs pkg)
+                                    (string-append dest-dir "/" pkg)))
+                         '("array"
+                           "bopomofo"
+                           "cangjie"
+                           "combo-pinyin"
+                           "double-pinyin"
+                           "emoji"
+                           "essay"
+                           "ipa"
+                           "jyutping"
+                           "luna-pinyin"
+                           "middle-chinese"
+                           "pinyin-simp"
+                           "prelude"
+                           "quick"
+                           "scj"
+                           "soutzoe"
+                           "stenotype"
+                           "stroke"
+                           "terra-pinyin"
+                           "wubi"
+                           "wugniu")))
+             #t))
+         (delete 'configure))))
+    (native-inputs
+     `(("array"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-array.git")
+                 (commit "906e923902147584b0b0247028a782abbfbfd8a0")))
+           (file-name "rime-array-checkout")
+           (sha256
+            (base32
+             "1alk6ghn4ji4kvp7lfm57bwm2gjh99i79r0w9naz6wkdim8idvb1"))))
+       ("bopomofo"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-bopomofo.git")
+                 (commit "8dc44ca1b6ef4e45b452e070b9da737f5da165e3")))
+           (file-name "rime-bopomofo-checkout")
+           (sha256
+            (base32
+             "16k6wfhcrw3a77rmbrp21ca0gmsmb3f68s193c1cfwr8i68k46nf"))))
+       ("cangjie"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-cangjie.git")
+                 (commit "ab085e90856b3399b374dc3c8b4cb40d11f307a8")))
+           (file-name "rime-cangjie-checkout")
+           (sha256
+            (base32
+             "11fgj0rbv9nyzfijwm2l8pm8fznhif4h27ndrrcaaylkp7p5zsx2"))))
+       ("combo-pinyin"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-combo-pinyin.git")
+                 (commit "f1bae63f20504f2b8113c5cbdf2700e858aa91eb")))
+           (file-name "rime-combo-pinyin-checkout")
+           (sha256
+            (base32
+             "1l1079akwm1hw4kkn0q6x9fpylnl2ka6z2fn7lmdpfpsr0xgn0n7"))))
+       ("double-pinyin"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-double-pinyin.git")
+                 (commit "2101a5cd40e511ec38835769aa66d2dddf059c2e")))
+           (file-name "rime-double-pinyin-checkout")
+           (sha256
+            (base32
+             "19hh2qm0njbfk2js678hfm2hw9b796s43vs11yy3m1v9m0gk2vi7"))))
+       ("emoji"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-emoji.git")
+                 (commit "6e6611b315f03ee4c33f958f9dbe960b13a0ed19")))
+           (file-name "rime-emoji-checkout")
+           (sha256
+            (base32
+             "1brfs3214w36j3345di9ygp468hbvbqdqpkjxxs1dbp437rayhyy"))))
+       ("essay"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-essay.git")
+                 (commit "5e5c7a0ef41c9b030abdad81a9df07b56b1661e9")))
+           (file-name "rime-essay-checkout")
+           (sha256
+            (base32
+             "0ana9is0zhh79m4gjshvmaxbrg3jiqysydx5bpm151i7i6vw5y1i"))))
+       ("ipa"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-ipa.git")
+                 (commit "02a9e2c181921a2e95e1a81f88188c41132755c3")))
+           (file-name "rime-ipa-checkout")
+           (sha256
+            (base32
+             "1szrxgvqlgmxapj2aflw2cvbv0p6pl0sw0gyxa13dvdhhf7s9rvr"))))
+       ("jyutping"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-jyutping.git")
+                 (commit "1402ec3d6cc0973f952fe3f9ef531294e4ffe9e0")))
+           (file-name "rime-jyutping-checkout")
+           (sha256
+            (base32
+             "17g03dy4gw6vyc9da1wjn3iy9hx64dfnwiwsfc7bkzan22x2m4dv"))))
+       ("luna-pinyin"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-luna-pinyin.git")
+                 (commit "3b05132576f5c347ff8a70857d2dae080936ac3b")))
+           (file-name "rime-luna-pinyin-checkout")
+           (sha256
+            (base32
+             "0kgnpxjn10dm2d9718r12rdjlwqd2s2h84jvkhxhh5v0dkv1anl2"))))
+       ("middle-chinese"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-middle-chinese.git")
+                 (commit "9ba8d70330654b9a730f882d35cfad7dbeddfd75")))
+           (file-name "rime-middle-chinese-checkout")
+           (sha256
+            (base32
+             "0hwg5zby5kphh0bcfay8mfxwr5bwqhamiw3cmmmf7kp9fbns5s23"))))
+       ("pinyin-simp"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-pinyin-simp.git")
+                 (commit "74357ffd62c05fb60edf6eab5b86bc8c8c1907d0")))
+           (file-name "rime-pinyin-simp-checkout")
+           (sha256
+            (base32
+             "1paw3c7pv5bl54abnp9pidfxrkchdacyxy5m9zb311p5sgm7fhxh"))))
+       ("prelude"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-prelude.git")
+                 (commit "33040568c3ddb2ee6340c9b669494317db21b77c")))
+           (file-name "rime-prelude-checkout")
+           (sha256
+            (base32
+             "1gwcasyyg6f0ib6s4qsrrjcqr1lcs7j3xqxl65rznsw44nhnbwwq"))))
+       ("quick"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-quick.git")
+                 (commit "910a97d403ad8e72f322488da146da79c19d623f")))
+           (file-name "rime-quick-checkout")
+           (sha256
+            (base32
+             "0yrq3gbfmm29xlr52rmxc41mqfrb0295q7sdhbc3ax71677mpr0y"))))
+       ("scj"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-scj.git")
+                 (commit "e0eae889f4376d2a434ac3b38523e0da7400db68")))
+           (file-name "rime-scj-checkout")
+           (sha256
+            (base32
+             "1whnv9zs349kvy0zi7dnmpqwil8i6gqwrzvhy3qdrjzy58y6gwxn"))))
+       ("soutzoe"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-soutzoe.git")
+                 (commit "e47841a8ad6341731c41cdb814b7a25c837603c4")))
+           (file-name "rime-soutzoe-checkout")
+           (sha256
+            (base32
+             "1rgpmkxa72jy6gyy44fn8azpk3amk9s9lrdf7za03nv95d0fvm0p"))))
+       ("stenotype"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-stenotype.git")
+                 (commit "d4ff379314fd95283853d1734854979cf3cbd287")))
+           (file-name "rime-stenotype-checkout")
+           (sha256
+            (base32
+             "1kckpi4l4884hvydr3d6vid3v7rsc1app29kmk7v8jf8vn16afhl"))))
+       ("stroke"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-stroke.git")
+                 (commit "cfd29c675c46cf70b7a7f0a3836a913059316a0a")))
+           (file-name "rime-stroke-checkout")
+           (sha256
+            (base32
+             "135is9c1p4lm98fd9l1gxyflkm69cv5an129ka7sk614bq84m08d"))))
+       ("terra-pinyin"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-terra-pinyin.git")
+                 (commit "15b5c73a796571cd6f9ef6c89f96656cb9df86f9")))
+           (file-name "rime-terra-pinyin-checkout")
+           (sha256
+            (base32
+             "1xsd84h1zw417h5hr4dbgyk5009zi7q2p9774w3ccr5sxgc3i3cm"))))
+       ("wubi"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-wubi.git")
+                 (commit "d44403728a0b1cd8b47cb1f81b83f58e5f790b74")))
+           (file-name "rime-wubi-checkout")
+           (sha256
+            (base32
+             "0ld31bdn94lncxd1ka44w4sbl03skh08mc927dhdmwq5bpvrgn36"))))
+       ("wugniu"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-wugniu.git")
+                 (commit "65bcc354ada3839591d7546a64c71dbdd0592b02")))
+           (file-name "rime-wugniu-checkout")
+           (sha256
+            (base32
+             "0g31awp40s778sp5c290x40s8np86n8aw011s17sslxrqhhb0bkx"))))))
+    (home-page "https://rime.im/")
+    (synopsis "Schema data of Rime Input Method Engine")
+    (description "@dfn{rime-data} provides the schema data of Rime Input
+Method Engine.")
+    (license lgpl3+)))

From d5b23d2b7ddcd94f073f3bac8d860895263e23c3 Mon Sep 17 00:00:00 2001
From: Meiyo Peng <meiyo.peng@gmail.com>
Date: Mon, 29 Oct 2018 11:46:03 +0800
Subject: [PATCH 055/181] gnu: Add ibus-rime.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/ibus.scm (ibus-rime): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/ibus.scm | 59 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index afb7602930..8ad1e09856 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -34,6 +34,7 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages freedesktop)
@@ -593,3 +594,61 @@ traditional Chinese output.")
     (description "@dfn{rime-data} provides the schema data of Rime Input
 Method Engine.")
     (license lgpl3+)))
+
+(define-public ibus-rime
+  (package
+    (name "ibus-rime")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/rime/" name
+                           "/archive/" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0mfbz0vwky7n4wvxrwabnn1i9n9adnql0dd1rx57w1anaslr5amj"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; no tests
+       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-source
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Define RIME_DATA_DIR. It's required but not used by the code.
+             (substitute* "Makefile"
+               (("cmake")
+                (string-append "cmake -DRIME_DATA_DIR="
+                               (assoc-ref inputs "rime-data")
+                               "/share/rime-data")))
+             ;; rime_config.h defines the actual data directory.
+             (substitute* "rime_config.h"
+               (("^#define IBUS_RIME_INSTALL_PREFIX .*$")
+                (string-append "#define IBUS_RIME_INSTALL_PREFIX \""
+                               (assoc-ref outputs "out")
+                               "\"\n"))
+               (("^#define IBUS_RIME_SHARED_DATA_DIR .*$")
+                (string-append "#define IBUS_RIME_SHARED_DATA_DIR \""
+                               (assoc-ref inputs "rime-data")
+                               "/share/rime-data\"\n")))
+             #t))
+         (delete 'configure))))
+    (inputs
+     `(("gdk-pixbuf" ,gdk-pixbuf)
+       ("glib" ,glib)
+       ("ibus" ,ibus)
+       ("libnotify" ,libnotify)
+       ("librime" ,librime)
+       ("rime-data" ,rime-data)))
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://rime.im/")
+    (synopsis "Rime Input Method Engine for IBus")
+    (description "@dfn{ibus-rime} provides the Rime input method engine for
+IBus.  Rime is a lightweight, extensible input method engine supporting
+various input schemas including glyph-based input methods, romanization-based
+input methods as well as those for Chinese dialects.  It has the ability to
+compose phrases and sentences intelligently and provide very accurate
+traditional Chinese output.")
+    (license gpl3+)))

From 78e3d554d15a565514d78a09d5dcd7f29e2f91ec Mon Sep 17 00:00:00 2001
From: Pierre Langlois <pierre.langlois@gmx.com>
Date: Sat, 3 Nov 2018 10:28:37 +0000
Subject: [PATCH 056/181] gnu: Add emacs-ivy-rich.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/emacs.scm (emacs-ivy-rich): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/emacs.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index e3808071a2..3e32998a9f 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -40,6 +40,7 @@
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
 ;;; Copyright © 2018 Thorsten Wilms <t_w_@freenet.de>
+;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3848,6 +3849,31 @@ use it, call @code{M-x ivy-yasnippet} (but make sure you have enabled
 @code{yas-minor-mode} first).")
       (license license:gpl3+))))
 
+(define-public emacs-ivy-rich
+  (package
+    (name "emacs-ivy-rich")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/Yevgnen/ivy-rich/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "14r3mx5rkd4wz0ls5pv5w6c7la3z9iy93d3jfind3xyg4kywy95c"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-ivy" ,emacs-ivy)))
+    (home-page "https://github.com/Yevgnen/ivy-rich")
+    (synopsis "More friendly interface for @code{ivy}")
+    (description
+     "This package extends @code{ivy} by showing more information in the
+minibuffer for each candidate.  It adds columns showing buffer modes, file
+sizes, docstrings, etc.  If @code{emacs-all-the-icons} is installed, it can
+show icons as well.")
+    (license license:gpl3+)))
+
 (define-public emacs-avy
   (package
     (name "emacs-avy")

From cdb4048d7201e509862b7e2a74e60c1d65a2ba42 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:34:53 +0100
Subject: [PATCH 057/181] gnu: portaudio: Remove custom bootstrap phase.

* gnu/packages/audio.scm (portaudio)[arguments]: Remove autoreconf phase.
---
 gnu/packages/audio.scm | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 5848411087..bf5ee3c65f 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2753,20 +2753,14 @@ portions of LAME.")
      ;; TODO: Add ASIHPI.
      `(("alsa-lib" ,alsa-lib)
        ("jack" ,jack-1)))
+    ;; Autoreconf is necessary because the audacity-compat patch modifies .in
+    ;; files.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
        ("libtool" ,libtool)
        ("pkg-config" ,pkg-config)))
-    (arguments
-     '(#:phases
-       ;; Autoreconf is necessary because the audacity-compat patch modifies
-       ;; .in files.
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _
-             (invoke "autoreconf" "-vif"))))
-       #:tests? #f))                    ;no 'check' target
+    (arguments '(#:tests? #f))                    ;no 'check' target
     (home-page "http://www.portaudio.com/")
     (synopsis "Audio I/O library")
     (description

From 7db147ec455b11c9717c4ac3730bf1139b370897 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:36:05 +0100
Subject: [PATCH 058/181] gnu: rtmidi: Remove custom bootstrap phase.

* gnu/packages/audio.scm (rtmidi)[arguments]: Remove autoconf phase.
---
 gnu/packages/audio.scm | 34 +++++++++++++++-------------------
 1 file changed, 15 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index bf5ee3c65f..e5b8f9ed79 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2285,25 +2285,21 @@ tempo and pitch of an audio recording independently of one another.")
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
-       #:phases (modify-phases %standard-phases
-                  (add-after
-                   'unpack 'autoconf
-                   (lambda _ (invoke "autoreconf" "-vfi")))
-                  (add-before
-                   'build 'fix-makefile
-                   (lambda _
-                     (substitute* "Makefile"
-                       (("/bin/ln") "ln")
-                       (("RtMidi.h RtError.h") "RtMidi.h"))
-                     #t))
-                  (add-before
-                   'install 'make-target-dirs
-                   (lambda _
-                     (let ((out (assoc-ref %outputs "out")))
-                       (mkdir-p (string-append out "/bin"))
-                       (mkdir (string-append out "/lib"))
-                       (mkdir (string-append out "/include")))
-                     #t)))))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'fix-makefile
+           (lambda _
+             (substitute* "Makefile"
+               (("/bin/ln") "ln")
+               (("RtMidi.h RtError.h") "RtMidi.h"))
+             #t))
+         (add-before 'install 'make-target-dirs
+           (lambda _
+             (let ((out (assoc-ref %outputs "out")))
+               (mkdir-p (string-append out "/bin"))
+               (mkdir (string-append out "/lib"))
+               (mkdir (string-append out "/include")))
+             #t)))))
     (inputs
      `(("jack" ,jack-1)
        ("alsa-lib" ,alsa-lib)))

From e17f867c62c687779a82d05db73ab63c25d49c4e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:37:48 +0100
Subject: [PATCH 059/181] gnu: wmbattery: Remove custom bootstrap phase.

* gnu/packages/gnustep.scm (wmbattery)[arguments]: Remove autoconf phase.
---
 gnu/packages/gnustep.scm | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/gnustep.scm b/gnu/packages/gnustep.scm
index bd28ceaa00..3cc5540ae7 100644
--- a/gnu/packages/gnustep.scm
+++ b/gnu/packages/gnustep.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -167,14 +168,7 @@ interface.  It is fast, feature rich, easy to configure, and easy to use.")
                (base32
                 "084a3irxbmgms4bqaga80mlx9wgvlkx6d2w0ns939yrpfzg87laj"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f              ; no "check" target
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _
-             (invoke "autoreconf" "-vfi")
-             #t)))))
+    (arguments '(#:tests? #f)) ; no "check" target
     (inputs
      `(("glib" ,glib)
        ("libx11" ,libx11)

From f116e1fcae18d07c116d5d96bdb4de20cd783b5f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:40:14 +0100
Subject: [PATCH 060/181] gnu: wmclock: Remove custom bootstrap phase.

* gnu/packages/gnustep.scm (wmclock)[arguments]: Remove.
---
 gnu/packages/gnustep.scm | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/gnu/packages/gnustep.scm b/gnu/packages/gnustep.scm
index 3cc5540ae7..dd7c67d553 100644
--- a/gnu/packages/gnustep.scm
+++ b/gnu/packages/gnustep.scm
@@ -256,18 +256,11 @@ on.")
                (base32
                 "1lx276ba8r2yydhmwj1g586jdqg695ad89ng36fr3mb067gvb2rz"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _
-             (invoke "autoreconf" "-vfi")
-             #t)))))
-    ;; wmclock requires autoreconf to generate its configure script.
     (inputs
      `(("libx11" ,libx11)
        ("libxext" ,libxext)
        ("libxpm" ,libxpm)))
+    ;; wmclock requires autoreconf to generate its configure script.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)

From 4cbbb16045d930b074268e9bc72922578ce31059 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Nov 2018 23:41:30 +0100
Subject: [PATCH 061/181] gnu: nxbelld: Remove custom bootstrap phase.

* gnu/packages/xdisorg.scm (nxbelld)[arguments]: Remove autoreconf phase.
---
 gnu/packages/xdisorg.scm | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index cf3e33eb5b..c54282b985 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -10,7 +10,7 @@
 ;;; Copyright © 2015 xd1le <elisp.vim@gmail.com>
 ;;; Copyright © 2015 Florian Paul Schmidt <mista.tapas@gmx.net>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
-;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Alex Kost <alezost@gmail.com>
@@ -1338,15 +1338,11 @@ invert colors on a specific display/screen.")
     (build-system gnu-build-system)
     (arguments '(#:configure-flags `("--enable-sound"
                                      "--enable-wave"
-                                     "--enable-alsa")
-                 #:phases (modify-phases %standard-phases
-                           (add-before 'configure 'autoreconf
-                             (lambda _
-                               (invoke "autoreconf" "-vfi"))))))
-   (native-inputs `(("autoconf" ,autoconf)
-                    ("automake" ,automake)
-                    ("pkg-config" ,pkg-config)
-                    ("perl" ,perl)))
+                                     "--enable-alsa")))
+    (native-inputs `(("autoconf" ,autoconf)
+                     ("automake" ,automake)
+                     ("pkg-config" ,pkg-config)
+                     ("perl" ,perl)))
     (inputs `(("libx11" ,libx11)
               ("alsa-lib" ,alsa-lib)))
     (synopsis "Daemon that performs an action every time the X11 bell is rung")

From fc43d6d4d9df9672b3a1047e5c81bed511dad8e4 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 10 Nov 2018 20:22:30 -0500
Subject: [PATCH 062/181] gnu: linux-libre@4.4: Update to 4.4.163.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.163.
---
 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 b1021d5624..cd7f61803d 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -445,8 +445,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.162"
-                    "1anb2k9i03369lvbwlw24vimxvk8zpcql4ryz0ydvf3pxv8lirm2"
+  (make-linux-libre "4.4.163"
+                    "05j0dm0cxilanp5z40n8kgjz9vn1p4rg63kksicd2v48w8ka82z6"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From 62168a555872aafccbc75d5681063c3f90d9a928 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 10 Nov 2018 20:23:15 -0500
Subject: [PATCH 063/181] gnu: linux-libre@4.9: Update to 4.9.136.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.136.
---
 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 cd7f61803d..132bc0d827 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -439,8 +439,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.135"
-                    "07v5s6hl08ls2z9xdkbqq1s210mqayfchqbckhp8hlaw089ap71f"
+  (make-linux-libre "4.9.136"
+                    "1kk6px1jcwbgkpfmf9pdklk6kz90h5l8fvdqwmvnk4bz6b2xrrfp"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From e22842f5ca7e8db772e9a8522d21b63bb7c81c4f Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 10 Nov 2018 20:23:57 -0500
Subject: [PATCH 064/181] gnu: linux-libre@4.14: Update to 4.14.80.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.80.
(%linux-libre-4.14-hash): 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 132bc0d827..b1dd5adc88 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -429,8 +429,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.19-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.79")
-(define %linux-libre-4.14-hash "000rd4h2yk6k68wjg37v53hqnqw1mgwhdxbcvy8iywy8za9r12c8")
+(define %linux-libre-4.14-version "4.14.80")
+(define %linux-libre-4.14-hash "0h4hi5lqizdx5nk0f3immbcv2n7p5jh26m80v4x6bw4wi5b44fra")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version

From 3b144946164641f806fbbf27ac592c7c717ea6c6 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 10 Nov 2018 13:42:50 -0500
Subject: [PATCH 065/181] gnu: icecat: Update to 60.3.0-gnu1.

* gnu/packages/gnuzilla.scm (icecat): Update to 60.3.0-gnu1.
[source]: Switch back to the normal source URI.  Remove patches that
are no longer applicable.
* gnu/packages/patches/icecat-CVE-2018-12383.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                  |   1 -
 gnu/packages/gnuzilla.scm                     |  68 +-----------
 .../patches/icecat-CVE-2018-12383.patch       | 103 ------------------
 3 files changed, 3 insertions(+), 169 deletions(-)
 delete mode 100644 gnu/packages/patches/icecat-CVE-2018-12383.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 68a87b1255..48ee438a6e 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -811,7 +811,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/hplip-remove-imageprocessor.patch	\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
-  %D%/packages/patches/icecat-CVE-2018-12383.patch		\
   %D%/packages/patches/icecat-use-system-graphite2+harfbuzz.patch	\
   %D%/packages/patches/icecat-use-system-media-libs.patch	\
   %D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch  \
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 1dd0e930d3..36ac0dfe6a 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -482,83 +482,21 @@ security standards.")
 (define-public icecat
   (package
     (name "icecat")
-    (version "60.2.0-gnu1")
+    (version "60.3.0-gnu1")
     (source
      (origin
       (method url-fetch)
-      ;; Temporary URL pending official release:
-      (uri "https://alpha.gnu.org/gnu/gnuzilla/60.2.0/icecat-60.2.0-gnu1.tar.bz2")
-      #;
       (uri (string-append "mirror://gnu/gnuzilla/"
                           (first (string-split version #\-))
                           "/" name "-" version ".tar.bz2"))
       (sha256
        (base32
-        "0lqx7g79x15941rhjr3qsfwsny6vzc7d7abdmvjy6jjbqkqlc1zl"))
+        "0icnl64nxcyf7dprpdpygxhabsvyhps8c3ixysj9bcdlj9q34ib1"))
       (patches
        (list
         (search-patch  "icecat-avoid-bundled-libraries.patch")
         (search-patch  "icecat-use-system-graphite2+harfbuzz.patch")
-        (search-patch  "icecat-use-system-media-libs.patch")
-        (mozilla-patch "icecat-CVE-2018-12385.patch"      "80a4a7ef2813" "1vgcbimpnfjqj934v0cryq1g13xac3wfmd4jyhcb5s60x8xyssf5")
-        (search-patch  "icecat-CVE-2018-12383.patch")
-        (mozilla-patch "icecat-bug-1489744.patch"         "6546ee839d30" "11mhvj77r789b428bfxqq5wdx8yr7lbrdjzr8qjj6fw197pldn51")
-        (mozilla-patch "icecat-CVE-2018-12386.patch"      "4808fcb2e6ca" "05sc881l7sh8bag8whd2ggdn198lskqcxq8f41scfpqscw6xs5d5")
-        (mozilla-patch "icecat-CVE-2018-12387.patch"      "b8f5c37486e1" "0lvmbh126m695kgdbasy1y5xh9n1j08cwdhn071mgvj6yn8cns5z")
-        (mozilla-patch "icecat-bug-1464751.patch"         "d5d00faf0465" "1mj7dbb06brwrk0mvap0z4lfl2hwz1cj6dwjvdrisxm046pdw98i")
-        (mozilla-patch "icecat-bug-1472538.patch"         "11462f2b98f2" "1nxgh0plzilylx8r73r7d74pv66qwjqxmd7nqii33p0snl2jjfzs")
-        (mozilla-patch "icecat-bug-1478685.patch"         "098585dc86fc" "1b0x4qdh6isvffmibvc8ad8z62m3iky9q6jq0z6gyvn8q252cqal")
-        (mozilla-patch "icecat-bug-1486080.patch"         "3f8d57d936ea" "0pz2c18wcgj44v0j8my9xbm90m4bsjcvzmavj569fi8bh6s6zz8p")
-        (mozilla-patch "icecat-bug-1423278.patch"         "878ceaee5634" "0i47s5nvrx9vqbnj6s9y9f4ffww20p8nviqa6frg676y1188xlyl")
-        (mozilla-patch "icecat-CVE-2018-12390-pt01.patch" "87be1b98ec9a" "15f4l18c7hz9aqn89gg3dwmdidfwgn10dywgpzydm8mps45amx7j")
-        (mozilla-patch "icecat-bug-1484559.patch"         "99e58b5307ce" "02fdgbliwzi2r2376wg6k1rky1isfka0smac4ii2cll01jhpfrn6")
-        (mozilla-patch "icecat-CVE-2018-12390-pt02.patch" "f25ce451a492" "18nzg39iyxza1686180qk9cc88l5j2hf1h35d62lrqmdgd9vcj33")
-        (mozilla-patch "icecat-CVE-2018-12390-pt03.patch" "35c26bc231df" "0qh8d4z6y03h5xh7djci26a01l6zq667lg2k11f6zzg7z2j0h67x")
-        (mozilla-patch "icecat-bug-1488061.patch"         "050d0cfa8e3d" "05ql798ynbyz5pvyri4b95j4ixmgnny3zl7sd2ckfrrbm9mxh627")
-        (mozilla-patch "icecat-bug-1434963-pt1.patch"     "1e6dad87efed" "1v00a6cmgswjk54041jyv1ib129fxshpzwk6mn6lr0v5hylk3bx9")
-        (mozilla-patch "icecat-bug-1434963-pt2.patch"     "6558c46df9ea" "0vdy9dm9w5k1flhcfxwvvff0aa415b5mgmmq5r37i83686768xfb")
-        (mozilla-patch "icecat-bug-1434963-pt3.patch"     "686fcfa8abd6" "0ihqr11aq4b0y7mx7bwn8yzn25mv3k2gdphm951mj1g85qg35ann")
-        (mozilla-patch "icecat-bug-1491132.patch"         "14120e0c74d6" "188c5fbhqqhmlk88p70l6d97skh7xy4jhqdby1ri3h9ix967515j")
-        (mozilla-patch "icecat-bug-1492065.patch"         "ec4b5969c6ae" "18gfwn15kh0826vlg6lhrx3q4gv82i7v1k3y5jp72mvrjq154gy0")
-        (mozilla-patch "icecat-bug-1492064.patch"         "528cabdd9665" "0rdwpkfma24hn8namfb9saw4rgi9yyyj4af5h2ijrvadw6r8lyyn")
-        (mozilla-patch "icecat-bug-1489757.patch"         "46f19852aaa6" "0dga7mw847klm8x6il2fyzpjxqxxgx1q5cya658f1w66kxms1f29")
-        (mozilla-patch "icecat-bug-1492897.patch"         "c3a48066f383" "09n6sdck4jzzmznzrq0iixg5nsgrc5ibpdfsh3i7ppwad3fsy2m3")
-        (mozilla-patch "icecat-bug-1492915.patch"         "2d280e557331" "11x2n61pw5way9cg8lbrfl3lqvgfnbmcs1fwm78i06kmfwj0msk3")
-        (mozilla-patch "icecat-CVE-2018-12390-pt04.patch" "b80f94262165" "1hw43h4sgf77x323745rixyp6cci3fb6d3fnp33q82m4ssdb5623")
-        (mozilla-patch "icecat-bug-1492484.patch"         "1b3e6759cf3a" "1yn2cd2227ncg90c88ymdi5fyfs4hk335bd16vkkgljs0924yy0m")
-        (mozilla-patch "icecat-bug-1493590.patch"         "d9fe3b2025fc" "06783hj1aqms2f9a3mp18bk8hgijk3pz70bpccn173v4w0zlbbd4")
-        (mozilla-patch "icecat-CVE-2018-12390-pt05.patch" "20c59797e994" "1vxnhpirjsj040hrq9xmq2xhkpq4l5mnnzqy0nda92dfh47zvidj")
-        (mozilla-patch "icecat-CVE-2018-12390-pt06.patch" "1749661dfd28" "0g0sj2fgp3asj0yvxksnhrc59yxncn35bz5nzlvkpgdf7h06gscd")
-        (mozilla-patch "icecat-CVE-2018-12390-pt07.patch" "a511a9242406" "1hhfrvdmkccnhs4skbi06174x37rmvf4ic86xawyyzr67yga73b2")
-        (mozilla-patch "icecat-bug-1495404.patch"         "3232bb3b622f" "1pnaxf8r9h0wldjc4qgl7z3rk34fpz9h1vd3zmhswa6mvyln5jhg")
-        (mozilla-patch "icecat-bug-1465388.patch"         "a9577451dcc2" "0v29s0v3vv9vblkcachhh46qvwjcrmv2bkcdb7sj2asc503l0lqv")
-        (mozilla-patch "icecat-CVE-2018-12390-pt08.patch" "e965f6f6ed75" "0hh091854xj5j0x1r8pg46xmn00fqi5n212xhzbdpgyf96rsf513")
-        (mozilla-patch "icecat-bug-1445528.patch"         "8a503e022a29" "1y2ll3h0yz8sfdddjmk90qjfxcr1ffhw7a9ww3yw26gyhnbpg404")
-        (mozilla-patch "icecat-bug-1409570.patch"         "8d326641d1c0" "0w29s6dixi7b7q3nicshrp29n9sj5awssdln00yx664m8a8a8ihs")
-        (mozilla-patch "icecat-bug-1496094.patch"         "6cdd6d88eca9" "1ssqa4fy2xpbr63ph3av3hkpl92g4yszx402fq9d2xn9482q43dp")
-        (mozilla-patch "icecat-CVE-2018-12391.patch"      "0fa07c704ca4" "055xdyb3g2l4rj188235i579qnr50v19q36jjpliws9nik129iqy")
-        (mozilla-patch "icecat-bug-1462162.patch"         "739e898cb7c8" "17m9y0pskmqx15dkgkw4k93njph14mpsf37wb1azwkq3xx7s0fhx")
-        (mozilla-patch "icecat-bug-1492764.patch"         "16310ab35452" "1kq5r3w9i4n6q9msmw2qsqa0jd4qw1mjlyyz8aq14fwlbkhvv199")
-        (mozilla-patch "icecat-CVE-2018-12390-pt09.patch" "9b669d047d55" "063ig49gx9468nvc9w8259j819qfdjvq0sbbz8n4kj5r6hcxjc5l")
-        (mozilla-patch "icecat-CVE-2018-12390-pt10.patch" "9d51e65c797a" "0m23cq9zl22w80dvx5rlgpbam1l3d6v56h7g9wzamzl21bwxq9fv")
-        (mozilla-patch "icecat-CVE-2018-12390-pt11.patch" "efc0596dd381" "1alvbb6wvawxxh6isisk9c40vhdiv59fy0af0n10yn1dgy8ffv5i")
-        (mozilla-patch "icecat-CVE-2018-12393.patch"      "c4fb48bb5d28" "09izww9dsg9n8cish8f3y7phxibsnd12bfkcxd7rzcdhg10nr4pl")
-        (mozilla-patch "icecat-CVE-2018-12390-pt12.patch" "b3359becd7b1" "188byxmbgrvrid2fcz34w5xdvaw571frxx1c6nqaa9k03iljdzjr")
-        (mozilla-patch "icecat-CVE-2018-12390-pt13.patch" "791c8ecf252d" "02h37594aba0pklxm3g7w1wv8vz9xmcf30fd0az8pfaccsklmx74")
-        (mozilla-patch "icecat-bug-1494328.patch"         "333276fac37c" "0qyq42jl0al63m6pwj9gva7nj82l76szzbj7sklsygx0a9mqs13z")
-        (mozilla-patch "icecat-CVE-2018-12397.patch"      "cb73374a0e4e" "0x2s1nwgwdag9df5hkwzvjj0qznp5c3d6w6y63rn2y287jn9m3vl")
-        (mozilla-patch "icecat-CVE-2018-12392.patch"      "f6bb138ad0ab" "0f0z9dsyw2a11p4p31mdyic571153jpfgy2q04i4v6dmmcz76pm3")
-        (mozilla-patch "icecat-CVE-2018-12396.patch"      "f27145bd5502" "0vznmlm1fbl3ynax2zpi6xxzr9qp9b83afr3mv90jgrhlgpzdbcz")
-        (mozilla-patch "icecat-CVE-2018-12395-pt1.patch"  "133a99a8f3ca" "0im7m4jmc273mg9kih0i70hxsgzy04j6ydm9zmaz2933hkhdf4iw")
-        (mozilla-patch "icecat-CVE-2018-12395-pt2.patch"  "82176a4a9b14" "0g3yqx4854d4mx5a0ghb7p7saj6y5d5bm2lfhabvkwybcd477zmc")
-        (mozilla-patch "icecat-bug-1474265.patch"         "e8abd9a8ce6e" "1q2sv5h081rvnhsx6g1y8a43hwv6hsg0cr6zdcij58mkgzf6hyvd")
-        (mozilla-patch "icecat-bug-1492737-pt1.patch"     "eeb9060379dc" "1d2mf0x4rni7anvi0sgra4dg87fmc6g7zhizzl9jv2x8va27ycbp")
-        (mozilla-patch "icecat-bug-1492737-pt2.patch"     "99eae0d15092" "0f9j6cvhrbrrxa95p4pkcn285r9wmi9yj13nwj5x0gkglwx6idbk")
-        (mozilla-patch "icecat-CVE-2018-12389-pt1.patch"  "23b23e12c548" "0nsdycggki5rhh59yvmh41nf1ahjmgii89fx38jryprhspy3wg62")
-        (mozilla-patch "icecat-CVE-2018-12390-pt14.patch" "023133ff02ec" "1g22qxnmgiy8bgrn2nv6har6vpz4p2h5pdas8ib1yyz7p2ic8652")
-        (mozilla-patch "icecat-CVE-2018-12390-pt15.patch" "9461988ff462" "0yq2cr5grqskr0kz4nxcwmnywy9g0xyv6k6q44i490jcj8x2y1vw")
-        (mozilla-patch "icecat-CVE-2018-12390-pt16.patch" "09939be135d8" "1546xlk368v4hnjd3hf4w868i6m8r4wfd34qxz4wg1cdpr4m5mik")
-        (mozilla-patch "icecat-CVE-2018-12389-pt2.patch"  "ea9412b18ca8" "0fmdncrylbmjh0bcb6dmw1rq7zww8a0v9v9p1pxqfz0vbc6v9l5d")))
+        (search-patch  "icecat-use-system-media-libs.patch")))
       (modules '((guix build utils)))
       (snippet
        '(begin
diff --git a/gnu/packages/patches/icecat-CVE-2018-12383.patch b/gnu/packages/patches/icecat-CVE-2018-12383.patch
deleted file mode 100644
index 17ca0f3773..0000000000
--- a/gnu/packages/patches/icecat-CVE-2018-12383.patch
+++ /dev/null
@@ -1,103 +0,0 @@
-Based on upstream changeset:
-  https://hg.mozilla.org/releases/mozilla-esr60/rev/300efdbc9fe1
-but with the git binary patch and related test changes omitted,
-and adapted to apply cleanly to GNU IceCat.
-
-# HG changeset patch
-# User David Keeler <dkeeler@mozilla.com>
-# Date 1531860660 25200
-# Node ID 300efdbc9fe1f9165428c7934861033935b5abfa
-# Parent  80a4a7ef281374dbb2afda8edac54665b14b9ef8
-Bug 1475775 - Clean up old NSS DB file after upgrade if necessary. r=franziskus, r=mattn, a=RyanVM
-
-Reviewers: franziskus, mattn
-
-Bug #: 1475775
-
-Differential Revision: https://phabricator.services.mozilla.com/D2202
-
-diff --git a/security/manager/ssl/nsNSSComponent.cpp b/security/manager/ssl/nsNSSComponent.cpp
---- a/security/manager/ssl/nsNSSComponent.cpp
-+++ b/security/manager/ssl/nsNSSComponent.cpp
-@@ -1935,16 +1935,61 @@ AttemptToRenameBothPKCS11ModuleDBVersion
-   NS_NAMED_LITERAL_CSTRING(sqlModuleDBFilename, "pkcs11.txt");
-   nsresult rv = AttemptToRenamePKCS11ModuleDB(profilePath,
-                                               legacyModuleDBFilename);
-   if (NS_FAILED(rv)) {
-     return rv;
-   }
-   return AttemptToRenamePKCS11ModuleDB(profilePath, sqlModuleDBFilename);
- }
-+
-+// When we changed from the old dbm database format to the newer sqlite
-+// implementation, the upgrade process left behind the existing files. Suppose a
-+// user had not set a password for the old key3.db (which is about 99% of
-+// users). After upgrading, both the old database and the new database are
-+// unprotected. If the user then sets a password for the new database, the old
-+// one will not be protected. In this scenario, we should probably just remove
-+// the old database (it would only be relevant if the user downgraded to a
-+// version of IceCat before 58, but we have to trade this off against the
-+// user's old private keys being unexpectedly unprotected after setting a
-+// password).
-+// This was never an issue on Android because we always used the new
-+// implementation.
-+static void
-+MaybeCleanUpOldNSSFiles(const nsACString& profilePath)
-+{
-+  UniquePK11SlotInfo slot(PK11_GetInternalKeySlot());
-+  if (!slot) {
-+    return;
-+  }
-+  // Unfortunately we can't now tell the difference between "there already was a
-+  // password when the upgrade happened" and "there was not a password but then
-+  // the user added one after upgrading".
-+  bool hasPassword = PK11_NeedLogin(slot.get()) &&
-+                     !PK11_NeedUserInit(slot.get());
-+  if (!hasPassword) {
-+    return;
-+  }
-+  nsCOMPtr<nsIFile> dbFile = do_CreateInstance("@mozilla.org/file/local;1");
-+  if (!dbFile) {
-+    return;
-+  }
-+  nsresult rv = dbFile->InitWithNativePath(profilePath);
-+  if (NS_FAILED(rv)) {
-+    return;
-+  }
-+  NS_NAMED_LITERAL_CSTRING(keyDBFilename, "key3.db");
-+  rv = dbFile->AppendNative(keyDBFilename);
-+  if (NS_FAILED(rv)) {
-+    return;
-+  }
-+  // Since this isn't a directory, the `recursive` argument to `Remove` is
-+  // irrelevant.
-+  Unused << dbFile->Remove(false);
-+}
- #endif // ifndef ANDROID
- 
- // Given a profile directory, attempt to initialize NSS. If nocertdb is true,
- // (or if we don't have a profile directory) simply initialize NSS in no DB mode
- // and return. Otherwise, first attempt to initialize in read/write mode, and
- // then read-only mode if that fails. If both attempts fail, we may be failing
- // to initialize an NSS DB collection that has FIPS mode enabled. Attempt to
- // ascertain if this is the case, and if so, rename the offending PKCS#11 module
-@@ -1966,16 +2011,19 @@ InitializeNSSWithFallbacks(const nsACStr
- 
-   // Try read/write mode. If we're in safeMode, we won't load PKCS#11 modules.
- #ifndef ANDROID
-   PRErrorCode savedPRErrorCode1;
- #endif // ifndef ANDROID
-   SECStatus srv = ::mozilla::psm::InitializeNSS(profilePath, false, !safeMode);
-   if (srv == SECSuccess) {
-     MOZ_LOG(gPIPNSSLog, LogLevel::Debug, ("initialized NSS in r/w mode"));
-+#ifndef ANDROID
-+    MaybeCleanUpOldNSSFiles(profilePath);
-+#endif // ifndef ANDROID
-     return NS_OK;
-   }
- #ifndef ANDROID
-   savedPRErrorCode1 = PR_GetError();
-   PRErrorCode savedPRErrorCode2;
- #endif // ifndef ANDROID
-   // That failed. Try read-only mode.
-   srv = ::mozilla::psm::InitializeNSS(profilePath, true, !safeMode);

From 717d29e25bab351c08e3bf391056f3b2e5edfdba Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 10 Nov 2018 13:43:22 -0500
Subject: [PATCH 066/181] gnu: icecat: Add more fixes from mozilla-esr60.

* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes
from the upstream mozilla-esr60 source repository.
---
 gnu/packages/gnuzilla.scm | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 36ac0dfe6a..e1abe8c2cd 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -496,7 +496,19 @@ security standards.")
        (list
         (search-patch  "icecat-avoid-bundled-libraries.patch")
         (search-patch  "icecat-use-system-graphite2+harfbuzz.patch")
-        (search-patch  "icecat-use-system-media-libs.patch")))
+        (search-patch  "icecat-use-system-media-libs.patch")
+        (mozilla-patch "icecat-bug-1464061.patch"         "d28761dbff18" "1f58rzwx4s1af66fdwn9lgkcd1ksmq8kn8imvf78p90jqi24h7b4")
+        (mozilla-patch "icecat-bug-1479853.patch"         "4faeb696dd06" "12891xx9c15s6kby6d3zk64v5nqgaq7sw597zv1fkd3a6x69hlva")
+        (mozilla-patch "icecat-bug-1488295.patch"         "12ba39f69876" "1piyq44f0xa0a9z2748aqwpaziaxwp61d86gyhalbyag8lcxfb3p")
+        (mozilla-patch "icecat-bug-1500011.patch"         "a0adabeedf26" "0f5wazha3zxzhy2j8f93hx62l9p02b1p40vi07qah3ar67h4ccj9")
+        (mozilla-patch "icecat-bug-1503082.patch"         "19604eb26230" "1wqxgph4z14ijhk2j2m4av5p6gx72d02lzz83q6yy0k065kw8psb")
+        (mozilla-patch "icecat-bug-1499861.patch"         "98737ab09270" "0fyl6wv0jxcxpkfpsff46y93k49n8lrw0k7c1p45g8da015dx27a")
+        (mozilla-patch "icecat-bug-1504452.patch"         "1cf7d80355d5" "19jp4x32vyxam54d1r9fm7jwf6krhhf3xazfqmxb9aw4iwdil7dl")
+        (mozilla-patch "icecat-bug-1494752.patch"         "c264774b8913" "1hxyi131x8jwawrq90cgkph833iv9ixrdrgzl1r978gbzwq10xz2")
+        (mozilla-patch "icecat-bug-1477773.patch"         "ec13fda7c9b0" "0zj7aylgw55g0y7plaafn5gq8jwcsdr1bpdxacs0hq914nm8zy9z")
+        (mozilla-patch "icecat-bug-1500759.patch"         "5e1a9644aeef" "1qimrpgyrd8zkiri7w57j0aymk20y9b34am5w7rvr6qj1lhrbfla")
+        (mozilla-patch "icecat-bug-1485655.patch"         "9055726e2d89" "1pppxr94zqh6zmi2mn1ih21qap09vk5ivbhnwxqr8iszvygjg44g")
+        (mozilla-patch "icecat-bug-1410214.patch"         "9e641345e2ef" "0542xss2jdb8drh4g50cfy32l300x69dyywgx3dqs03vgr3qplxy")))
       (modules '((guix build utils)))
       (snippet
        '(begin

From cab70d4c2ae8c92337501b19dd938792447ad5b8 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 10 Nov 2018 21:48:26 +0200
Subject: [PATCH 067/181] gnu: perl-autovivification: Update to 0.18.

* gnu/packages/perl.scm (perl-autovivification): Update to 0.18.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index f556d19f3c..cbdf070e89 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -364,7 +364,7 @@ sometimes even without using a single syscall.")
 (define-public perl-autovivification
   (package
     (name "perl-autovivification")
-    (version "0.16")
+    (version "0.18")
     (source
      (origin
        (method url-fetch)
@@ -372,7 +372,7 @@ sometimes even without using a single syscall.")
                            "autovivification-" version ".tar.gz"))
        (sha256
         (base32
-         "1422kw9fknv7rbjkgdfflg1q3mb69d3yryszp38dn0bgzkqhwkc1"))))
+         "01giacr2sx6b9bgfz6aqw7ndcnf08j8n6kwhm7880a94hmb9g69d"))))
     (build-system perl-build-system)
     (home-page "https://metacpan.org/release/autovivification")
     (synopsis "Lexically disable autovivification")

From 863742856c663aace968f2c84876b4528074dd2c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 09:58:55 +0100
Subject: [PATCH 068/181] gnu: librime: Fetch sources from git.

* gnu/packages/ibus.scm (librime)[source]: Fetch from git.
---
 gnu/packages/ibus.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index 8ad1e09856..3abdd4fab0 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -295,12 +295,13 @@ Japanese language input in most graphical applications.")
     (version "1.3.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/rime/" name
-                           "/archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rime/librime.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0qh0hy8bvj17bnzaxk0bmv4gsnbsd6jx8csr84936xmhkrysdday"))))
+        (base32 "1y0h3nnz97smx9z8h5fzk4c27mvrwv8kajxffqc43bhyvxvb2jd6"))))
     (build-system cmake-build-system)
     (inputs
      `(("boost" ,boost)

From 487e3f5a807581c5b1558590e3f54cd06b7214d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 09:59:28 +0100
Subject: [PATCH 069/181] gnu: ibus-rime: Fetch sources from git.

* gnu/packages/ibus.scm (ibus-rime)[source]: Fetch from git.
---
 gnu/packages/ibus.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index 3abdd4fab0..a2687ac8c3 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -602,12 +602,13 @@ Method Engine.")
     (version "1.3.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/rime/" name
-                           "/archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rime/ibus-rime.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0mfbz0vwky7n4wvxrwabnn1i9n9adnql0dd1rx57w1anaslr5amj"))))
+        (base32 "1nqi7ymv34a9kx24say3xj98lkrs9nkpv1n2ijb91wdz3cr012ly"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests

From 1410e178bb66479de1ae859b03f8a00be6ddfdd3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 10:02:40 +0100
Subject: [PATCH 070/181] gnu: pianobar: Fetch sources from git.

* gnu/packages/music.scm (pianobar)[source]: Fetch from git.
---
 gnu/packages/music.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index c405ea8511..be988b107a 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -2443,13 +2443,14 @@ tune-in sender list from @url{http://opml.radiotime.com}.")
     (name "pianobar")
     (version "2016.06.02")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/PromyLOPh/"
-                                  name "/archive/" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/PromyLOPh/pianobar.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1hi5rr6jcr0kwf4xfz007ndwkjkp287lhwlsgfz6iryqa5n6jzcp"))))
+                "058fbdxp7n35hxwy3b8slfy4pb4n63cb173vfmywqa06wh1dv6f6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no tests

From f626b7192394b96b012d5872cc623ef6adbb8981 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 10:05:56 +0100
Subject: [PATCH 071/181] gnu: mdbtools: Remove custom bootstrap phase.

* gnu/packages/databases.scm (mdbtools)[arguments]: Remove.
---
 gnu/packages/databases.scm | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index dc7e2aa53d..aacf5465c1 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2088,12 +2088,6 @@ for ODBC.")
        ("pkg-config" ,pkg-config)
        ("txt2man" ,txt2man)
        ("which" ,which)))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vfi")))))))
     (home-page "http://mdbtools.sourceforge.net/")
     (synopsis "Read Microsoft Access databases")
     (description "MDB Tools is a set of tools and applications to read the

From f1f1cebdd3f2ca18d77e8f8a1f5760a65e7137fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 10:09:54 +0100
Subject: [PATCH 072/181] gnu: mdbtools: Fetch sources from git.

* gnu/packages/databases.scm (mdbtools)[source]: Fetch from git.
---
 gnu/packages/databases.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index aacf5465c1..46bd728b1b 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2071,13 +2071,14 @@ for ODBC.")
     (version "0.7.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/brianb/mdbtools/archive/"
-                           version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/brianb/mdbtools.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "05hbmxcq173kzb899gdi3bz2qcc1vi3n1qbbkwpsvrq7ggf11wyw"))
-       (file-name (string-append name "-" version ".tar.gz"))))
+         "0gwcpp9y09xhs21g7my2fs8ncb8i6ahlyixcx8jd3q97jbzj441l"))))
     (build-system gnu-build-system)
     (inputs
      `(("glib" ,glib)))

From a49b5322c56cd5b7778a8c8ffea95f9c28339cc7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 10:16:43 +0100
Subject: [PATCH 073/181] gnu: lxsession: Remove custom bootstrap phase.

* gnu/packages/lxde.scm (lxsession)[arguments]: Remove autoreconf phase and
end rm-stamp phase with #T.
---
 gnu/packages/lxde.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/lxde.scm b/gnu/packages/lxde.scm
index c45beb8bbb..1f32ec3bb1 100644
--- a/gnu/packages/lxde.scm
+++ b/gnu/packages/lxde.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Ison111 <ison111@protonmail.com>
 ;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -419,10 +420,10 @@ in LXDE.")
        (modify-phases %standard-phases
          (add-after 'unpack 'rm-stamp
            (lambda _
-             (for-each delete-file (find-files "." "\\.stamp$"))))
-         (add-after 'rm-stamp 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vfi")))))))
+             (for-each delete-file (find-files "." "\\.stamp$"))
+             ;; Force regeneration of configure script.
+             (delete-file "configure")
+             #t)))))
     (inputs
      `(("gtk+-2" ,gtk+-2)
        ("polkit" ,polkit)))

From 974056c05e3515deb9cf616c2a4d1265a0d55f17 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 10:20:36 +0100
Subject: [PATCH 074/181] gnu: opendht: Fetch sources from git.

* gnu/packages/crypto.scm (opendht)[source]: Fetch from git.
---
 gnu/packages/crypto.scm | 47 +++++++++++++++++++----------------------
 1 file changed, 22 insertions(+), 25 deletions(-)

diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 29d9a3d6ab..393d8f84b9 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 David Thompson <davet@gnu.org>
-;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -164,34 +164,31 @@ OpenBSD tool of the same name.")
                                           "See base64.c in the distribution for
                                            the license from IBM.")))))
 
-
 (define-public opendht
   (package
     (name "opendht")
     (version "0.6.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append
-         "https://github.com/savoirfairelinux/" name
-         "/archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           (delete-file-recursively "src/argon2")
-           (substitute* "src/Makefile.am"
-             (("./argon2/libargon2.la") "")
-             (("SUBDIRS = argon2") ""))
-           (substitute* "src/crypto.cpp"
-             (("argon2/argon2.h") "argon2.h"))
-           (substitute* "configure.ac"
-             (("src/argon2/Makefile") ""))
-           #t))
-       (sha256
-        (base32
-         "09yvkmbqbym3b5md4n96qc1s9sf2n8ji404hagih45rmsj49599x"))))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/savoirfairelinux/opendht.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "src/argon2")
+                  (substitute* "src/Makefile.am"
+                    (("./argon2/libargon2.la") "")
+                    (("SUBDIRS = argon2") ""))
+                  (substitute* "src/crypto.cpp"
+                    (("argon2/argon2.h") "argon2.h"))
+                  (substitute* "configure.ac"
+                    (("src/argon2/Makefile") ""))
+                  #t))
+              (sha256
+               (base32
+                "1akk613f18rc8kqs0cxdm34iq7wwc9kffhgp5rng09arwlw8gw3w"))))
     (build-system gnu-build-system)
     (inputs
      `(("gnutls" ,gnutls)

From 5ad728e04c652d157039128ac7fc510a8530076c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 10:21:02 +0100
Subject: [PATCH 075/181] gnu: opendht: Remove custom bootstrap phase.

* gnu/packages/crypto.scm (opendht)[arguments]: Remove autoconf phase.
---
 gnu/packages/crypto.scm | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 393d8f84b9..e8062f0e1f 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -203,11 +203,7 @@ OpenBSD tool of the same name.")
        ("automake" ,automake)
        ("libtool" ,libtool)))
     (arguments
-     `(#:configure-flags '("--disable-tools" "--disable-python")
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'autoconf
-                    (lambda _
-                      (zero? (system* "autoreconf" "-vfi")))))))
+     `(#:configure-flags '("--disable-tools" "--disable-python")))
     (home-page "https://github.com/savoirfairelinux/opendht/")
     (synopsis "Distributed Hash Table (DHT) library")
     (description "OpenDHT is a Distributed Hash Table (DHT) library.  It may

From 34da5c394bb8aedb9a054d4738dc8d471f8b77cd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 10:22:45 +0100
Subject: [PATCH 076/181] gnu: guile-dsv: Remove custom bootstrap phase.

* gnu/packages/guile.scm (guile-dsv)[arguments]: Remove autoreconf phase.
---
 gnu/packages/guile.scm | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 6ae0fe2e77..cbdd5b1e0f 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -1573,10 +1573,7 @@ $(datadir)/guile/site/$(GUILE_EFFECTIVE_VERSION)\n"))
                         (("^guilesitedir =.*$")
                          "guilesitedir = \
 $(datadir)/guile/site/$(GUILE_EFFECTIVE_VERSION)\n"))
-                      #t))
-                  (add-after 'unpack 'autoreconf
-                    (lambda _
-                      (zero? (system* "autoreconf" "-vfi")))))))
+                      #t)))))
     (home-page "https://github.com/artyom-poptsov/guile-dsv")
     (synopsis "DSV module for Guile")
     (description

From 2cabd29323382d72cc3bc5f21a81c293df84ea3f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 10:38:00 +0100
Subject: [PATCH 077/181] gnu: guildhall: Remove custom bootstrap phase.

* gnu/packages/guile.scm (guildhall)[arguments]: Remove autogen phase.
---
 gnu/packages/guile.scm | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index cbdd5b1e0f..c41c27466b 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -517,10 +517,7 @@ AM_SCM_LOG_FLAGS =  --no-auto-compile -s")
                  ;; FIXME: one of the database tests fails for unknown
                  ;; reasons.  It does not fail when run outside of Guix.
                  (("tests/database.scm") ""))
-               #t))
-           (add-after 'fix-bug-22 'autogen
-             (lambda _
-               (zero? (system* "sh" "autogen.sh")))))))
+               #t)))))
       (inputs
        `(("guile" ,guile-2.0)))
       (native-inputs

From d212ed2f00e6639c95b4185685617285c8cafdfd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 11:21:55 +0100
Subject: [PATCH 078/181] gnu: lrdf: Fetch sources from git.

* gnu/packages/rdf.scm (lrdf)[source]: Fetch from git.
---
 gnu/packages/rdf.scm | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm
index 48dc3cddb9..e48a4fb08c 100644
--- a/gnu/packages/rdf.scm
+++ b/gnu/packages/rdf.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -22,6 +22,7 @@
   #:use-module ((guix licenses)
                 #:select (non-copyleft isc gpl2 lgpl2.1 lgpl2.1+))
   #:use-module (guix packages)
+  #:use-module (guix git-download)
   #:use-module (guix download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
@@ -122,13 +123,14 @@ Java Lucene text search engine API to C++.")
     (name "lrdf")
     (version "0.6.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/swh/LRDF/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/swh/LRDF.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1vxii4mlcpyi16dizcmnqfl2j9gffgr986yd8ic67hvs8xy42yfm"))))
+                "00wzkfb8y0aqd519ypz067cq099dpc89w69zw8ln39vl6f9x2pd4"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

From a69cc70deaa641baa50d580fb1315a69615cc381 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 11:22:22 +0100
Subject: [PATCH 079/181] gnu: lrdf: Replace bootstrap phase.

* gnu/packages/rdf.scm (lrdf)[arguments]: Remove autoreconf phase; replace
bootstrap phase instead.
---
 gnu/packages/rdf.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm
index e48a4fb08c..22ea21dd94 100644
--- a/gnu/packages/rdf.scm
+++ b/gnu/packages/rdf.scm
@@ -142,9 +142,9 @@ Java Lucene text search engine API to C++.")
                (("instances_test remove_test") "instances_test")
                (("\\$\\(TESTS\\) remove_test") "$(TESTS)"))
              #t))
-         (add-after 'remove-out-of-tree-references 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vfi")))))))
+         ;; The default bootstrap phase executes autogen.sh, which fails.
+         (replace 'bootstrap
+           (lambda _ (invoke "autoreconf" "-vif") #t)))))
     (inputs
      `(("raptor" ,raptor2)
        ("cyrus-sasl" ,cyrus-sasl)

From 4cd6ab1b1f6808b9146105a81a2b28620939aa44 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 11:23:39 +0100
Subject: [PATCH 080/181] gnu: libjaylink: Remove custom bootstrap phase.

* gnu/packages/embedded.scm (libjaylink)[arguments]: Remove.
---
 gnu/packages/embedded.scm | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm
index 38c76cd737..ddf3c340ab 100644
--- a/gnu/packages/embedded.scm
+++ b/gnu/packages/embedded.scm
@@ -321,12 +321,6 @@ languages are C and C++.")
          ("pkg-config" ,pkg-config)))
       (inputs
        `(("libusb" ,libusb)))
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'autoreconf
-             (lambda _
-               (zero? (system* "autoreconf" "-vfi")))))))
       (home-page "http://repo.or.cz/w/libjaylink.git")
       (synopsis "Library to interface Segger J-Link devices")
       (description "libjaylink is a shared library written in C to access

From 867d9de690c77b232af843106779523fe5d370cc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 11:32:12 +0100
Subject: [PATCH 081/181] gnu: openocd: Use INVOKE.

* gnu/packages/embedded.scm (openocd)[arguments]: Use INVOKE and return #T
unconditionally.
---
 gnu/packages/embedded.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm
index ddf3c340ab..f20d1e17c7 100644
--- a/gnu/packages/embedded.scm
+++ b/gnu/packages/embedded.scm
@@ -398,9 +398,9 @@ language.")
                       "presto" "openjtag")))
        #:phases
        (modify-phases %standard-phases
+         ;; Required because of patched sources.
          (add-before 'configure 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vfi"))))
+           (lambda _ (invoke "autoreconf" "-vfi") #t))
          (add-after 'autoreconf 'change-udev-group
            (lambda _
              (substitute* "contrib/60-openocd.rules"
@@ -411,7 +411,8 @@ language.")
              (install-file "contrib/60-openocd.rules"
                            (string-append
                             (assoc-ref outputs "out")
-                            "/lib/udev/rules.d/")))))))
+                            "/lib/udev/rules.d/"))
+             #t)))))
     (home-page "http://openocd.org")
     (synopsis "On-Chip Debugger")
     (description "OpenOCD provides on-chip programming and debugging support

From fab455840ea883237d2715bde313e07558f4bfba Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 11:33:39 +0100
Subject: [PATCH 082/181] gnu: libtoxcore: Remove custom bootstrap phase.

* gnu/packages/messaging.scm (libtoxcore)[arguments]: Remove autoconf phase.
---
 gnu/packages/messaging.scm | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index de33d737e2..1a7560bd72 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -855,13 +855,7 @@ protocols.")
        `(("libsodium" ,libsodium)
          ("opus" ,opus)
          ("libvpx" ,libvpx)))
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'autoconf
-             (lambda _
-               (zero? (system* "autoreconf" "-vfi")))))
-         #:tests? #f)) ; FIXME: Testsuite fails, reasons unspecific.
+      (arguments `(#:tests? #f)) ; FIXME: Testsuite fails, reasons unspecific.
       (synopsis "Library for the Tox encrypted messenger protocol")
       (description
        "C library implementation of the Tox encrypted messenger protocol.")

From d68a15806b26ee23bf83c92ed29d2d4b1024b919 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 11:34:55 +0100
Subject: [PATCH 083/181] gnu: libgtextutils: Remove custom bootstrap phase.

* gnu/packages/textutils.scm (libgtextutils)[arguments]: Remove.
---
 gnu/packages/textutils.scm | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 1d498b5a75..d4e306483e 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Jelle Licht <jlicht@fsfe.org>
@@ -198,11 +198,6 @@ encoding, supporting Unicode version 9.0.0.")
        (sha256
         (base32 "0jiybkb2z58wa2msvllnphr4js2hvjvh988pavb3mzkgr6ihwbkr"))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)

From 7a52d0e075baebe2c04331b82d5974f2db9bf9f0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 11:36:39 +0100
Subject: [PATCH 084/181] gnu: dotconf: Remove custom bootstrap phase.

* gnu/packages/textutils.scm (dotconf)[arguments]: Remove autoreconf phase.
---
 gnu/packages/textutils.scm | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index d4e306483e..c814e988b1 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -577,13 +577,7 @@ categories.")
                (base32
                 "0lsnh0yaw44psmx59hq94cj1932gscp5h8d3cnh05l0svr0cy7kz"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f ; FIXME maketest.sh does not work.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vif")))))))
+    (arguments `(#:tests? #f))  ; FIXME maketest.sh does not work.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)

From 08bc7f26653a407ccd7f07c07a81a538e9f44313 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 11:37:01 +0100
Subject: [PATCH 085/181] gnu: dotconf: Fetch sources from git.

* gnu/packages/textutils.scm (dotconf)[source]: Fetch from git.
---
 gnu/packages/textutils.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index c814e988b1..e9a4ab3d68 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -568,14 +568,14 @@ categories.")
     (name "dotconf")
     (version "1.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/williamh/dotconf/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/williamh/dotconf.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0lsnh0yaw44psmx59hq94cj1932gscp5h8d3cnh05l0svr0cy7kz"))))
+                "1sc95hw5k2xagpafny0v35filmcn05k1ds5ghkldfpf6xw4hakp7"))))
     (build-system gnu-build-system)
     (arguments `(#:tests? #f))  ; FIXME maketest.sh does not work.
     (native-inputs

From caa39e56f7d10f00893b00279e28c9c834a9a53f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 11:44:24 +0100
Subject: [PATCH 086/181] gnu: milkytracker: Fetch sources from git.

* gnu/packages/music.scm (milkytracker)[source]: Fetch from git.
---
 gnu/packages/music.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index be988b107a..479b9e40ff 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -2731,14 +2731,14 @@ of tools for manipulating and accessing your music.")
     (name "milkytracker")
     (version "1.02.00")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/milkytracker/"
-                                  "MilkyTracker/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/milkytracker/MilkyTracker.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "08v0l4ipvvwkwv4ywkc6c8a6xnpkyb02anj36w8q6gikxrs6xjvb"))
+                "05a6d7l98k9i82dwrgi855dnccm3f2lkb144gi244vhk1156n0ca"))
               (modules '((guix build utils)))
               ;; Remove non-FSDG compliant sample songs.
               (snippet

From 3a0592ae314184b44ea96cb10ff57710cca10af1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:00:55 +0100
Subject: [PATCH 087/181] gnu: lmms: Fetch sources from git.

* gnu/packages/music.scm (lmms)[source]: Fetch from git.
---
 gnu/packages/music.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 479b9e40ff..af24c96600 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -3532,13 +3532,14 @@ are a C compiler and glib.  Full API documentation and examples are included.")
     (version "1.1.3")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/LMMS/lmms/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/LMMS/lmms.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1g76z7ha3hd53vbqaq9n1qg6s3lw8zzaw51iny6y2bz0j1xqwcsr"))))
+         "03hhymc6d73fa3wbcqb7rm1l03zkw605k5i9kvkvjmv488bqh3pd"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; no tests

From 234a1825b20ebee516cbd23af1dbcb07be7f2be8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:01:25 +0100
Subject: [PATCH 088/181] gnu: clyrics: Fetch sources from git.

* gnu/packages/music.scm (clyrics)[source]: Fetch from git.
[native-inputs]: Remove.
[arguments]: Adjust builder.
---
 gnu/packages/music.scm | 21 +++++++--------------
 1 file changed, 7 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index af24c96600..012d67ae67 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4156,17 +4156,15 @@ at @code{musicbrainz.org}.")
     (version "0.10")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/trizen/clyrics/archive/"
-             version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/trizen/clyrics.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1l0cg26afnjv8cgk0jbiavbyvq55q1djyigzmi526rpcjjwq9jwn"))
-       (file-name (string-append name "-" version ".tar.gz"))))
+         "1qvj4dyipkkdccx5hci4z0q23i54ldk6hh7x5m35a7f70rrj6fbk"))))
     (build-system trivial-build-system)
-    (native-inputs `(("tar" ,tar)
-                     ("gzip" ,gzip)))
     (inputs
      `(("bash" ,bash)                             ;for the wrapped program
        ("perl" ,perl)
@@ -4183,17 +4181,12 @@ at @code{musicbrainz.org}.")
                                 (ice-9 match)
                                 (srfi srfi-26))
                    (let* ((source (assoc-ref %build-inputs "source"))
-                          (tar (assoc-ref %build-inputs "tar"))
-                          (gzip (assoc-ref %build-inputs "gzip"))
                           (output (assoc-ref %outputs "out")))
                      (setenv "PATH"
                              (string-append
-                              (assoc-ref %build-inputs "gzip") "/bin" ":"
                               (assoc-ref %build-inputs "bash") "/bin" ":"
                               (assoc-ref %build-inputs "perl") "/bin" ":"))
-                     (invoke (string-append tar "/bin/tar") "xvf"
-                             source)
-                     (chdir ,(string-append "clyrics-" version))
+                     (copy-recursively source (getcwd))
                      (patch-shebang "clyrics")
                      (substitute* "clyrics"
                        (("/usr/share") output))

From 3b9e9415faec1566dc989493030a76fc382e0a41 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:07:21 +0100
Subject: [PATCH 089/181] gnu: schismtracker: Fetch sources from git.

* gnu/packages/music.scm (schismtracker)[source]: Fetch from git.
---
 gnu/packages/music.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 012d67ae67..3b7fd54f31 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -2773,14 +2773,14 @@ for improved Amiga ProTracker 2/3 compatibility.")
     (name "schismtracker")
     (version "20180513")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/" name "/" name "/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/schismtracker/schismtracker.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yjfd02arb51n0vyv11qgpn6imh7hcqnc3953cbvgwb4cnrswk9f"))
+                "0fayix1zbl96zhkfszgj71qr25dnddgy9hr6149nslww4gl7jk36"))
               (modules '((guix build utils)))
               (snippet
                ;; Remove use of __DATE__ and __TIME__ for reproducibility.

From 88659738487e553447f66177b2df722db0e84ff9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:15:03 +0100
Subject: [PATCH 090/181] gnu: lilypond: Use INVOKE.

* gnu/packages/music.scm (lilypond)[arguments]: Use INVOKE and return #T
unconditionally.
---
 gnu/packages/music.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 3b7fd54f31..7474dac74b 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -886,9 +886,10 @@ Sega Master System/Mark III, Sega Genesis/Mega Drive, BBC Micro
             #t))
          (add-after 'install 'install-info
            (lambda _
-             (zero? (system* "make"
-                             "-j" (number->string (parallel-job-count))
-                             "conf=www" "install-info")))))))
+             (invoke "make"
+                     "-j" (number->string (parallel-job-count))
+                     "conf=www" "install-info")
+             #t)))))
     (inputs
      `(("guile" ,guile-1.8)
        ("font-dejavu" ,font-dejavu)

From cbb6a15056bd90c3fa9d03a50a347ac148ab64d9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:19:23 +0100
Subject: [PATCH 091/181] gnu: schismtracker: Remove custom bootstrap phase.

* gnu/packages/music.scm (schismtracker)[arguments]: Remove autoconf phase.
---
 gnu/packages/music.scm | 2 --
 1 file changed, 2 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 7474dac74b..b789d67f7f 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -2794,8 +2794,6 @@ for improved Amiga ProTracker 2/3 compatibility.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _ (invoke "autoreconf" "-vfi")))
          (add-before 'configure 'link-libm
            (lambda _ (setenv "LIBS" "-lm") #t)))))
     (native-inputs

From 2fef54fd64495148e0c546ef4ecaacf9503e62db Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:27:01 +0100
Subject: [PATCH 092/181] gnu: hpcguix-web: Do not re-bootstrap.

* gnu/packages/web.scm (hpcguix-web)[arguments]: Do not run autoreconf after
the bootstrap phase; remove "autoconf" phase to "set-variables"; end phase
with #T.
---
 gnu/packages/web.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index b0ab4add8d..03deab422d 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -6761,14 +6761,14 @@ compressed JSON header blocks.
                     (srfi srfi-26)
                     (ice-9 popen)
                     (ice-9 rdelim))
-
          #:phases
          (modify-phases %standard-phases
-           (add-before 'configure 'autoconf
+           (add-before 'configure 'set-variables
              (lambda _
+               ;; This prevents a few warnings
                (setenv "GUILE_AUTO_COMPILE" "0")
                (setenv "XDG_CACHE_HOME" (getcwd))
-               (invoke "autoreconf" "-vif")))
+               #t))
            (add-after 'install 'wrap-program
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((out      (assoc-ref outputs "out"))

From 5cdbdc2b138b0dd6237f9116af894b9d7dbf429b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:31:18 +0100
Subject: [PATCH 093/181] gnu: par2cmdline: Fetch sources from git.

* gnu/packages/backup.scm (par2cmdline)[source]: Fetch from git.
---
 gnu/packages/backup.scm | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 52afcbc676..b81d790642 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,6 +31,7 @@
 (define-module (gnu packages backup)
   #:use-module (guix packages)
   #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix git-download)
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
@@ -132,13 +134,14 @@ spying and/or modification by the server.")
     (name "par2cmdline")
     (version "0.8.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/Parchive/par2cmdline/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Parchive/par2cmdline.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1jpshmmcr81mxly0md2rr231qz9c8c680bbvcmhh100dg9i4a6s6"))))
+                "0f1jsd5sw2wynjzi7yjqjaf13yhyjfdid91p8yh0jn32y03kjyrz"))))
     (native-inputs
      `(("automake" ,automake)
        ("autoconf" ,autoconf)))

From 2286107f60e403c8d2f41cc4ba66ed89d14ab762 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:31:35 +0100
Subject: [PATCH 094/181] gnu: par2cmdline: Remove custom bootstrap phase.

* gnu/packages/backup.scm (par2cmdline)[arguments]: Remove.
---
 gnu/packages/backup.scm | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index b81d790642..ab95aea727 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -146,11 +146,6 @@ spying and/or modification by the server.")
      `(("automake" ,automake)
        ("autoconf" ,autoconf)))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _ (invoke "autoreconf" "-vfi"))))))
     (synopsis "File verification and repair tools")
     (description "Par2cmdline uses Reed-Solomon error-correcting codes to
 generate and verify PAR2 recovery files.  These files can be distributed

From 88f9fea72395ea7c00ce4070c1e55f6a82aa7357 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:36:15 +0100
Subject: [PATCH 095/181] gnu: inotify-tools: Fetch sources from git.

* gnu/packages/linux.scm (inotify-tools)[source]: Fetch from git.
---
 gnu/packages/linux.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b1dd5adc88..9833ff543d 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -1967,14 +1967,14 @@ for systems using the Linux kernel.  This includes commands such as
     (name "inotify-tools")
     (version "3.20.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/rvoicilas/inotify-tools/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rvoicilas/inotify-tools.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1b22c8x4pjnz3abx4dikpbj43zprjw79pdkd4xw111dsxlfwqcx4"))))
+                "14dci1i4mhsd5sa33k8h3ayphk19kizynh5ql9ryibdpmcanfiyq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases

From 4078beab938d5043098d42cd051a6db1e85c5d2b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:36:35 +0100
Subject: [PATCH 096/181] gnu: inotify-tools: Remove custom bootstrap phase.

* gnu/packages/linux.scm (inotify-tools)[arguments]: Remove.
---
 gnu/packages/linux.scm | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 9833ff543d..6b7aa89931 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -1976,11 +1976,6 @@ for systems using the Linux kernel.  This includes commands such as
                (base32
                 "14dci1i4mhsd5sa33k8h3ayphk19kizynh5ql9ryibdpmcanfiyq"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'bootstrap
-                    (lambda _
-                      (invoke "autoreconf" "-vif"))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)

From 34789459484993becfef3c4996b76709dcedb164 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:45:52 +0100
Subject: [PATCH 097/181] gnu: minizip: Remove custom bootstrap phase.

* gnu/packages/compression.scm (minizip)[arguments]: Remove autoreconf phase.
---
 gnu/packages/compression.scm | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 464402ec6c..2beda19a10 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -124,10 +124,7 @@ in compression.")
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-source
-           (lambda _ (chdir "contrib/minizip") #t))
-         (add-after 'enter-source 'autoreconf
-           (lambda _
-             (invoke "autoreconf" "-vif"))))))
+           (lambda _ (chdir "contrib/minizip") #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)

From 112fcafbae40cbae66b55eac02119799051fc354 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:47:51 +0100
Subject: [PATCH 098/181] gnu: libtar: Remove custom bootstrap phase.

* gnu/packages/compression.scm (libtar)[arguments]: Remove autoconf phase.
---
 gnu/packages/compression.scm | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 2beda19a10..f831535578 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -176,12 +176,7 @@ utility.  Instead of being written in Java, FastJar is written in C.")
               "02cihzl77ia0dcz7z2cga2412vyhhs5pa2355q4wpwbyga2lrwjh"))
             (patches (search-patches "libtar-CVE-2013-4420.patch"))))
    (build-system gnu-build-system)
-   (arguments
-    `(#:tests? #f ;no "check" target
-      #:phases
-      (modify-phases %standard-phases
-        (add-after 'unpack 'autoconf
-          (lambda _ (invoke "sh" "autoreconf" "-vfi"))))))
+   (arguments `(#:tests? #f)) ; no "check" target
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)

From 0633c77b1bea9ca671dc1e6495bd1835b99e18fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:52:30 +0100
Subject: [PATCH 099/181] gnu: xdelta: Fetch sources from git.

* gnu/packages/compression.scm (xdelta)[source]: Fetch from git.
---
 gnu/packages/compression.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index f831535578..3fd219e5f4 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1047,13 +1047,14 @@ smaller than those produced by @code{Xdelta}.")
     (version "3.1.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/jmacd/xdelta/archive/v"
-                           version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jmacd/xdelta.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "17g2pbbqy6h20qgdjq7ykib7kg5ajh8fwbsfgyjqg8pwg19wy5bm"))
-       (file-name (string-append name "-" version ".tar.gz"))
+         "09mmsalc7dwlvgrda56s2k927rpl3a5dzfa88aslkqcjnr790wjy"))
        (snippet
         ;; This file isn't freely distributable and has no effect on building.
         '(begin

From e5ff963a6d89e4c4902e1f5ffeef2319b05d5d57 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:52:46 +0100
Subject: [PATCH 100/181] gnu: xdelta: Remove custom bootstrap phase.

* gnu/packages/compression.scm (xdelta)[arguments]: Remove autoconf phase.
---
 gnu/packages/compression.scm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 3fd219e5f4..9c94ff09cd 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1068,9 +1068,7 @@ smaller than those produced by @code{Xdelta}.")
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-build-directory
-           (lambda _ (chdir "xdelta3") #t))
-         (add-after 'enter-build-directory 'autoconf
-           (lambda _ (invoke "autoreconf" "-vfi"))))))
+           (lambda _ (chdir "xdelta3") #t)))))
     (home-page "http://xdelta.org")
     (synopsis "Delta encoder for binary files")
     (description "xdelta encodes only the differences between two binary files

From bc74e9e4cd409ec31a227ad3c6ddd1c45a3e5d36 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 12:56:22 +0100
Subject: [PATCH 101/181] gnu: scsh: Remove custom bootstrap phase.

* gnu/packages/shells.scm (scsh)[arguments]: Remove autoreconf phase.
---
 gnu/packages/shells.scm | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index 3e9d797e2c..38eeaa7831 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 Stefan Reichör <stefan@xsteve.at>
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2018 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
@@ -414,10 +414,7 @@ use of experts and novices alike.")
                                              "/rx")))
                  (delete-file-recursively "rx")
                  (symlink rxpath "rx"))
-               #t))
-           (add-after 'unpack 'autoreconf
-             (lambda _
-               (invoke "autoreconf"))))))
+               #t)))))
       (inputs
        `(("scheme48" ,scheme48)
          ("scheme48-rx" ,scheme48-rx)))

From 2b2ab39cfc694e3c0cb37c0136bb606b20d41661 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 13:00:35 +0100
Subject: [PATCH 102/181] gnu: libharu: Fetch sources from git.

* gnu/packages/pdf.scm (libharu)[source]: Fetch from git.
---
 gnu/packages/pdf.scm | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 1d37de70d7..1ecd49215b 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -223,15 +223,16 @@ Poppler PDF rendering library.")
    (name "libharu")
    (version "2.3.0")
    (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/libharu/libharu/archive/"
-                                 "RELEASE_"
-                                 (string-join (string-split version #\.) "_")
-                                 ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/libharu/libharu.git")
+                   (commit (string-append
+                            "RELEASE_"
+                            (string-join (string-split version #\.) "_")))))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "1lm4v539y9cb1lvbq387j57sy7yxda3yv8b1pk8m6zazbp66i7lg"))))
+               "15s9hswnl3qqi7yh29jyrg0hma2n99haxznvcywmsp8kjqlyg75q"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags

From 6f3dd09f8d5e2bd16bd26891d71829f4dd19f772 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 13:00:53 +0100
Subject: [PATCH 103/181] gnu: libharu: Remove custom bootstrap phase.

* gnu/packages/pdf.scm (libharu)[arguments]: Remove autogen phase.
---
 gnu/packages/pdf.scm | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 1ecd49215b..dc966b64d8 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -239,11 +239,7 @@ Poppler PDF rendering library.")
       (list (string-append "--with-zlib="
                            (assoc-ref %build-inputs "zlib"))
             (string-append "--with-png="
-                           (assoc-ref %build-inputs "libpng")))
-      #:phases
-      (modify-phases %standard-phases
-        (add-after 'unpack 'autogen
-          (lambda _ (invoke "autoreconf" "-vif"))))))
+                           (assoc-ref %build-inputs "libpng")))))
    (inputs
     `(("zlib" ,zlib)
       ("libpng" ,libpng)))

From 5a103bb84ecc1ddc221bdcdba4f3cdf79117a2f0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 13:04:08 +0100
Subject: [PATCH 104/181] gnu: libiax2: Remove custom bootstrap phase.

* gnu/packages/telephony.scm (libiax2)[arguments]: Remove.
---
 gnu/packages/telephony.scm | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm
index 05916cde5c..15c07beed9 100644
--- a/gnu/packages/telephony.scm
+++ b/gnu/packages/telephony.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
 ;;; Copyright © 2016 Francesco Frassinelli <fraph24@gmail.com>
 ;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is>
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Jovany Leandro G.C <bit4bit@riseup.net>
 ;;;
@@ -310,11 +310,6 @@ protocol (RFC 3550).")
        `(("autoconf" ,autoconf)
          ("automake" ,automake)
          ("libtool" ,libtool)))
-      (arguments
-       `(#:phases (modify-phases %standard-phases
-                    (add-after 'unpack 'autoconf
-                      (lambda _
-                        (invoke "autoreconf" "-vfi"))))))
       (home-page "https://gitlab.savoirfairelinux.com/sflphone/libiax2")
       (synopsis "Inter-Asterisk-Protocol library")
       (description "LibIAX2 implements the Inter-Asterisk-Protocol for relaying

From cd1f661e827dd6fd5b05f8219a61aa466069a5a5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 13:06:31 +0100
Subject: [PATCH 105/181] gnu: libiax2: Fetch sources from git.

* gnu/packages/telephony.scm (libiax2)[source]: Fetch from git.
---
 gnu/packages/telephony.scm | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm
index 15c07beed9..63709935c3 100644
--- a/gnu/packages/telephony.scm
+++ b/gnu/packages/telephony.scm
@@ -295,16 +295,14 @@ protocol (RFC 3550).")
       (version (string-append "0.0.0-1." (string-take commit 7)))
       (source
        (origin
-         (method url-fetch)
-         (uri
-          (string-append
-           "https://gitlab.savoirfairelinux.com/sflphone/libiax2/"
-           "repository/archive.tar.gz?ref="
-           commit))
-         (file-name (string-append name "-" version ".tar.gz"))
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.savoirfairelinux.com/sflphone/libiax2.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
-           "0cj5293bixp3k5x3hjwyd0iq7z8w5p7yavxvvkqk5817hjq386y2"))))
+           "0d269474kk1933c55hx4azw3sak5ycfrxkw6ida0sb2cm00kfich"))))
       (build-system gnu-build-system)
       (native-inputs
        `(("autoconf" ,autoconf)

From 2b61cd37b44400c881ec2dc20202f3505ef1d25b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 13:08:56 +0100
Subject: [PATCH 106/181] gnu: cifs-utils: Remove autoreconf phase.

* gnu/packages/samba.scm (cifs-utils)[arguments]: Remove autoreconf phase.
---
 gnu/packages/samba.scm | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm
index 458ff50ae8..ff237c96ce 100644
--- a/gnu/packages/samba.scm
+++ b/gnu/packages/samba.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -73,10 +74,6 @@
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         ;; The 6.7 tarball is missing ‘install.sh’. Create it.
-         (add-after 'unpack 'autoreconf
-           (lambda _
-             (invoke "autoreconf" "-i")))
          (add-before 'configure 'set-root-sbin
            (lambda _ ; Don't try to install in "/sbin".
              (setenv "ROOTSBINDIR"

From 9066424778d2b7b7b73968a91e64ce2b53a163fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 13:10:56 +0100
Subject: [PATCH 107/181] gnu: privoxy: Remove custom bootstrap phase.

* gnu/packages/tor.scm (privoxy)[arguments]: Remove autoconf phase.
---
 gnu/packages/tor.scm | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index 61b0c82e30..e28a6d4f48 100644
--- a/gnu/packages/tor.scm
+++ b/gnu/packages/tor.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -140,14 +141,6 @@ rejects UDP traffic from the application you're using.")
        #:configure-flags (list (string-append "--sysconfdir="
                                               (assoc-ref %outputs "out")
                                               "/etc/privoxy"))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _
-             ;; Unfortunately, this is not a tarball produced by
-             ;; "make dist".
-             (invoke "autoreconf" "-vfi")
-             #t)))
        #:tests? #f))
     (inputs
      `(("w3m" ,w3m)

From 902068b43664b862dfcbb9172f41778d576e3ae0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 13:18:27 +0100
Subject: [PATCH 108/181] gnu: tiled: Fetch sources from git.

* gnu/packages/game-development.scm (tiled)[source]: Fetch from git.
---
 gnu/packages/game-development.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index da1675820b..1f73025db7 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -399,13 +399,14 @@ support.")
     (name "tiled")
     (version "1.2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/bjorn/tiled/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/bjorn/tiled.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "13dlf5kzvhhjkhy19118x3diakmraz4m9kxrsdam8dms6xivb6lp"))))
+                "1rra48hlkcgqxwxi802fb182p1q0723c9hhfvkd5inz9467idd4c"))))
     (build-system gnu-build-system)
     (inputs
      `(("qtbase" ,qtbase)

From 4ad3786b7b61073005f024f33465e6b7a4a952ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Sun, 11 Nov 2018 12:26:44 +0100
Subject: [PATCH 109/181] gnu: Add python-precis-i18n.

* gnu/packages/messaging.scm (python-precis-i18n): New variable.
---
 gnu/packages/python.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5f81c428ff..b6b0ad75a4 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14611,3 +14611,22 @@ on regular expressions.")
              (propagated-inputs
               `(("python2-enum34" ,python2-enum34)
                 ,@(package-propagated-inputs reparser))))))
+
+(define-public python-precis-i18n
+  (package
+    (name "python-precis-i18n")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "precis_i18n" version))
+       (sha256
+        (base32
+         "0gjhvwd8aifx94rl1ag08vlmndyx2q3fkyqb0c4i46x3p2bc2yi2"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/byllyfish/precis_i18n")
+    (synopsis "Implementation of the PRECIS framework")
+    (description
+     "This module implements the PRECIS Framework as described in RFC 8264,
+RFC 8265 and RFC 8266.")
+    (license license:expat)))

From a311f42e1bcb71b59e3ce51ee3c8f6148d939168 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Sun, 11 Nov 2018 12:26:03 +0100
Subject: [PATCH 110/181] gnu: python-nbxmpp: Update to 0.6.8.

* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.8.
---
 gnu/packages/messaging.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 1a7560bd72..987426794b 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -549,14 +549,14 @@ simultaneously and therefore appear under the same nickname on IRC.")
 (define-public python-nbxmpp
   (package
     (name "python-nbxmpp")
-    (version "0.6.7")
+    (version "0.6.8")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "nbxmpp" version))
        (sha256
         (base32
-         "0fas4iawjfdmkz8vr042wpq6b2qispi6fy35g4a62jw50jb1saav"))))
+         "1iip8ijxp86fx4bl1h67p2lp02p2zm1ga2p3q43nv30smj54nawc"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f))                    ; no tests

From 992a496503a49ef7977f097a1390f8536b06dee4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Thu, 8 Nov 2018 10:13:44 +0100
Subject: [PATCH 111/181] gnu: gajim: Update to 1.1.0.

* gnu/packages/messaging.scm (gajim): Update to 1.1.0.
[arguments]: Set #:test-target to "test_nogui".  Remove the
'remove-test-resolver' and 'start-xserver' phases.
[inputs]: Remove python-pyasn1.  Add python-cssutils, python-keyring and
python-precis-i18n.
---
 gnu/packages/messaging.scm | 25 +++++++------------------
 1 file changed, 7 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 987426794b..5f1aa7ce58 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -574,7 +574,7 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
 (define-public gajim
   (package
     (name "gajim")
-    (version "1.0.3")
+    (version "1.1.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gajim.org/downloads/"
@@ -582,10 +582,11 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
                                   "/gajim-" version ".tar.bz2"))
               (sha256
                (base32
-                "0ds4rqwfrpj89a489w6yih8gx5zi7qa4ffgld950fk7s0qxvcfnb"))))
+                "1qis8vs7y7g1zn5i5dshwrszidc22qpflycwb4nixvp9lbmkq0va"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     `(#:test-target "test_nogui"
+       #:phases
        (modify-phases %standard-phases
          (add-after 'install 'wrap-program
            (lambda* (#:key outputs #:allow-other-keys)
@@ -598,20 +599,6 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
                       `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))))
                 '("gajim" "gajim-remote" "gajim-history-manager")))
              #t))
-         (add-before 'check 'remove-test-resolver
-           ;; This test requires network access.
-           (lambda _
-             (substitute* "test/runtests.py"
-               (("'integration.test_resolver',") ""))
-             #t))
-         (add-before 'check 'start-xserver
-           ;; Tests require a running X server.
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((xorg-server (assoc-ref inputs "xorg-server"))
-                   (display ":1"))
-               (setenv "DISPLAY" display)
-               (zero? (system (string-append xorg-server "/bin/Xvfb "
-                                             display " &"))))))
          (add-after 'install 'install-icons
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -648,12 +635,14 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
        ("hicolor-icon-theme" ,hicolor-icon-theme)
        ("libsecret" ,libsecret)
        ("python-axolotl" ,python-axolotl)
+       ("python-cssutils" ,python-cssutils)
        ("python-dbus" ,python-dbus)
        ("python-docutils" ,python-docutils)
        ("python-gnupg" ,python-gnupg)
+       ("python-keyring" ,python-keyring)
        ("python-nbxmpp" ,python-nbxmpp)
        ("python-pillow" ,python-pillow)
-       ("python-pyasn1" ,python-pyasn1)
+       ("python-precis-i18n" ,python-precis-i18n)
        ("python-pycairo" ,python-pycairo)
        ("python-pygobject" ,python-pygobject)
        ("python-pyopenssl" ,python-pyopenssl)

From 60c5b4448961ce1745b7f0bfada1e7620f238ea0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Sun, 11 Nov 2018 15:34:06 +0100
Subject: [PATCH 112/181] gnu: gajim: Get the second 'wrap-program' phase to
 return #t.

* gnu/packages/messaging.scm (gajim)[arguments]: Get the second 'wrap-program'
phase to return #t.
---
 gnu/packages/messaging.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 5f1aa7ce58..c276bc03ea 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -623,7 +623,8 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
                ;; For GtkFileChooserDialog.
                `("GSETTINGS_SCHEMA_DIR" =
                  (,(string-append (assoc-ref inputs "gtk+")
-                                  "/share/glib-2.0/schemas")))))))))
+                                  "/share/glib-2.0/schemas"))))
+             #t)))))
     (native-inputs
      `(("intltool" ,intltool)
        ("xorg-server" ,xorg-server)))

From 37a350eccee7b36cba779c6a6841448b8deaed72 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Sun, 11 Nov 2018 15:24:00 +0100
Subject: [PATCH 113/181] gnu: gajim: Move python-docutils from inputs to
 native-inputs.

* gnu/packages/messaging.scm (gajim): Move python-docutils from inputs to
native-inputs.
---
 gnu/packages/messaging.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index c276bc03ea..9d652486f2 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -627,6 +627,7 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
              #t)))))
     (native-inputs
      `(("intltool" ,intltool)
+       ("python-docutils" ,python-docutils)
        ("xorg-server" ,xorg-server)))
     (inputs
      `(("adwaita-icon-theme" ,adwaita-icon-theme)
@@ -638,7 +639,6 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
        ("python-axolotl" ,python-axolotl)
        ("python-cssutils" ,python-cssutils)
        ("python-dbus" ,python-dbus)
-       ("python-docutils" ,python-docutils)
        ("python-gnupg" ,python-gnupg)
        ("python-keyring" ,python-keyring)
        ("python-nbxmpp" ,python-nbxmpp)

From 89c7894805329023754512c9b30e67ceb1753cb0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 16:18:24 +0100
Subject: [PATCH 114/181] gnu: faust-2: Update to 2.5.23.

* gnu/packages/audio.scm (faust-2): Update to 2.5.23.
[native-inputs]: Replace llvm-with-rtti with llvm-3.8-with-rtti.
* gnu/packages/llvm.scm (llvm-with-rtti): Rename this variable...
(llvm-3.8-with-rtti): ...to this variable; inherit from llvm-3.8.
---
 gnu/packages/audio.scm | 18 +++++++-----------
 gnu/packages/llvm.scm  | 23 ++++++++++++-----------
 2 files changed, 19 insertions(+), 22 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index e5b8f9ed79..91f55a3544 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1176,19 +1176,15 @@ PS, and DAB+.")
 (define-public faust-2
   (package
     (inherit faust)
-    (version "2.1.0")
+    (version "2.5.23")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/grame-cncm/faust.git")
-                    (commit (string-append "v"
-                                           (string-map (lambda (c)
-                                                         (if (char=? c #\.) #\- c))
-                                                       version)))))
-              (file-name (string-append "faust-" version "-checkout"))
+              (method url-fetch)
+              (uri (string-append "https://github.com/grame-cncm/faust/"
+                                  "releases/download/" version
+                                  "/faust-" version ".tar.gz"))
               (sha256
                (base32
-                "06km0ygwxxwgw1lqldccqidxhmjfz8ck0wnbd95qk5sg8sbpc068"))))
+                "1yz5jnr76hh7rmxkpdi7gyrw1wp4gyqfpq8zyl97qdi5ga5gjznq"))))
     (build-system gnu-build-system)
     (arguments
      (substitute-keyword-arguments (package-arguments faust)
@@ -1196,7 +1192,7 @@ PS, and DAB+.")
         `(list (string-append "prefix=" (assoc-ref %outputs "out"))
                "world"))))
     (native-inputs
-     `(("llvm" ,llvm-with-rtti)
+     `(("llvm" ,llvm-3.8-with-rtti)
        ("which" ,which)
        ("xxd" ,xxd)
        ("ctags" ,emacs-minimal)  ; for ctags
diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm
index d0791d00cc..a809180e29 100644
--- a/gnu/packages/llvm.scm
+++ b/gnu/packages/llvm.scm
@@ -90,17 +90,6 @@ languages is in development.  The compiler infrastructure includes mirror sets
 of programming tools as well as libraries with equivalent functionality.")
     (license license:ncsa)))
 
-(define-public llvm-with-rtti
-  (package (inherit llvm)
-    (name "llvm-with-rtti")
-    (arguments
-     (substitute-keyword-arguments (package-arguments llvm)
-       ((#:configure-flags flags)
-        `(append '("-DCMAKE_SKIP_BUILD_RPATH=FALSE"
-                   "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE"
-                   "-DLLVM_REQUIRES_RTTI=1")
-                 ,flags))))))
-
 (define* (clang-runtime-from-llvm llvm hash
                                   #:optional (patches '()))
   (package
@@ -290,6 +279,18 @@ code analysis tools.")
        (base32
         "1ybmnid4pw2hxn12ax5qa5kl1ldfns0njg8533y3mzslvd5cx0kf"))))))
 
+;; This is for Faust 2
+(define-public llvm-3.8-with-rtti
+  (package (inherit llvm-3.8)
+    (name "llvm-with-rtti")
+    (arguments
+     (substitute-keyword-arguments (package-arguments llvm)
+       ((#:configure-flags flags)
+        `(append '("-DCMAKE_SKIP_BUILD_RPATH=FALSE"
+                   "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE"
+                   "-DLLVM_REQUIRES_RTTI=1")
+                 ,flags))))))
+
 (define-public clang-runtime-3.8
   (clang-runtime-from-llvm
    llvm-3.8

From 50ee7e93fcd881d3bf996954bcd5176aa7c54d21 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 9 Nov 2018 19:17:05 +0100
Subject: [PATCH 115/181] gnu: gtk-doc: Use local docbook-xsl.

* gnu/packages/gtk.scm (gtk-doc): Use local docbook-xsl.
---
 gnu/packages/gtk.scm | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 640bd75da4..0d62b80833 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -19,6 +19,7 @@
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1411,7 +1412,12 @@ information.")
                (string-append (assoc-ref inputs "docbook-xsl")
                               "/xml/xsl/docbook-xsl-"
                               ,(package-version docbook-xsl)
-                              "/html/chunk.xsl")))
+                              "/html/chunk.xsl"))
+              (("http://docbook.sourceforge.net/release/xsl/current/common/en.xml")
+               (string-append (assoc-ref inputs "docbook-xsl")
+                              "/xml/xsl/docbook-xsl-"
+                              ,(package-version docbook-xsl)
+                              "/common/en.xml")))
              #t))
          (add-after 'patch-gtk-doc-scan 'patch-test-out
            (lambda _

From 0ead0b4d2c025ad1b4a293fb6cbb8a578b7dd87d Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 9 Nov 2018 19:18:55 +0100
Subject: [PATCH 116/181] gnu: webkitgtk: Include documentation.

* gnu/packages/webkit.scm (webkitgtk): Include documentation.
---
 gnu/packages/webkit.scm | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm
index d1890c8b32..dfff53c627 100644
--- a/gnu/packages/webkit.scm
+++ b/gnu/packages/webkit.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,6 +32,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages docbook)
   #:use-module (gnu packages enchant)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gcc)
@@ -66,11 +68,13 @@
                (base32
                 "147r7an41920zl4x9srdva7fxvw2znjin5ldjkhay1cndv9gih0m"))))
     (build-system cmake-build-system)
+    (outputs '("out" "doc"))
     (arguments
      '(#:tests? #f ; no tests
        #:build-type "Release" ; turn off debugging symbols to save space
        #:configure-flags (list
                           "-DPORT=GTK"
+                          "-DENABLE_GTKDOC=ON" ; No doc by default
                           (string-append ; uses lib64 by default
                            "-DLIB_INSTALL_DIR="
                            (assoc-ref %outputs "out") "/lib")
@@ -87,7 +91,28 @@
                           ;; XXX Disable WOFF2 ‘web fonts’.  These were never
                           ;; supported in our previous builds.  Enabling them
                           ;; requires building libwoff2 and possibly woff2dec.
-                          "-DUSE_WOFF2=OFF")))
+                          "-DUSE_WOFF2=OFF")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-gtk-doc-scan
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "Source/WebKit/WebProcess/InjectedBundle/API/gtk/DOM/docs/webkitdomgtk-docs.sgml"
+               (("http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd")
+                (string-append (assoc-ref inputs "docbook-xml")
+                               "/xml/dtd/docbook/docbookx.dtd")))
+             (substitute* "Source/WebKit/UIProcess/API/gtk/docs/webkit2gtk-docs.sgml"
+               (("http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd")
+                (string-append (assoc-ref inputs "docbook-xml")
+                               "/xml/dtd/docbook/docbookx.dtd")))
+             #t))
+         (add-after 'install 'move-doc-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (doc (assoc-ref outputs "doc")))
+               (mkdir-p (string-append doc "/share"))
+               (rename-file (string-append out "/share/gtk-doc")
+                            (string-append doc "/share/gtk-doc"))
+               #t))))))
     (native-inputs
      `(("bison" ,bison)
        ("gettext" ,gettext-minimal)
@@ -97,6 +122,8 @@
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("python" ,python-2) ; incompatible with Python 3 (print syntax)
+       ("gtk-doc" ,gtk-doc) ; For documentation generation
+       ("docbook-xml" ,docbook-xml) ; For documentation generation
        ("ruby" ,ruby)))
     (propagated-inputs
      `(("gtk+" ,gtk+)

From ec350676315e3ec5fb4b5a9865b8cc3aa76d2681 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 8 Nov 2018 13:22:52 -0500
Subject: [PATCH 117/181] gnu: PostgreSQL: Update to 10.6 [fixes
 CVE-2018-16850].

* gnu/packages/databases.scm (postgresql): Update to 10.6.
---
 gnu/packages/databases.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 46bd728b1b..7258622f42 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -804,14 +804,14 @@ as a drop-in replacement of MySQL.")
 (define-public postgresql
   (package
     (name "postgresql")
-    (version "10.5")
+    (version "10.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "04a07jkvc5s6zgh6jr78149kcjmsxclizsqabjw44ld4j5n633kc"))))
+                "0jv26y3f10svrjxzsgqxg956c86b664azyk2wppzpa5x11pjga38"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-uuid=e2fs")

From e874f34d3f65ced7bee226b07210cdfc81dece30 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 20:48:34 +0100
Subject: [PATCH 118/181] gnu: mumi: Update to 0.0.0-2.bfd96ce7.

* gnu/packages/mail.scm (mumi): Update to 0.0.0-2.bfd96ce7.
---
 gnu/packages/mail.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 978b22333e..fa545da3b2 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -2645,8 +2645,8 @@ replacement for the @code{urlview} program.")
     (license gpl2+)))
 
 (define-public mumi
-  (let ((commit "648311b9b9d9d974fb2d76dacfe956fc7b842401")
-        (revision "1"))
+  (let ((commit "bfd96ce76b4600ae232e6548b26c9365095fd174")
+        (revision "2"))
     (package
       (name "mumi")
       (version (git-version "0.0.0" revision commit))
@@ -2658,7 +2658,7 @@ replacement for the @code{urlview} program.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "081yvjhy8ig3xyixkdklrzf3bf2bczn92g5hpxmsl8m9cpcj77vv"))))
+                  "05miwfi1bh0v9x2gvn15bwkb3gn4xy53z506ysjzns2y497zkc5h"))))
       (build-system gnu-build-system)
       (arguments
        `(#:phases

From aaf0e47f6dbe4245ef5d38f69e0e4eb2855de15b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 20:50:30 +0100
Subject: [PATCH 119/181] gnu: libtoxcore: Update to 0.0.0-2.bf69b54.

* gnu/packages/messaging.scm (libtoxcore): Update to 0.0.0-2.bf69b54.
[native-inputs]: Add check.
---
 gnu/packages/messaging.scm | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 9d652486f2..a7b868ccc0 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -818,8 +818,8 @@ protocols.")
     (license license:x11)))
 
 (define-public libtoxcore
-  (let ((revision "1")
-        (commit "755f084e8720b349026c85afbad58954cb7ff1d4"))
+  (let ((revision "2")
+        (commit "bf69b54f64003d160d759068f4816b2d9b2e1e21"))
     (package
       (name "libtoxcore")
       (version (string-append "0.0.0" "-"
@@ -832,20 +832,19 @@ protocols.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "0ap1gvlyihnfivv235dbrgsxsiiz70bhlmlr5gn1027w3h5kqz8w"))))
+                  "11lqra4yd7v293cp286ynff5lqz1pprzg8vn3wq6vryj08g88zqb"))))
       (build-system gnu-build-system)
+      (arguments `(#:tests? #f)) ; FIXME: tests hang, some fail.
       (native-inputs
        `(("autoconf" ,autoconf)
          ("automake" ,automake)
          ("libtool" ,libtool)
-         ;; TODO: Add when test suite is capable of passing.
-         ;; ("check" ,check)
+         ("check" ,check)
          ("pkg-config" ,pkg-config)))
       (inputs
        `(("libsodium" ,libsodium)
          ("opus" ,opus)
          ("libvpx" ,libvpx)))
-      (arguments `(#:tests? #f)) ; FIXME: Testsuite fails, reasons unspecific.
       (synopsis "Library for the Tox encrypted messenger protocol")
       (description
        "C library implementation of the Tox encrypted messenger protocol.")

From a509b180870cf7bffe65a1cd6099487469fae39f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 11 Nov 2018 18:09:55 +0100
Subject: [PATCH 120/181] gnu: webkitgtk@2.22: Adjust to documentation output.

This is a follow-up to commit 0ead0b4d2c025ad1b4a293fb6cbb8a578b7dd87d.

* gnu/packages/webkit.scm (webkitgtk)[arguments]: Remove hard coded file list.
(webkitgtk-2.22)[arguments]: Inherit phases using SUBSTITUTE-KEYWORD-ARGUMENTS.
---
 gnu/packages/webkit.scm | 33 ++++++++++++++++-----------------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm
index dfff53c627..82f03c7f94 100644
--- a/gnu/packages/webkit.scm
+++ b/gnu/packages/webkit.scm
@@ -96,14 +96,12 @@
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-gtk-doc-scan
            (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* "Source/WebKit/WebProcess/InjectedBundle/API/gtk/DOM/docs/webkitdomgtk-docs.sgml"
-               (("http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd")
-                (string-append (assoc-ref inputs "docbook-xml")
-                               "/xml/dtd/docbook/docbookx.dtd")))
-             (substitute* "Source/WebKit/UIProcess/API/gtk/docs/webkit2gtk-docs.sgml"
-               (("http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd")
-                (string-append (assoc-ref inputs "docbook-xml")
-                               "/xml/dtd/docbook/docbookx.dtd")))
+             (for-each (lambda (file)
+                         (substitute* file
+                           (("http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd")
+                            (string-append (assoc-ref inputs "docbook-xml")
+                                           "/xml/dtd/docbook/docbookx.dtd"))))
+                       (find-files "Source" "\\.sgml$"))
              #t))
          (add-after 'install 'move-doc-files
            (lambda* (#:key outputs #:allow-other-keys)
@@ -182,12 +180,13 @@ HTML/CSS applications to full-fledged web browsers.")
      `(("gcc" ,gcc-7)  ; webkitgtk-2.22 requires gcc-6 or newer
        ,@(package-native-inputs webkitgtk)))
     (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-before 'configure 'work-around-gcc-7-include-path-issue
-                    ;; FIXME: Work around a problem with gcc-7 includes (see
-                    ;; <https://bugs.gnu.org/30756>).
-                    (lambda _
-                      (unsetenv "C_INCLUDE_PATH")
-                      (unsetenv "CPLUS_INCLUDE_PATH")
-                      #t)))
-       ,@(package-arguments webkitgtk)))))
+     (substitute-keyword-arguments (package-arguments webkitgtk)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-before 'configure 'work-around-gcc-7-include-path-issue
+             ;; FIXME: Work around a problem with gcc-7 includes (see
+             ;; <https://bugs.gnu.org/30756>).
+             (lambda _
+               (unsetenv "C_INCLUDE_PATH")
+               (unsetenv "CPLUS_INCLUDE_PATH")
+               #t))))))))

From 7865c8c460272b1375b8dc544459d8c282ef3984 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 23:11:19 +0100
Subject: [PATCH 121/181] gnu: r-lme4: Update to 1.1-19.

* gnu/packages/statistics.scm (r-lme4): Update to 1.1-19.
---
 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 f363d9a473..b5d230d02a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5123,14 +5123,14 @@ algorithms.")
 (define-public r-lme4
   (package
     (name "r-lme4")
-    (version "1.1-18-1")
+    (version "1.1-19")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lme4" version))
        (sha256
         (base32
-         "01ar4fak8zj7c1vmh9m576wchxj5qzpfqn637s7fh3fl6cpz0alq"))))
+         "0j8xhkkcdv45ilab960s9jrcjk6jbzvd7w7myswv5fmalrpq52pf"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-rcpp" ,r-rcpp)

From 23dd886a95379a8aaed5d58025e603e7f9ea659e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 23:11:33 +0100
Subject: [PATCH 122/181] gnu: r-rtsne: Update to 0.15.

* gnu/packages/statistics.scm (r-rtsne): Update to 0.15.
---
 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 b5d230d02a..71472cb974 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3268,14 +3268,14 @@ the way current RNG settings can be changed.")
 (define-public r-rtsne
   (package
     (name "r-rtsne")
-    (version "0.13")
+    (version "0.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rtsne" version))
        (sha256
         (base32
-         "17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw"))))
+         "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
     (properties `((upstream-name . "Rtsne")))
     (build-system r-build-system)
     (propagated-inputs

From 41d2c26e675cad3240fe7a5ddd5a286ceb9bc710 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 23:11:43 +0100
Subject: [PATCH 123/181] gnu: r-rcpparmadillo: Update to 0.9.200.4.0.

* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.4.0.
---
 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 71472cb974..024e90f3e5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2528,13 +2528,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.100.5.0")
+    (version "0.9.200.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1iyjqhfjip1nxrkllzh7r1m01jjnx7cahqkf3s557w34p987f2l1"))))
+                "1ayvpyi4hgaqrhx1kqi640iillc2byj4kam7vydlgqmdrzpgrfvz"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (native-inputs

From 441cf11de1ddbe7b9d4b5b70d9b67456ac6bfa63 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 23:11:57 +0100
Subject: [PATCH 124/181] gnu: r-dplyr: Update to 0.7.8.

* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.8.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 024e90f3e5..bd581c154b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1620,13 +1620,13 @@ and printing capabilities than traditional data frames.")
 (define-public r-dplyr
   (package
     (name "r-dplyr")
-    (version "0.7.7")
+    (version "0.7.8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "dplyr" version))
               (sha256
                (base32
-                "196lwck3i3m25jnn1f1nrda9svnjqqi89s0is79gbrphamddnlq5"))))
+                "06p59nhli8c1sarghzxq0y4pk6lyyz3xwkarp55b252dfg2rly9p"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)

From 2a4c5877a996007f2c6e058fb973fa7d5dcfdbff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 23:12:10 +0100
Subject: [PATCH 125/181] gnu: r-ggpubr: Update to 0.1.9.

* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.9.
---
 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 45526c7072..2c1151bf6e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4450,14 +4450,14 @@ and adds the annotation to the plot.")
 (define-public r-ggpubr
   (package
     (name "r-ggpubr")
-    (version "0.1.8")
+    (version "0.1.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggpubr" version))
        (sha256
         (base32
-         "0psl2zndm4wk6nnj1nv305islpxfvfgd87gjh2ph8yqn4mxpnfi1"))))
+         "0rvfgii2gxarra7d33n6c63ky0mivxxyx35acsrn94xkbd8mbcsj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cowplot" ,r-cowplot)

From 06910a86896aba25adad104c96303624e7479938 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 23:12:22 +0100
Subject: [PATCH 126/181] gnu: r-rcmdcheck: Update to 1.3.2.

* gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.2.
---
 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 2c1151bf6e..a74ffa773f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6943,14 +6943,14 @@ directories or URLs with their associated programs.")
 (define-public r-rcmdcheck
   (package
     (name "r-rcmdcheck")
-    (version "1.3.1")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rcmdcheck" version))
        (sha256
         (base32
-         "1ga19jqix0zs7xyz2j155zyagwbv22r6dgv55g6wdjigc67qfsix"))))
+         "0ys1nd7690mhwzslyzg8fq1wxr28nz8g6av5iykkrshb8lkxg7ly"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)

From 5f9b38ba3438c7bba9203757391c256507573b7b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Nov 2018 23:12:32 +0100
Subject: [PATCH 127/181] gnu: r-s4vectors: Update to 0.20.1.

* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
---
 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 55631530ca..bf49f4e1dc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7268,13 +7268,13 @@ abnormal copy number.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.20.0")
+    (version "0.20.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0qgiykjhnsvvpcp3zwmrnpx3bv3msvj0szchyvb1yb0fxw716xc5"))))
+                "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)

From 9c001c07d4c483a4a6b7c7ff50b1119d3fd4b90f Mon Sep 17 00:00:00 2001
From: Laura Lazzati <laura.lazzati.15@gmail.com>
Date: Sun, 11 Nov 2018 18:12:34 -0300
Subject: [PATCH 128/181] doc: Fix typo.

* doc/guix.texi (Porting to a New Platform): Fix typo.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 doc/guix.texi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index c74351dd87..4b082c5f87 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -24216,7 +24216,7 @@ to be updated to refer to these binaries on the target platform.  That
 is, the hashes and URLs of the bootstrap tarballs for the new platform
 must be added alongside those of the currently supported platforms.  The
 bootstrap Guile tarball is treated specially: it is expected to be
-available locally, and @file{gnu/local.mk} has rules do download it for
+available locally, and @file{gnu/local.mk} has rules to download it for
 the supported architectures; a rule for the new platform must be added
 as well.
 

From 652163154c06b47936a453f44ea35938789718de Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 11 Nov 2018 17:13:20 +0100
Subject: [PATCH 129/181] guix package: '--show' errors when asked for a
 non-existent package.

Fixes <https://bugs.gnu.org/33323>.
Reported by swedebugia <swedebugia@riseup.net>.

* guix/scripts/package.scm (process-query): Call 'leave' when
'find-packages-by-name' returns the empty list.
* tests/guix-package.sh: Test it.
---
 guix/scripts/package.scm | 10 +++++++---
 tests/guix-package.sh    |  4 ++++
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm
index 500fc9ac90..5743816324 100644
--- a/guix/scripts/package.scm
+++ b/guix/scripts/package.scm
@@ -771,9 +771,13 @@ processed, #f otherwise."
       (('show requested-name)
        (let-values (((name version)
                      (package-name->name+version requested-name)))
-         (leave-on-EPIPE
-          (for-each (cute package->recutils <> (current-output-port))
-                    (find-packages-by-name name version)))
+         (match (find-packages-by-name name version)
+           (()
+            (leave (G_ "~a~@[@~a~]: package not found~%") name version))
+           (packages
+            (leave-on-EPIPE
+             (for-each (cute package->recutils <> (current-output-port))
+                       packages))))
          #t))
 
       (('search-paths kind)
diff --git a/tests/guix-package.sh b/tests/guix-package.sh
index f7dfbfad00..7eeb4304d1 100644
--- a/tests/guix-package.sh
+++ b/tests/guix-package.sh
@@ -106,6 +106,10 @@ guix package --show=guile | grep "^name: guile"
 # Ensure `--show' doesn't fail for packages with non-package inputs.
 guix package --show=texlive
 
+# Fail for non-existent packages or package/version pairs.
+if guix package --show=does-not-exist; then false; else true; fi
+if guix package --show=emacs@42; then false; else true; fi
+
 # Search.
 LC_MESSAGES=C
 export LC_MESSAGES

From 6c843907e90c9f6a1af389f9624cac8b6b01ecbb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 11 Nov 2018 23:48:53 +0100
Subject: [PATCH 130/181] guix system: Invoking 'guix system init' twice keeps
 timestamps zeroed.

Fixes a bug whereby running 'guix system init config.scm /mnt' twice
would, on the second run, change timestamps in /mnt/gnu/store from the
Epoch to now.  This is because the 'register-path' call would bypass the
'reset-timestamps' phase altogether in that case, as a consequence of
commit bb3b6ccb05550fbfbeb459c68819a752327d6e1e.

Reported by Christopher Baines.

* guix/scripts/system.scm (install): When TARGET/var/guix exists, delete
it.  As a side-effect, this ensures that later on, the 'register-path'
call invokes 'reset-timestamps' on all the copied store items.
---
 guix/scripts/system.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm
index d2be0cf8fb..9ba9428a08 100644
--- a/guix/scripts/system.scm
+++ b/guix/scripts/system.scm
@@ -235,6 +235,13 @@ When INSTALL-BOOTLOADER? is true, install bootloader using BOOTCFG."
 the ownership of '~a' may be incorrect!~%")
                target))
 
+  ;; If a previous installation was attempted, make sure we start anew; in
+  ;; particular, we don't want to keep a store database that might not
+  ;; correspond to what we're actually putting in the store.
+  (let ((state (string-append target "/var/guix")))
+    (when (file-exists? state)
+      (delete-file-recursively state)))
+
   (chmod target #o755)
   (let ((os-dir   (derivation->output-path os-drv))
         (format   (lift format %store-monad))

From 9a65a052016572b61e3c4247fcdf9e0478656f71 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Sun, 11 Nov 2018 22:02:18 +0100
Subject: [PATCH 131/181] gnu: go: Update default to 1.11.

* gnu/packages/golang.scm (go): Update default to 1.11.
---
 gnu/packages/golang.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index e49372d435..5b84ced804 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -528,7 +528,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                  (setenv "GOGC" "400")
                  #t)))))))))
 
-(define-public go go-1.9)
+(define-public go go-1.11)
 
 (define-public go-github-com-alsm-ioprogress
   (let ((commit "063c3725f436e7fba0c8f588547bee21ffec7ac5")

From 0fd115d536d59e5160329546f09943c278b15cdb Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Sun, 11 Nov 2018 22:03:08 +0100
Subject: [PATCH 132/181] build-system/go: Plan removal of the pkg folder for
 go-1.11 onward.

* guix/build/go-build-system.scm (install): New comment.
---
 guix/build/go-build-system.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/guix/build/go-build-system.scm b/guix/build/go-build-system.scm
index 6be0167063..022d4fe16b 100644
--- a/guix/build/go-build-system.scm
+++ b/guix/build/go-build-system.scm
@@ -204,6 +204,9 @@ respectively."
 $GOPATH/pkg, so we have to copy them into the output directory manually.
 Compiled executable files should have already been installed to the store based
 on $GOBIN in the build phase."
+  ;; TODO: From go-1.10 onward, the pkg folder should not be needed (see
+  ;; https://lists.gnu.org/archive/html/guix-devel/2018-11/msg00208.html).
+  ;; Remove it?
   (when (file-exists? "pkg")
     (copy-recursively "pkg" (string-append (assoc-ref outputs "out") "/pkg")))
   #t)

From 46a37b5966298e26d91d2a660c3f2c84f111f826 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 6 Nov 2018 18:09:16 +0100
Subject: [PATCH 133/181] gnu: go-github-com-prometheus-common-expfmt: Fix
 tests for go-1.11.

* gnu/packages/syncthing.scm (go-github-com-prometheus-common-expfmt): Fix tests for go-1.11.
---
 gnu/packages/syncthing.scm | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 5d681b816e..46211d27d8 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1097,7 +1097,14 @@ message streaming.")
                       (string-append (assoc-ref outputs "out")
                                      "/src/github.com/prometheus/common/expfmt/testdata/")
                       ".*\\.gz$"))
-               #t)))))
+               #t))
+           (replace 'check
+             ;; Tests don't pass "vet" on go-1.11.  See
+             ;; https://github.com/syncthing/syncthing/issues/5311.
+             (lambda* (#:key import-path #:allow-other-keys)
+               (invoke "go" "test"
+                       "-vet=off"
+                       import-path))))))
       (propagated-inputs
        `(("go-github-com-golang-protobuf-proto"
           ,go-github-com-golang-protobuf-proto)

From d4780c82387f226658bc8bf073ce8610bf37433b Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 6 Nov 2018 18:10:09 +0100
Subject: [PATCH 134/181] gnu: go-github-com-audriusbutkevicius-cli: Fix tests
 for go-1.11.

* gnu/packages/syncthing.scm (go-github-com-audriusbutkevicius-cli): Fix tests for go-1.11.
---
 gnu/packages/syncthing.scm | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 46211d27d8..7e4ff0ed84 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -900,7 +900,16 @@ the current goroutine's ID.")
                   "0bg26pfg25vr16jmczig2m493mja2nxjxyswz3hha7avxw20rpi5"))))
       (build-system go-build-system)
       (arguments
-       '(#:import-path "github.com/AudriusButkevicius/cli"))
+       '(#:import-path "github.com/AudriusButkevicius/cli"
+         ;; Tests don't pass "vet" on go-1.11.  See
+         ;; https://github.com/AudriusButkevicius/cli/pull/1.
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'check
+             (lambda* (#:key import-path #:allow-other-keys)
+               (invoke "go" "test"
+                       "-vet=off"
+                       import-path))))))
       (synopsis "Library for building command-line interfaces in Go")
       (description "This package provides a library for building command-line
 interfaces in Go.")

From 66fa8f0f77ac26766e5547ffdaa67cf6c261bd8e Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 6 Nov 2018 18:10:42 +0100
Subject: [PATCH 135/181] gnu: go-gopkg.in-asn1-ber.v1: Fix tests for go-1.11.

* gnu/packages/syncthing.scm (go-gopkg.in-asn1-ber.v1): Fix tests for go-1.11.
---
 gnu/packages/syncthing.scm | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 7e4ff0ed84..c29c88a588 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1267,7 +1267,16 @@ Prometheus HTTP API.")
                 "1y8bvzbxpw0lfnn7pbcdwzqj4l90qj6xf88dvv9pxd9yl5g6cskx"))))
     (build-system go-build-system)
     (arguments
-     '(#:import-path "gopkg.in/asn1-ber.v1"))
+     '(#:import-path "gopkg.in/asn1-ber.v1"
+       ;; Tests don't pass "vet" on go-1.11.  See
+       ;; https://github.com/go-asn1-ber/asn1-ber/issues/20.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key import-path #:allow-other-keys)
+             (invoke "go" "test"
+                     "-vet=off"
+                     import-path))))))
     (synopsis "ASN.1 BER encoding and decoding in Go")
     (description "This package provides ASN.1 BER encoding and decoding in the
 Go language.")

From 46a4ae2212d72d38dc55188e35a7441964694f91 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 6 Nov 2018 18:11:21 +0100
Subject: [PATCH 136/181] gnu: go-github-com-wtolson-go-taglib: Fix tests and
 build for go-1.11.

* gnu/packages/golang.scm (go-github-com-wtolson-go-taglib)[arguments]: Fix tests for go-1.11.
[native-inputs]: Remove pkg-config and taglib.
[propagated-inputs]: Add pkg-config and taglib.
---
 gnu/packages/golang.scm | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 5b84ced804..2fd8bf487c 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -2419,11 +2419,24 @@ and lookup requests.  Browse requests are not supported yet.")
           (base32
            "1cpjqnrviwflz150g78iir5ndrp3hh7a93zbp4dwbg6sb2q141p2"))))
       (build-system go-build-system)
-      (native-inputs
+      ;; From go-1.10 onward, "pkg" compiled libraries are not re-used, so
+      ;; when this package required as input for another one, it will have to
+      ;; be built again.  Thus its CGO requirements must be made available in
+      ;; the environment, that is, they must be propagated.
+      (propagated-inputs
        `(("pkg-config" ,pkg-config)
          ("taglib" ,taglib)))
       (arguments
-       `(#:import-path "github.com/wtolson/go-taglib"))
+       `(#:import-path "github.com/wtolson/go-taglib"
+         ;; Tests don't pass "vet" on go-1.11.  See
+         ;; https://github.com/wtolson/go-taglib/issues/12.
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'check
+             (lambda* (#:key import-path #:allow-other-keys)
+               (invoke "go" "test"
+                       "-vet=off"
+                       import-path))))))
       (home-page "https://github.com/wtolson/go-taglib")
       (synopsis "Go wrapper for taglib")
       (description "Go wrapper for taglib")

From 5c4758415d4b2565d3ec4a6d89c525d85dafb53a Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Sun, 11 Nov 2018 22:28:05 +0100
Subject: [PATCH 137/181] gnu: go-github-com-aarzilli-golua: Fix for go-1.11.

* gnu/packages/golang.scm (go-github-com-aarzilli-golua)[arguments]: Fix for go-1.11.
[native-inputs]: Remove lua.
[propagated-inputs]: Add lua.
---
 gnu/packages/golang.scm | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 2fd8bf487c..38df23a6c1 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -2152,26 +2152,28 @@ generate ANSI colored strings.")
           (base32
            "1d9hr29i36cza98afj3g6rs3l7xbkprwzz0blcxsr9dd7nak20di"))))
       (build-system go-build-system)
-      (native-inputs
+      ;; From go-1.10 onward, "pkg" compiled libraries are not re-used, so
+      ;; when this package required as input for another one, it will have to
+      ;; be built again.  Thus its CGO requirements must be made available in
+      ;; the environment, that is, they must be propagated.
+      (propagated-inputs
        `(("lua" ,lua)))
       (arguments
        `(#:unpack-path "github.com/aarzilli/golua"
          #:import-path "github.com/aarzilli/golua/lua"
          #:phases
          (modify-phases %standard-phases
-           (replace 'build
-             (lambda* (#:key import-path #:allow-other-keys)
-               (invoke "go" "install"
-                       "-v"  ; print the name of packages as they are compiled
-                       "-x"  ; print each command as it is invoked
-                       "-ldflags=-s -w" ; strip the symbol table and debug
-                       "-tags" "llua" ; Latest Lua on Guix does not have a version number.
-                       import-path)))
-           (replace 'check
-             (lambda* (#:key import-path #:allow-other-keys)
-               (invoke "go" "test"
-                       "-tags" "llua" ; Latest Lua on Guix does not have a version number.
-                       import-path))))))
+           ;; While it's possible to fix the CGO_LDFLAGS with the "-tags"
+           ;; command line argument, go-1.10+ does not re-use the produced pkg
+           ;; for dependencies, which means we would need to propagate the
+           ;; same "-tags" argument to all golua referrers.  A substitution is
+           ;; more convenient here.  We also need to propagate the lua
+           ;; dependency to make it available to referrers.
+           (add-after 'unpack 'fix-lua-ldflags
+             (lambda _
+               (substitute* "src/github.com/aarzilli/golua/lua/lua.go"
+                 (("#cgo linux,!llua,!luaa LDFLAGS: -llua5.3")
+                  "#cgo linux,!llua,!luaa LDFLAGS: -llua")))))))
       (home-page "https://github.com/aarzilli/golua")
       (synopsis "Go Bindings for the Lua C API")
       (description "This package provides @code{lua}, a Go module that can

From 53bcee9ea7e885e756ad4689381aa2bdfbac97ef Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 12 Nov 2018 12:36:15 +0200
Subject: [PATCH 138/181] gnu: vifm: Update to 0.10.

* gnu/packages/vim.scm (vifm): Update to 0.10.
---
 gnu/packages/vim.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm
index c6906b12cf..c974ebc439 100644
--- a/gnu/packages/vim.scm
+++ b/gnu/packages/vim.scm
@@ -718,7 +718,7 @@ refactor Vim in order to:
 (define-public vifm
   (package
     (name "vifm")
-    (version "0.9.1")
+    (version "0.10")
     (source
       (origin
         (method url-fetch)
@@ -729,7 +729,7 @@ refactor Vim in order to:
                               "vifm-" version ".tar.bz2")))
         (sha256
          (base32
-          "1cz7vjjmghgdxd1lvsdwv85gvx4kz8idq14qijpwkpfrf2va9f98"))))
+          "1f380xcyjnm4xmcdazs6dj064bwddhywvn3mgm36k7r7b2gnjnp0"))))
     (build-system gnu-build-system)
     (arguments
     '(#:configure-flags '("--disable-build-timestamp")

From e740a902281bb3bde369cc04f26656de608d3614 Mon Sep 17 00:00:00 2001
From: Arun Isaac <arunisaac@systemreboot.net>
Date: Mon, 12 Nov 2018 22:09:12 +0530
Subject: [PATCH 139/181] gnu: youtube-dl: Update to 2018.11.07.

* gnu/packages/video.scm (youtube-dl): Update to 2018.11.07.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index a482ef2515..94c5cf3a67 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1269,7 +1269,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.11.03")
+    (version "2018.11.07")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1277,7 +1277,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "11phhwhr1g050h4625d5jsgcsjnnv7jc6xcrbn7zdzd32f6gy2lj"))))
+                "1rvc2m2kbm2kycqsa7fkcg5gql9f0w3hn1a7jg48zzl06ayggxk9"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion

From 9ed86fe175c15c819d6d86681c8136ff6bc927c0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sat, 4 Apr 2015 21:59:25 +0200
Subject: [PATCH 140/181] tests: Add 'test-assertm' to (guix tests).

* guix/tests.scm (test-assertm): New macro.
* tests/gexp.scm (test-assertm): Remove.
* tests/profiles.scm (test-assertm): Remove.
* tests/challenge.scm (%store, test-assertm): Remove.
* tests/debug-link.scm (%store, test-assertm): Remove.
* tests/size.scm (%store, test-assertm): Remove.
---
 guix/tests.scm       | 25 +++++++++++++++++++++++++
 tests/challenge.scm  |  8 --------
 tests/debug-link.scm |  8 --------
 tests/gexp.scm       |  5 -----
 tests/profiles.scm   | 11 -----------
 tests/size.scm       |  8 --------
 6 files changed, 25 insertions(+), 40 deletions(-)

diff --git a/guix/tests.scm b/guix/tests.scm
index bcf9b990e5..66524ddc2f 100644
--- a/guix/tests.scm
+++ b/guix/tests.scm
@@ -27,6 +27,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages bootstrap)
   #:use-module (srfi srfi-34)
+  #:use-module (srfi srfi-64)
   #:use-module (rnrs bytevectors)
   #:use-module (ice-9 binary-ports)
   #:use-module (web uri)
@@ -39,6 +40,8 @@
             shebang-too-long?
             mock
             %test-substitute-urls
+            test-assertm
+            test-equalm
             %substitute-directory
             with-derivation-narinfo
             with-derivation-substitute
@@ -161,6 +164,28 @@ given by REPLACEMENT."
       (lambda () body ...)
       (lambda () (module-set! m 'proc original)))))
 
+(define-syntax-rule (test-assertm name exp)
+  "Like 'test-assert', but EXP is a monadic value.  A new connection to the
+store is opened."
+  (test-assert name
+    (let ((store (open-connection-for-tests)))
+      (dynamic-wind
+        (const #t)
+        (lambda ()
+          (run-with-store store exp
+                          #:guile-for-build (%guile-for-build)))
+        (lambda ()
+          (close-connection store))))))
+
+(define-syntax-rule (test-equalm name value exp)
+  "Like 'test-equal', but EXP is a monadic value.  A new connection to the
+store is opened."
+  (test-equal name
+    value
+    (with-store store
+      (run-with-store store exp
+                      #:guile-for-build (%guile-for-build)))))
+
 
 ;;;
 ;;; Narinfo files, as used by the substituter.
diff --git a/tests/challenge.scm b/tests/challenge.scm
index 4b13ec278e..c962800f3f 100644
--- a/tests/challenge.scm
+++ b/tests/challenge.scm
@@ -31,17 +31,9 @@
   #:use-module (rnrs bytevectors)
   #:use-module (ice-9 match))
 
-(define %store
-  (open-connection-for-tests))
-
 (define query-path-hash*
   (store-lift query-path-hash))
 
-(define-syntax-rule (test-assertm name exp)
-  (test-assert name
-    (run-with-store %store exp
-                    #:guile-for-build (%guile-for-build))))
-
 (define* (call-with-derivation-narinfo* drv thunk hash)
   (lambda (store)
     (with-derivation-narinfo drv (sha256 => hash)
diff --git a/tests/debug-link.scm b/tests/debug-link.scm
index 2dde3cb460..a1ae4f141c 100644
--- a/tests/debug-link.scm
+++ b/tests/debug-link.scm
@@ -43,14 +43,6 @@
 (define read-elf
   (compose parse-elf get-bytevector-all))
 
-(define %store
-  (open-connection-for-tests))
-
-(define-syntax-rule (test-assertm name exp)
-  (test-assert name
-    (run-with-store %store exp
-                    #:guile-for-build (%guile-for-build))))
-
 
 (test-begin "debug-link")
 
diff --git a/tests/gexp.scm b/tests/gexp.scm
index 467370f8cb..ab60bdab68 100644
--- a/tests/gexp.scm
+++ b/tests/gexp.scm
@@ -62,11 +62,6 @@
                                      #:target target)
                   #:guile-for-build (%guile-for-build)))
 
-(define-syntax-rule (test-assertm name exp)
-  (test-assert name
-    (run-with-store %store exp
-                    #:guile-for-build (%guile-for-build))))
-
 (define %extension-package
   ;; Example of a package to use when testing 'with-extensions'.
   (dummy-package "extension"
diff --git a/tests/profiles.scm b/tests/profiles.scm
index 9f366a04ef..1f9bbd099d 100644
--- a/tests/profiles.scm
+++ b/tests/profiles.scm
@@ -47,17 +47,6 @@
 ;; Globally disable grafts because they can trigger early builds.
 (%graft? #f)
 
-(define-syntax-rule (test-assertm name exp)
-  (test-assert name
-    (run-with-store %store exp
-                    #:guile-for-build (%guile-for-build))))
-
-(define-syntax-rule (test-equalm name value exp)
-  (test-equal name
-    value
-    (run-with-store %store exp
-                    #:guile-for-build (%guile-for-build))))
-
 ;; Example manifest entries.
 
 (define guile-1.8.8
diff --git a/tests/size.scm b/tests/size.scm
index 575b1abfdd..0aaa8fbc29 100644
--- a/tests/size.scm
+++ b/tests/size.scm
@@ -30,14 +30,6 @@
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-64))
 
-(define %store
-  (open-connection-for-tests))
-
-(define-syntax-rule (test-assertm name exp)
-  (test-assert name
-    (run-with-store %store exp
-                    #:guile-for-build (%guile-for-build))))
-
 
 (test-begin "size")
 

From c6080c3249560ef777b9a4eb6a78e7605b8b98d8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 20 Nov 2015 18:44:29 +0100
Subject: [PATCH 141/181] store: Add a functional object cache and use it in
 'lower-object'.

This leads to ~25% improvements on things like:

  guix system build desktop.tmpl --no-grafts -d

* guix/store.scm (<nix-server>)[object-cache]: New field.
* guix/store.scm (open-connection): Initialize it.
(cache-object-mapping, lookup-cached-object, %mcached): New procedures.
(mcached): New macro.
* guix/gexp.scm (lower-object): Use it.
* guix/grafts.scm (grafting?): New procedure.
---
 guix/gexp.scm   |  7 ++++-
 guix/grafts.scm |  8 +++++-
 guix/store.scm  | 68 ++++++++++++++++++++++++++++++++++++++++++++-----
 3 files changed, 74 insertions(+), 9 deletions(-)

diff --git a/guix/gexp.scm b/guix/gexp.scm
index 537875b6b7..f33fb198e4 100644
--- a/guix/gexp.scm
+++ b/guix/gexp.scm
@@ -211,7 +211,12 @@ OBJ must be an object that has an associated gexp compiler, such as a
     (#f
      (raise (condition (&gexp-input-error (input obj)))))
     (lower
-     (lower obj system target))))
+     ;; Cache in STORE the result of lowering OBJ.
+     (mlet %store-monad ((graft? (grafting?)))
+       (mcached (let ((lower (lookup-compiler obj)))
+                  (lower obj system target))
+                obj
+                system target graft?)))))
 
 (define-syntax define-gexp-compiler
   (syntax-rules (=> compiler expander)
diff --git a/guix/grafts.scm b/guix/grafts.scm
index f303e925f1..01e245d8eb 100644
--- a/guix/grafts.scm
+++ b/guix/grafts.scm
@@ -40,7 +40,8 @@
             graft-derivation/shallow
 
             %graft?
-            set-grafting))
+            set-grafting
+            grafting?))
 
 (define-record-type* <graft> graft make-graft
   graft?
@@ -328,6 +329,11 @@ it otherwise.  It returns the previous setting."
   (lambda (store)
     (values (%graft? enable?) store)))
 
+(define (grafting?)
+  "Return a Boolean indicating whether grafting is enabled."
+  (lambda (store)
+    (values (%graft?) store)))
+
 ;; Local Variables:
 ;; eval: (put 'with-cache 'scheme-indent-function 1)
 ;; End:
diff --git a/guix/store.scm b/guix/store.scm
index b1bdbf3813..9dc651b26c 100644
--- a/guix/store.scm
+++ b/guix/store.scm
@@ -23,6 +23,7 @@
   #:use-module (guix memoization)
   #:use-module (guix serialization)
   #:use-module (guix monads)
+  #:use-module (guix records)
   #:use-module (guix base16)
   #:use-module (guix base32)
   #:use-module (gcrypt hash)
@@ -30,6 +31,7 @@
   #:autoload   (guix build syscalls) (terminal-columns)
   #:use-module (rnrs bytevectors)
   #:use-module (ice-9 binary-ports)
+  #:use-module ((ice-9 control) #:select (let/ec))
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-9)
   #:use-module (srfi srfi-9 gnu)
@@ -55,6 +57,7 @@
             nix-server-minor-version
             nix-server-socket
             current-store-protocol-version        ;for internal use
+            mcached
 
             &nix-error nix-error?
             &nix-connection-error nix-connection-error?
@@ -332,10 +335,7 @@
 
 ;; remote-store.cc
 
-(define-record-type <nix-server>
-  (%make-nix-server socket major minor
-                    buffer flush
-                    ats-cache atts-cache)
+(define-record-type* <nix-server> nix-server %make-nix-server
   nix-server?
   (socket nix-server-socket)
   (major  nix-server-major-version)
@@ -348,7 +348,9 @@
   ;; during the session are temporary GC roots kept for the duration of
   ;; the session.
   (ats-cache  nix-server-add-to-store-cache)
-  (atts-cache nix-server-add-text-to-store-cache))
+  (atts-cache nix-server-add-text-to-store-cache)
+  (object-cache nix-server-object-cache
+                (default vlist-null)))            ;vhash
 
 (set-record-type-printer! <nix-server>
                           (lambda (obj port)
@@ -523,7 +525,8 @@ for this connection will be pinned.  Return a server object."
                                                     (protocol-minor v)
                                                     output flush
                                                     (make-hash-table 100)
-                                                    (make-hash-table 100))))
+                                                    (make-hash-table 100)
+                                                    vlist-null)))
                         (let loop ((done? (process-stderr conn)))
                           (or done? (process-stderr conn)))
                         conn)))))))))
@@ -543,7 +546,8 @@ connection.  Use with care."
                       (protocol-minor version)
                       output flush
                       (make-hash-table 100)
-                      (make-hash-table 100))))
+                      (make-hash-table 100)
+                      vlist-null)))
 
 (define (nix-server-version store)
   "Return the protocol version of STORE as an integer."
@@ -1486,6 +1490,56 @@ This makes sense only when the daemon was started with '--cache-failures'."
 ;; from %STATE-MONAD.
 (template-directory instantiations %store-monad)
 
+(define* (cache-object-mapping object keys result)
+  "Augment the store's object cache with a mapping from OBJECT/KEYS to RESULT.
+KEYS is a list of additional keys to match against, for instance a (SYSTEM
+TARGET) tuple.
+
+OBJECT is typically a high-level object such as a <package> or an <origin>,
+and RESULT is typically its derivation."
+  (lambda (store)
+    (values result
+            (nix-server
+             (inherit store)
+             (object-cache (vhash-consq object (cons result keys)
+                                        (nix-server-object-cache store)))))))
+
+(define* (lookup-cached-object object #:optional (keys '()))
+  "Return the cached object in the store connection corresponding to OBJECT
+and KEYS.  KEYS is a list of additional keys to match against, and which are
+compared with 'equal?'.  Return #f on failure and the cached result
+otherwise."
+  (lambda (store)
+    ;; Escape as soon as we find the result.  This avoids traversing the whole
+    ;; vlist chain and significantly reduces the number of 'hashq' calls.
+    (values (let/ec return
+              (vhash-foldq* (lambda (item result)
+                              (match item
+                                ((value . keys*)
+                                 (if (equal? keys keys*)
+                                     (return value)
+                                     result))))
+                            #f object
+                            (nix-server-object-cache store)))
+            store)))
+
+(define* (%mcached mthunk object #:optional (keys '()))
+  "Bind the monadic value returned by MTHUNK, which supposedly corresponds to
+OBJECT/KEYS, or return its cached value."
+  (mlet %store-monad ((cached (lookup-cached-object object keys)))
+    (if cached
+        (return cached)
+        (>>= (mthunk)
+             (lambda (result)
+               (cache-object-mapping object keys result))))))
+
+(define-syntax-rule (mcached mvalue object keys ...)
+  "Run MVALUE, which corresponds to OBJECT/KEYS, and cache it; or return the
+value associated with OBJECT/KEYS in the store's object cache if there is
+one."
+  (%mcached (lambda () mvalue)
+            object (list keys ...)))
+
 (define (preserve-documentation original proc)
   "Return PROC with documentation taken from ORIGINAL."
   (set-object-property! proc 'documentation

From 0dd60c1c9bb07bb3488761c95b5f4aab16061602 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Mon, 12 Nov 2018 23:56:22 +0100
Subject: [PATCH 142/181] gnu: php: Update to 7.2.12.

* gnu/packages/php.scm (php): Update to 7.2.12.
---
 gnu/packages/php.scm | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
index c78902c97c..a22591d377 100644
--- a/gnu/packages/php.scm
+++ b/gnu/packages/php.scm
@@ -63,7 +63,7 @@
 (define-public php
   (package
     (name "php")
-    (version "7.2.10")
+    (version "7.2.12")
     (home-page "https://secure.php.net/")
     (source (origin
               (method url-fetch)
@@ -71,7 +71,7 @@
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1w0432i5wjga9z8x3rhc72h2ij1jd2aimg5xmhc0hg4f7951bhh1"))
+                "1qbz2j9kzqxxp0mmx02zavvz20ji7izqdnri25g1mrwyhz60974q"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "ext"
@@ -186,6 +186,11 @@
              (substitute* "ext/standard/tests/streams/bug60602.phpt"
                (("'ls'") (string-append "'" (which "ls") "'")))
 
+             ;; The expected output is slightly different from what is given,
+             ;; in a section that's not related to the actual test
+             (substitute* "sapi/cli/tests/upload_2G.phpt"
+               (("Test\\\\n") "Test\n\n"))
+
              ;; Drop tests that are known to fail.
              (for-each delete-file
                        '("ext/posix/tests/posix_getgrgid.phpt"    ; Requires /etc/group.

From 7fed5481fe4029e4f85d90ee163a0fb1c5d617f5 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Tue, 13 Nov 2018 10:23:15 +0100
Subject: [PATCH 143/181] gnu: wine-staging: Update to 3.20.

* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.20.
* gnu/packages/wine.scm (wine-staging): Update to 3.20.
---
 gnu/packages/wine.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index 60b2a81de8..85c71b5abb 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -225,7 +225,7 @@ integrate Windows applications into your desktop.")
 (define-public wine-staging-patchset-data
   (package
    (name "wine-staging-patchset-data")
-   (version "3.19")
+   (version "3.20")
    (source
     (origin
       (method git-fetch)
@@ -235,7 +235,7 @@ integrate Windows applications into your desktop.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-        "0nmlhc6jamz0zb4b1w165l8j1a1b0j5ad1sv06aasc9jy8s12b22"))))
+        "049cwllf4aybrhj4l2i3vd5jvagjz4d448404zkyy0lfxr08id3p"))))
    (build-system trivial-build-system)
    (native-inputs
     `(("bash" ,bash)
@@ -281,7 +281,7 @@ integrate Windows applications into your desktop.")
               (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0slwgbxclx2dx0glj8az3mv0bqxmx119v9s0jvg1b5zhmqkcc8gg"))))
+                "063garmflbna3mhph8k0dv0bkzq8x75x5xrd0j8y0mjh10i13mik"))))
     (inputs `(("autoconf" ,autoconf) ; for autoreconf
               ("gtk+" ,gtk+)
               ("libva" ,libva)

From 6018683683ac49765ee0eda4cb09606f1d3689fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Nov 2018 10:51:21 +0100
Subject: [PATCH 144/181] gnu: c-toxcore: Fetch sources from git.

* gnu/packages/messaging.scm (c-toxcore)[source]: Fetch from git.
---
 gnu/packages/messaging.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index a7b868ccc0..c22cacfd36 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -860,13 +860,14 @@ protocols.")
     (version "0.2.8")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/TokTok/c-toxcore/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/TokTok/c-toxcore.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0qlkimlvbd24nlj7w9b5rpz1r807magqxmfylc1mlxsqhmfi5zj7"))))
+         "0xgnraysz25fbws5zwjk92mwnl8k1yih701qam8kgm3rxh50kyhm"))))
     (arguments
      `(#:tests? #f)) ; FIXME: Testsuite seems to stay stuck on test 3. Disable
                      ; for now.

From 155956449af6d42cdf739b0922b34bdaae639aa7 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Tue, 13 Nov 2018 15:03:15 +0300
Subject: [PATCH 145/181] gnu: restic: Fix build phase.

* gnu/packages/backup.scm (restic)[arguments]: Set "HOME" environment variable
in build phase.
---
 gnu/packages/backup.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index ab95aea727..c927a14673 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -887,6 +887,7 @@ is like a time machine for your data. ")
                                         ,version)
                ;; Disable 'restic self-update'.  It makes little sense in Guix.
                (substitute* "build.go" (("selfupdate") ""))
+               (setenv "HOME" (getcwd)) ; for $HOME/.cache/go-build
                (invoke "go" "run" "build.go"))))
 
          (replace 'check

From 1afe1985f5bffef76872f4c9e87115b46a4a3d47 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 13 Nov 2018 09:46:40 +0100
Subject: [PATCH 146/181] nar: Access the database instead of connecting to the
 daemon.

* guix/store/database.scm (%default-database-file): New variable.
(path-id): Export.
* guix/nar.scm (finalize-store-file): Use 'with-database' instead of
'with-store', and use 'path-id' instead of 'valid-path?'.
---
 guix/nar.scm            | 13 +++++++------
 guix/store/database.scm |  6 ++++++
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/guix/nar.scm b/guix/nar.scm
index 0495b4a40c..8894f10d2b 100644
--- a/guix/nar.scm
+++ b/guix/nar.scm
@@ -22,8 +22,12 @@
   #:use-module (guix build syscalls)
   #:use-module ((guix build utils)
                 #:select (delete-file-recursively with-directory-excursion))
+
+  ;; XXX: Eventually we should use (guix store database) exclusively, and not
+  ;; (guix store) since this is "daemon-side" code.
   #:use-module (guix store)
   #:use-module (guix store database)
+
   #:use-module (guix ui)                          ; for '_'
   #:use-module (gcrypt hash)
   #:use-module (guix pki)
@@ -88,15 +92,12 @@
 REFERENCES and DERIVER.  When LOCK? is true, acquire exclusive locks on TARGET
 before attempting to register it; otherwise, assume TARGET's locks are already
 held."
-
-  ;; XXX: Currently we have to call out to the daemon to check whether TARGET
-  ;; is valid.
-  (with-store store
-    (unless (valid-path? store target)
+  (with-database %default-database-file db
+    (unless (path-id db target)
       (when lock?
         (lock-store-file target))
 
-      (unless (valid-path? store target)
+      (unless (path-id db target)
         ;; If FILE already exists, delete it (it's invalid anyway.)
         (when (file-exists? target)
           (delete-file-recursively target))
diff --git a/guix/store/database.scm b/guix/store/database.scm
index 341276bc30..38796910da 100644
--- a/guix/store/database.scm
+++ b/guix/store/database.scm
@@ -36,7 +36,9 @@
   #:use-module (ice-9 match)
   #:use-module (system foreign)
   #:export (sql-schema
+            %default-database-file
             with-database
+            path-id
             sqlite-register
             register-path
             register-items
@@ -85,6 +87,10 @@ create it and initialize it as a new database."
                   (lambda ()
                     (sqlite-close db)))))
 
+(define %default-database-file
+  ;; Default location of the store database.
+  (string-append %store-database-directory "/db.sqlite"))
+
 (define-syntax-rule (with-database file db exp ...)
   "Open DB from FILE and close it when the dynamic extent of EXP... is left.
 If FILE doesn't exist, create it and initialize it as a new database."

From 190877748eeadff475dca822847fb3a5cc4467b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 13 Nov 2018 10:36:37 +0100
Subject: [PATCH 147/181] services: mcron: Fix typo in comment.

* gnu/services/mcron.scm (shepherd-schedule-action): Fix typo in comment.
---
 gnu/services/mcron.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/services/mcron.scm b/gnu/services/mcron.scm
index 5757bf8cf6..120b663e3e 100644
--- a/gnu/services/mcron.scm
+++ b/gnu/services/mcron.scm
@@ -86,7 +86,7 @@ files."
                  (lambda ()
                    (zero? (close-pipe pipe)))
                  (lambda args
-                   ;; There's with race between the SIGCHLD handler, which
+                   ;; There's a race with the SIGCHLD handler, which
                    ;; could call 'waitpid' before 'close-pipe' above does.  If
                    ;; we get ECHILD, that means we lost the race, but that's
                    ;; fine.

From d3f75179e5741db29358e3e723146fd20ec79de9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 13 Nov 2018 11:02:13 +0100
Subject: [PATCH 148/181] services: nscd: Add 'invalidate' and 'statistics'
 actions.

* gnu/services/base.scm (nscd-action-procedure, nscd-actions): New
procedures.
(nscd-shepherd-service): Add 'modules' and 'actions' fields.
* gnu/tests/base.scm (run-basic-test)["nscd invalidate action"]
["nscd invalidate action, wrong table"]: New tests.
* doc/guix.texi (Services): Mention 'herd doc nscd action'.
(Base Services): Document the actions.
---
 doc/guix.texi         | 26 ++++++++++++++++++++-
 gnu/services/base.scm | 54 +++++++++++++++++++++++++++++++++++++++----
 gnu/tests/base.scm    | 14 +++++++++++
 3 files changed, 88 insertions(+), 6 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 4b082c5f87..0ba034e822 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -10563,11 +10563,14 @@ Start,,, shepherd, The GNU Shepherd Manual}).  For example:
 
 The above command, run as @code{root}, lists the currently defined
 services.  The @command{herd doc} command shows a synopsis of the given
-service:
+service and its associated actions:
 
 @example
 # herd doc nscd
 Run libc's name service cache daemon (nscd).
+
+# herd doc nscd action invalidate
+invalidate: Invalidate the given cache--e.g., 'hosts' for host name lookups.
 @end example
 
 The @command{start}, @command{stop}, and @command{restart} sub-commands
@@ -10965,6 +10968,27 @@ The Kmscon package to use.
 Return a service that runs the libc name service cache daemon (nscd) with the
 given @var{config}---an @code{<nscd-configuration>} object.  @xref{Name
 Service Switch}, for an example.
+
+For convenience, the Shepherd service for nscd provides the following actions:
+
+@table @code
+@item invalidate
+@cindex cache invalidation, nscd
+@cindex nscd, cache invalidation
+This invalidate the given cache.  For instance, running:
+
+@example
+herd invalidate nscd hosts
+@end example
+
+@noindent
+invalidates the host name lookup cache of nscd.
+
+@item statistics
+Running @command{herd statistics nscd} displays information about nscd usage
+and caches.
+@end table
+
 @end deffn
 
 @defvr {Scheme Variable} %nscd-default-configuration
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 3409bd352c..228d3c5926 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -1252,18 +1252,57 @@ the tty to run, among other things."
                                 (string-concatenate
                                  (map cache->config caches)))))))
 
+(define (nscd-action-procedure nscd config option)
+  ;; XXX: This is duplicated from mcron; factorize.
+  #~(lambda (_ . args)
+      ;; Run 'nscd' in a pipe so we can explicitly redirect its output to
+      ;; 'current-output-port', which at this stage is bound to the client
+      ;; connection.
+      (let ((pipe (apply open-pipe* OPEN_READ #$nscd
+                         "-f" #$config #$option args)))
+        (let loop ()
+          (match (read-line pipe 'concat)
+            ((? eof-object?)
+             (catch 'system-error
+               (lambda ()
+                 (zero? (close-pipe pipe)))
+               (lambda args
+                 ;; There's a race with the SIGCHLD handler, which could
+                 ;; call 'waitpid' before 'close-pipe' above does.  If we
+                 ;; get ECHILD, that means we lost the race, but that's
+                 ;; fine.
+                 (or (= ECHILD (system-error-errno args))
+                     (apply throw args)))))
+            (line
+             (display line)
+             (loop)))))))
+
+(define (nscd-actions nscd config)
+  "Return Shepherd actions for NSCD."
+  ;; Make this functionality available as actions because that's a simple way
+  ;; to run the right 'nscd' binary with the right config file.
+  (list (shepherd-action
+         (name 'statistics)
+         (documentation "Display statistics about nscd usage.")
+         (procedure (nscd-action-procedure nscd config "--statistics")))
+        (shepherd-action
+         (name 'invalidate)
+         (documentation
+          "Invalidate the given cache--e.g., 'hosts' for host name lookups.")
+         (procedure (nscd-action-procedure nscd config "--invalidate")))))
+
 (define (nscd-shepherd-service config)
   "Return a shepherd service for CONFIG, an <nscd-configuration> object."
-  (let ((nscd.conf     (nscd.conf-file config))
+  (let ((nscd          (file-append (nscd-configuration-glibc config)
+                                    "/sbin/nscd"))
+        (nscd.conf     (nscd.conf-file config))
         (name-services (nscd-configuration-name-services config)))
     (list (shepherd-service
            (documentation "Run libc's name service cache daemon (nscd).")
            (provision '(nscd))
            (requirement '(user-processes))
            (start #~(make-forkexec-constructor
-                     (list #$(file-append (nscd-configuration-glibc config)
-                                          "/sbin/nscd")
-                           "-f" #$nscd.conf "--foreground")
+                     (list #$nscd "-f" #$nscd.conf "--foreground")
 
                      ;; Wait for the PID file.  However, the PID file is
                      ;; written before nscd is actually listening on its
@@ -1277,7 +1316,12 @@ the tty to run, among other things."
                                                   (string-append dir "/lib"))
                                                 (list #$@name-services))
                                            ":")))))
-           (stop #~(make-kill-destructor))))))
+           (stop #~(make-kill-destructor))
+           (modules `((ice-9 popen)               ;for the actions
+                      (ice-9 rdelim)
+                      (ice-9 match)
+                      ,@%default-modules))
+           (actions (nscd-actions nscd nscd.conf))))))
 
 (define nscd-activation
   ;; Actions to take before starting nscd.
diff --git a/gnu/tests/base.scm b/gnu/tests/base.scm
index 896d4a8f88..02882f4b46 100644
--- a/gnu/tests/base.scm
+++ b/gnu/tests/base.scm
@@ -335,6 +335,20 @@ info --version")
               (x
                (pk 'failure x #f))))
 
+          (test-equal "nscd invalidate action"
+            '(#t)                                 ;one value, #t
+            (marionette-eval '(with-shepherd-action 'nscd ('invalidate "hosts")
+                                                    result
+                                                    result)
+                             marionette))
+
+          (test-equal "nscd invalidate action, wrong table"
+            '(#f)                                 ;one value, #f
+            (marionette-eval '(with-shepherd-action 'nscd ('invalidate "xyz")
+                                                    result
+                                                    result)
+                             marionette))
+
           (test-equal "host not found"
             #f
             (marionette-eval

From 3ed56ad09b1d2be15e98d195b56886ec14899518 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 13 Nov 2018 11:15:41 +0100
Subject: [PATCH 149/181] tests: Remove check for a feature that appeared in
 Guile 2.0.10.

* tests/nar.scm: Remove test for 'open-sha256-input-port'.
---
 tests/nar.scm | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/tests/nar.scm b/tests/nar.scm
index d610ea53f7..ff16c3c400 100644
--- a/tests/nar.scm
+++ b/tests/nar.scm
@@ -332,13 +332,6 @@
       (lambda ()
         (rmdir input)))))
 
-;; 'restore-file-set' depends on 'open-sha256-input-port', which in turn
-;; relies on a Guile 2.0.10+ feature.
-(test-skip (if (false-if-exception
-                (open-sha256-input-port (%make-void-port "r")))
-               0
-               3))
-
 (test-assert "restore-file-set (signed, valid)"
   (with-store store
     (let* ((texts (unfold (cut >= <> 10)

From 8390869811f56f5b2ff947efb9d48bcf219a0444 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 13 Nov 2018 11:38:00 +0100
Subject: [PATCH 150/181] tests: Check file canonicalization for
 'restore-file-set'.

* guix/tests.scm (canonical-file?): New procedure.
* tests/nar.scm ("restore-file-set (signed, valid)"): Check that every
item of FILES matches 'canonical-file?'.
---
 guix/tests.scm | 9 +++++++++
 tests/nar.scm  | 5 ++++-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/guix/tests.scm b/guix/tests.scm
index 66524ddc2f..f4948148c4 100644
--- a/guix/tests.scm
+++ b/guix/tests.scm
@@ -36,6 +36,7 @@
             random-text
             random-bytevector
             file=?
+            canonical-file?
             network-reachable?
             shebang-too-long?
             mock
@@ -150,6 +151,14 @@ too expensive to build entirely in the test store."
          (else
           (error "what?" (lstat a))))))
 
+(define (canonical-file? file)
+  "Return #t if FILE is in the store, is read-only, and its mtime is 1."
+  (let ((st (lstat file)))
+    (or (not (string-prefix? (%store-prefix) file))
+        (eq? 'symlink (stat:type st))
+        (and (= 1 (stat:mtime st))
+             (zero? (logand #o222 (stat:mode st)))))))
+
 (define (network-reachable?)
   "Return true if we can reach the Internet."
   (false-if-exception (getaddrinfo "www.gnu.org" "80" AI_NUMERICSERV)))
diff --git a/tests/nar.scm b/tests/nar.scm
index ff16c3c400..bf1b066687 100644
--- a/tests/nar.scm
+++ b/tests/nar.scm
@@ -25,6 +25,8 @@
                 #:select (open-sha256-port open-sha256-input-port))
   #:use-module ((guix packages)
                 #:select (base32))
+  #:use-module ((guix build utils)
+                #:select (find-files))
   #:use-module (rnrs bytevectors)
   #:use-module (rnrs io ports)
   #:use-module (srfi srfi-1)
@@ -354,7 +356,8 @@
                           (map (lambda (file)
                                  (call-with-input-file file
                                    get-string-all))
-                               files))))))))
+                               files))
+                  (every canonical-file? files)))))))
 
 (test-assert "restore-file-set (missing signature)"
   (let/ec return

From f5a2724ae453f4a4b55ff848f4ad7e30efb6eef8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 13 Nov 2018 14:20:27 +0100
Subject: [PATCH 151/181] deduplication: Restore directory mtime and
 permissions after deduplication.

Fixes <https://bugs.gnu.org/33361>.

* guix/store/deduplication.scm (replace-with-link): Call 'set-file-time'
and 'chmod' after 'rename-file'.
* tests/nar.scm ("restore-file-set with directories (signed, valid)"):
New test.
---
 guix/store/deduplication.scm | 12 +++++++++---
 tests/nar.scm                | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 44 insertions(+), 3 deletions(-)

diff --git a/guix/store/deduplication.scm b/guix/store/deduplication.scm
index 53810c680f..21b0c81f3d 100644
--- a/guix/store/deduplication.scm
+++ b/guix/store/deduplication.scm
@@ -102,11 +102,17 @@ LINK-PREFIX."
 SWAP-DIRECTORY as the directory to store temporary hard links.
 
 Note: TARGET, TO-REPLACE, and SWAP-DIRECTORY must be on the same file system."
-  (let ((temp-link (get-temp-link target swap-directory)))
-    (make-file-writable (dirname to-replace))
+  (let* ((temp-link (get-temp-link target swap-directory))
+         (parent    (dirname to-replace))
+         (stat      (stat parent)))
+    (make-file-writable parent)
     (catch 'system-error
       (lambda ()
-        (rename-file temp-link to-replace))
+        (rename-file temp-link to-replace)
+
+        ;; Restore PARENT's mtime and permissions.
+        (set-file-time parent stat)
+        (chmod parent (stat:mode stat)))
       (lambda args
         (delete-file temp-link)
         (unless (= EMLINK (system-error-errno args))
diff --git a/tests/nar.scm b/tests/nar.scm
index bf1b066687..5ffe68c9e2 100644
--- a/tests/nar.scm
+++ b/tests/nar.scm
@@ -359,6 +359,41 @@
                                files))
                   (every canonical-file? files)))))))
 
+(test-assert "restore-file-set with directories (signed, valid)"
+  ;; <https://bugs.gnu.org/33361> describes a bug whereby directories
+  ;; containing files subject to deduplication were not canonicalized--i.e.,
+  ;; their mtime and permissions were not reset.  Ensure that this bug is
+  ;; gone.
+  (with-store store
+    (let* ((text1 (random-text))
+           (text2 (random-text))
+           (tree  `("tree" directory
+                    ("a" regular (data ,text1))
+                    ("b" directory
+                     ("c" regular (data ,text2))
+                     ("d" regular (data ,text1))))) ;duplicate
+           (file  (add-file-tree-to-store store tree))
+           (dump  (call-with-bytevector-output-port
+                   (cute export-paths store (list file) <>))))
+      (delete-paths store (list file))
+      (and (not (file-exists? file))
+           (let* ((source   (open-bytevector-input-port dump))
+                  (imported (restore-file-set source)))
+             (and (equal? imported (list file))
+                  (file-exists? file)
+                  (valid-path? store file)
+                  (string=? text1
+                            (call-with-input-file (string-append file "/a")
+                              get-string-all))
+                  (string=? text2
+                            (call-with-input-file
+                                (string-append file "/b/c")
+                              get-string-all))
+                  (= (stat:ino (stat (string-append file "/a"))) ;deduplication
+                     (stat:ino (stat (string-append file "/b/d"))))
+                  (every canonical-file?
+                         (find-files file #:directories? #t))))))))
+
 (test-assert "restore-file-set (missing signature)"
   (let/ec return
     (with-store store

From 3483f8241354935ffd56c03005f407b39c4cea45 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 13 Nov 2018 15:44:25 +0100
Subject: [PATCH 152/181] gnu: guix: Update to f5a2724.

* gnu/packages/package-management.scm (guix): Update to f5a2724.
---
 gnu/packages/package-management.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 28437224c4..1fd071b32f 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -102,8 +102,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "0.15.0")
-        (commit "f9a8fce10f2d99efec7cb1dd0f6c5f0df9d1b2df")
-        (revision 6))
+        (commit "f5a2724ae453f4a4b55ff848f4ad7e30efb6eef8")
+        (revision 7))
     (package
       (name "guix")
 
@@ -119,7 +119,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "1733d5id0h44rrkyj9xw4fcqr1wawcfi8igpgk5wsn1iq4qqwv5f"))
+                  "12glmvifbwvl6lmxh1mc8nbcp0f5qgw40rmf8n1icxvj0mnjrwp4"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments

From 8263b9f71f2ee4f8b0d765b0c38b1d812ea8168c Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Mon, 12 Nov 2018 13:27:56 -0500
Subject: [PATCH 153/181] gnu: certbot, python-acme: Update to 0.28.0.

* gnu/packages/tls.scm (certbot, python-acme): Update to 0.28.0.
---
 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 715148c432..6c2c11501f 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -538,13 +538,13 @@ netcat implementation that supports TLS.")
   (package
     (name "python-acme")
     ;; Remember to update the hash of certbot when updating python-acme.
-    (version "0.27.1")
+    (version "0.28.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "acme" version))
               (sha256
                (base32
-                "142gynlfx7yv0sdba3gpdxlnhg9chhz7hpdxdrp630z17h1bk9ri"))))
+                "11dvcbdifn5d02p4k5li8r6r39bl3p5ap9p3zjwvasm24hf2yz5z"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -595,7 +595,7 @@ netcat implementation that supports TLS.")
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "0anh3vjy9sif1bkp25nj76ii37xx8hh0igcx60ppag12xlabsw1m"))))
+                "02h959qkq7z0s13ivgf7jyl3gnc55wcck6n546k0kh155bpf5qri"))))
     (build-system python-build-system)
     (arguments
      `(,@(substitute-keyword-arguments (package-arguments python-acme)

From 021bf6af182099dbb0178e19a2f461aeb0eef686 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 13 Nov 2018 10:33:27 -0500
Subject: [PATCH 154/181] gnu: Poppler: Fix CVE-2018-19149.

* gnu/packages/patches/poppler-CVE-2018-19149.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pdf.scm (poppler)[replacement]: New field.
(poppler/fixed): New variable.
(poppler-qt4, poppler-qt5): Use package/inherit.
---
 gnu/local.mk                                  |  1 +
 .../patches/poppler-CVE-2018-19149.patch      | 80 +++++++++++++++++++
 gnu/packages/pdf.scm                          | 13 ++-
 3 files changed, 92 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/poppler-CVE-2018-19149.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 48ee438a6e..23a6cb34b5 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1046,6 +1046,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/plink-1.07-unclobber-i.patch		\
   %D%/packages/patches/plink-endian-detection.patch		\
   %D%/packages/patches/plotutils-libpng-jmpbuf.patch		\
+  %D%/packages/patches/poppler-CVE-2018-19149.patch		\
   %D%/packages/patches/portaudio-audacity-compat.patch		\
   %D%/packages/patches/portmidi-modular-build.patch		\
   %D%/packages/patches/potrace-tests.patch			\
diff --git a/gnu/packages/patches/poppler-CVE-2018-19149.patch b/gnu/packages/patches/poppler-CVE-2018-19149.patch
new file mode 100644
index 0000000000..3641f5f078
--- /dev/null
+++ b/gnu/packages/patches/poppler-CVE-2018-19149.patch
@@ -0,0 +1,80 @@
+Fix CVE-2018-19149:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-19149
+https://gitlab.freedesktop.org/poppler/poppler/issues/664
+
+Patch copied from upstream source repository:
+
+https://gitlab.freedesktop.org/poppler/poppler/commit/f162ecdea0dda5dbbdb45503c1d55d9afaa41d44
+
+From f162ecdea0dda5dbbdb45503c1d55d9afaa41d44 Mon Sep 17 00:00:00 2001
+From: Marek Kasik <mkasik@redhat.com>
+Date: Fri, 20 Apr 2018 11:38:13 +0200
+Subject: [PATCH] Fix crash on missing embedded file
+
+Check whether an embedded file is actually present in the PDF
+and show warning in that case.
+
+https://bugs.freedesktop.org/show_bug.cgi?id=106137
+https://gitlab.freedesktop.org/poppler/poppler/issues/236
+---
+ glib/poppler-attachment.cc | 26 +++++++++++++++++---------
+ glib/poppler-document.cc   |  3 ++-
+ 2 files changed, 19 insertions(+), 10 deletions(-)
+
+diff --git a/glib/poppler-attachment.cc b/glib/poppler-attachment.cc
+index c6502e9d..11ba5bb5 100644
+--- a/glib/poppler-attachment.cc
++++ b/glib/poppler-attachment.cc
+@@ -111,17 +111,25 @@ _poppler_attachment_new (FileSpec *emb_file)
+     attachment->description = _poppler_goo_string_to_utf8 (emb_file->getDescription ());
+ 
+   embFile = emb_file->getEmbeddedFile();
+-  attachment->size = embFile->size ();
++  if (embFile != NULL && embFile->streamObject()->isStream())
++    {
++      attachment->size = embFile->size ();
+ 
+-  if (embFile->createDate ())
+-    _poppler_convert_pdf_date_to_gtime (embFile->createDate (), (time_t *)&attachment->ctime);
+-  if (embFile->modDate ())
+-    _poppler_convert_pdf_date_to_gtime (embFile->modDate (), (time_t *)&attachment->mtime);
++      if (embFile->createDate ())
++        _poppler_convert_pdf_date_to_gtime (embFile->createDate (), (time_t *)&attachment->ctime);
++      if (embFile->modDate ())
++        _poppler_convert_pdf_date_to_gtime (embFile->modDate (), (time_t *)&attachment->mtime);
+ 
+-  if (embFile->checksum () && embFile->checksum ()->getLength () > 0)
+-    attachment->checksum = g_string_new_len (embFile->checksum ()->getCString (),
+-                                             embFile->checksum ()->getLength ());
+-  priv->obj_stream = embFile->streamObject()->copy();
++      if (embFile->checksum () && embFile->checksum ()->getLength () > 0)
++        attachment->checksum = g_string_new_len (embFile->checksum ()->getCString (),
++                                                 embFile->checksum ()->getLength ());
++      priv->obj_stream = embFile->streamObject()->copy();
++    }
++  else
++    {
++      g_warning ("Missing stream object for embedded file");
++      g_clear_object (&attachment);
++    }
+ 
+   return attachment;
+ }
+diff --git a/glib/poppler-document.cc b/glib/poppler-document.cc
+index 83f6aea6..ea319344 100644
+--- a/glib/poppler-document.cc
++++ b/glib/poppler-document.cc
+@@ -670,7 +670,8 @@ poppler_document_get_attachments (PopplerDocument *document)
+       attachment = _poppler_attachment_new (emb_file);
+       delete emb_file;
+ 
+-      retval = g_list_prepend (retval, attachment);
++      if (attachment != NULL)
++        retval = g_list_prepend (retval, attachment);
+     }
+   return g_list_reverse (retval);
+ }
+-- 
+2.19.1
+
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index dc966b64d8..9ffc5cb9bb 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -82,6 +82,7 @@
 (define-public poppler
   (package
    (name "poppler")
+   (replacement poppler/fixed)
    (version "0.63.0")
    (source (origin
             (method url-fetch)
@@ -127,6 +128,14 @@
    (license license:gpl2+)
    (home-page "https://poppler.freedesktop.org/")))
 
+(define poppler/fixed
+  (package
+    (inherit poppler)
+    (source (origin
+              (inherit (package-source poppler))
+              (patches (append (origin-patches (package-source poppler))
+                               (search-patches "poppler-CVE-2018-19149.patch")))))))
+
 (define-public poppler-data
   (package
     (name "poppler-data")
@@ -158,14 +167,14 @@ When present, Poppler is able to correctly render CJK and Cyrillic text.")
                    license:gpl2))))
 
 (define-public poppler-qt4
-  (package (inherit poppler)
+  (package/inherit poppler
    (name "poppler-qt4")
    (inputs `(("qt-4" ,qt-4)
              ,@(package-inputs poppler)))
    (synopsis "Qt4 frontend for the Poppler PDF rendering library")))
 
 (define-public poppler-qt5
-  (package (inherit poppler)
+  (package/inherit poppler
    (name "poppler-qt5")
    (inputs `(("qtbase" ,qtbase)
              ,@(package-inputs poppler)))

From 978d59737acaadbb0d2aa02ed071bb5d3f555973 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 13 Nov 2018 11:25:54 -0500
Subject: [PATCH 155/181] gnu: direnv: Build with Go 1.9.

* gnu/packages/shellutils.scm (direnv)[native-inputs]: Remove go.
[inputs]: Add go-1.9.
---
 gnu/packages/shellutils.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm
index 3020fdd210..0978300c9b 100644
--- a/gnu/packages/shellutils.scm
+++ b/gnu/packages/shellutils.scm
@@ -116,9 +116,10 @@ are already there.")
      '(#:test-target "test"
        #:make-flags (list (string-append "DESTDIR=" (assoc-ref %outputs "out")))
        #:phases (modify-phases %standard-phases (delete 'configure))))
+    (inputs
+     `(("go" ,go-1.9)))
     (native-inputs
-      `(("go" ,go)
-        ("which" ,which)))
+      `(("which" ,which)))
     (home-page "https://direnv.net/")
     (synopsis "Environment switcher for the shell")
     (description

From d5401375099f6e4562b849121265bb1c3e85874f Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 13 Nov 2018 11:43:16 -0500
Subject: [PATCH 156/181] gnu: libssh: Fetch source over HTTPS.

* gnu/packages/ssh.scm (libssh)[source]: Use HTTPS URL.
---
 gnu/packages/ssh.scm | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm
index 80564a9e19..5ea5148cbc 100644
--- a/gnu/packages/ssh.scm
+++ b/gnu/packages/ssh.scm
@@ -71,13 +71,7 @@
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                     ;; git.libssh.org does not support the fast "smart" HTTP
-                     ;; Git protocol. The "dumb" HTTP Git protocol is extremely
-                     ;; slow, and does not support shallow clones, so we use the
-                     ;; plain Git protocol despite its flaws. This offers an
-                     ;; incredible speedup and reduces the size of the the
-                     ;; source by more than half.
-                     (url "git://git.libssh.org/projects/libssh.git")
+                     (url "https://git.libssh.org/projects/libssh.git")
                      (commit (string-append "libssh-" version))))
               (patches (search-patches "libssh-hostname-parser-bug.patch"))
               (sha256

From c991806a7d9817c8c204dfd0813144aa0ea96c57 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Mon, 12 Nov 2018 03:53:50 +0800
Subject: [PATCH 157/181] gnu: ImageMagick: Update to 6.9.10-14.

* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14.
---
 gnu/packages/imagemagick.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index e29ec6255b..fe0923f479 100644
--- a/gnu/packages/imagemagick.scm
+++ b/gnu/packages/imagemagick.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -47,14 +48,14 @@
     ;; The 7 release series has an incompatible API, while the 6 series is still
     ;; maintained. Don't update to 7 until we've made sure that the ImageMagick
     ;; users are ready for the 7-series API.
-    (version "6.9.10-12")
+    (version "6.9.10-14")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://imagemagick/ImageMagick-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0ri96yqihdk921k5qx23y2sbhraxbp2avdccxiy6m3srjkirym2l"))))
+               "0vcfjvdk9in92x808djvy94l5gylpgds4a7mlr8jrxsv9snx88yi"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")

From 3f995aaf2101c1c7b00d473a7a81881dd50973e3 Mon Sep 17 00:00:00 2001
From: Taegil Bae <esrevinu@gmail.com>
Date: Tue, 13 Nov 2018 15:23:22 -0500
Subject: [PATCH 158/181] gnu: spice-vdagent: Fix typo in desktop file.

Fixes <https://bugs.gnu.org/33346>.

* gnu/packages/spice.scm (spice-vdagent)[arguments]: Fix typo in
'patch-spice-vdagent.desktop' phase.
---
 gnu/packages/spice.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm
index e708d726bb..fb121a0581 100644
--- a/gnu/packages/spice.scm
+++ b/gnu/packages/spice.scm
@@ -250,7 +250,7 @@ Internet and from a wide variety of machine architectures.")
          (add-after 'unpack 'patch-spice-vdagent.desktop
            (lambda* (#:key outputs #:allow-other-keys)
             (substitute* "data/spice-vdagent.desktop"
-              (("Exec=/usr/bin/spice-vdagent\n")
+              (("Exec=/usr/bin/spice-vdagent")
                (string-append "Exec=" (assoc-ref outputs "out")
                               "/bin/spice-vdagent")))
              #t)))))

From 13a574652bf2f9843b37a9ec6ae2c9204a3662b4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Nov 2018 23:27:06 +0100
Subject: [PATCH 159/181] gnu: r-genomeinfodbdata: Update to 1.2.0.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bf49f4e1dc..f48b6bd0e3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7349,7 +7349,7 @@ possible.")
 (define-public r-genomeinfodbdata
   (package
     (name "r-genomeinfodbdata")
-    (version "1.1.0")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -7359,7 +7359,7 @@ possible.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0k1hsjx6n2i1sf14hyrgdhxqxm5mxk0bgnivhiax944whcicmzbf"))))
+                "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
     (properties
      `((upstream-name . "GenomeInfoDbData")))
     (build-system r-build-system)

From 13e70f6304e9b13bdadc15bff33357f44173fe89 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Nov 2018 23:27:24 +0100
Subject: [PATCH 160/181] gnu: r-go-db: Update to 3.7.0.

* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f48b6bd0e3..2b3fc0acd8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7910,7 +7910,7 @@ extracting the desired features in a convenient format.")
 (define-public r-go-db
   (package
     (name "r-go-db")
-    (version "3.6.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.bioconductor.org/packages/"
@@ -7918,7 +7918,7 @@ extracting the desired features in a convenient format.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0fi2qywr9apg5lwfqfq9qq6bgrnv4rdhxx25656qn4bsy62i838j"))))
+                "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
     (properties
      `((upstream-name . "GO.db")))
     (build-system r-build-system)

From cb9e6ed7029a546202f6ddebe49aafd9287ff85a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Nov 2018 23:27:36 +0100
Subject: [PATCH 161/181] gnu: r-genomationdata: Update to 1.14.0.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2b3fc0acd8..7101f28ba0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8121,7 +8121,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomationdata
   (package
     (name "r-genomationdata")
-    (version "1.10.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8131,7 +8131,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
                                   "genomationData_" version ".tar.gz"))
               (sha256
                (base32
-                "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
+                "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
     (build-system r-build-system)
     ;; As this package provides little more than large data files, it doesn't
     ;; make sense to build substitutes.

From fc7683fa30035221612d883dea82413c048f3454 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Nov 2018 23:27:49 +0100
Subject: [PATCH 162/181] gnu: r-org-hs-eg-db: Update to 3.7.0.

* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7101f28ba0..b7f1970ad5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8149,7 +8149,7 @@ downloaded from Encode.")
 (define-public r-org-hs-eg-db
   (package
     (name "r-org-hs-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8159,7 +8159,7 @@ downloaded from Encode.")
                                   "org.Hs.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
+                "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
     (properties
      `((upstream-name . "org.Hs.eg.db")))
     (build-system r-build-system)

From 76bd16bcf6e42e3192b8aaefce26cef56d8bfc40 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Nov 2018 23:28:05 +0100
Subject: [PATCH 163/181] gnu: r-org-ce-eg-db: Update to 3.7.0.

* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b7f1970ad5..fe61fc601e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8175,7 +8175,7 @@ on mapping using Entrez Gene identifiers.")
 (define-public r-org-ce-eg-db
   (package
     (name "r-org-ce-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8185,7 +8185,7 @@ on mapping using Entrez Gene identifiers.")
                                   "org.Ce.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
+                "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
     (properties
      `((upstream-name . "org.Ce.eg.db")))
     (build-system r-build-system)

From 314511b86273ff1cb61a476cdb825f80b96dde0b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Nov 2018 23:28:19 +0100
Subject: [PATCH 164/181] gnu: r-org-dm-eg-db: Update to 3.7.0.

* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fe61fc601e..a4402b2737 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8201,7 +8201,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
 (define-public r-org-dm-eg-db
   (package
     (name "r-org-dm-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8211,7 +8211,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
                                   "org.Dm.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
+                "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
     (properties
      `((upstream-name . "org.Dm.eg.db")))
     (build-system r-build-system)

From d34959b8d4f4f20b3110fa6d6c54fa6f755a7a7c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Nov 2018 23:28:33 +0100
Subject: [PATCH 165/181] gnu: r-org-mm-eg-db: Update to 3.7.0.

* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a4402b2737..a1d87fc686 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8227,7 +8227,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
 (define-public r-org-mm-eg-db
   (package
     (name "r-org-mm-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8237,7 +8237,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
                                   "org.Mm.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
+                "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
     (properties
      `((upstream-name . "org.Mm.eg.db")))
     (build-system r-build-system)

From 51b262f3109fe8aba112b7cc49521c5c6810ce54 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Nov 2018 23:28:46 +0100
Subject: [PATCH 166/181] gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to
 3.4.4.

* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a1d87fc686..674bbb107d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8368,7 +8368,7 @@ in Biostrings objects.")
 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
   (package
     (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
-    (version "3.4.0")
+    (version "3.4.4")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8379,7 +8379,7 @@ in Biostrings objects.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
+                "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
     (properties
      `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
     (build-system r-build-system)

From 0bca8643a2afa3e88333d86a4a5194edc7a60455 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 14 Nov 2018 14:33:06 +0100
Subject: [PATCH 167/181] gnu: Add jags.

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index bd581c154b..0020dd02d0 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -115,6 +115,36 @@ can be imported from spreadsheets, text files and database sources and it can
 be output in text, PostScript, PDF or HTML.")
     (license license:gpl3+)))
 
+(define-public jags
+  (package
+    (name "jags")
+    (version "4.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
+                                  (version-major version) ".x/Source/"
+                                  "JAGS-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
+    (build-system gnu-build-system)
+    (home-page "http://mcmc-jags.sourceforge.net/")
+    (native-inputs
+     `(("gfortran" ,gfortran)
+       ("lapack" ,lapack)))
+    (synopsis "Gibbs sampler")
+    (description "JAGS is Just Another Gibbs Sampler.  It is a program for
+analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
+simulation not wholly unlike BUGS.  JAGS was written with three aims in mind:
+
+@enumerate
+@item To have a cross-platform engine for the BUGS language;
+@item To be extensible, allowing users to write their own functions,
+  distributions and samplers;
+@item To be a platform for experimentation with ideas in Bayesian modelling.
+@end enumerate\n")
+    (license license:gpl2)))
+
 ;; Update this package together with the set of recommended packages: r-boot,
 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.

From 0c92f3734e64086599940cf32a37b4cdd3be3648 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 14 Nov 2018 14:32:54 +0100
Subject: [PATCH 168/181] gnu: Add r-rjags.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a74ffa773f..093c51ee9a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4728,6 +4728,32 @@ Extract argument descriptions and other parts of the help pages of
 functions.")
     (license license:gpl2+)))
 
+(define-public r-rjags
+  (package
+    (name "r-rjags")
+    (version "4-8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rjags" version))
+       (sha256
+        (base32
+         "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-coda" ,r-coda)))
+    (inputs
+     `(("jags" ,jags)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://mcmc-jags.sourceforge.net")
+    (synopsis "Bayesian graphical models using MCMC")
+    (description
+     "This package provides an R interface to the JAGS MCMC library.  JAGS is
+Just Another Gibbs Sampler.  It is a program for analysis of Bayesian
+hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
+    (license license:gpl2)))
+
 (define-public r-rdpack
   (package
     (name "r-rdpack")

From 488dc4e1e27327831d08cb8f33a9128dc1b7eb26 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 12 Nov 2018 16:22:28 +0100
Subject: [PATCH 169/181] gnu: Add r-abn.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 093c51ee9a..446062cce6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4816,6 +4816,43 @@ be added or removed.  When working with Word documents, a cursor can be used
 to help insert or delete content at a specific location in the document.")
     (license license:gpl3)))
 
+(define-public r-abn
+  (package
+    (name "r-abn")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abn" version))
+       (sha256
+        (base32
+         "00k0razgdb5y5f62622fm7rxkcxrxg470nyyb02dvpfp60254kvs"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gsl" ,gsl)))
+    (propagated-inputs
+     `(("r-cairo" ,r-cairo)
+       ("r-lme4" ,r-lme4)
+       ("r-mass" ,r-mass)
+       ("r-nnet" ,r-nnet)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rjags" ,r-rjags)))
+    (home-page "http://www.r-bayesian-networks.org")
+    (synopsis "Modelling multivariate data with additive bayesian networks")
+    (description
+     "Bayesian network analysis is a form of probabilistic graphical models
+which derives from empirical data a directed acyclic graph, DAG, describing
+the dependency structure between random variables.  An additive Bayesian
+network model consists of a form of a DAG where each node comprises a
+@dfn{generalized linear model} (GLM).  Additive Bayesian network models are
+equivalent to Bayesian multivariate regression using graphical modelling, they
+generalises the usual multivariable regression, GLM, to multiple dependent
+variables.  This package provides routines to help determine optimal Bayesian
+network models for a given data set, where these models are used to identify
+statistical dependencies in messy, complex data.")
+    (license license:gpl2+)))
+
 (define-public r-snakecase
   (package
     (name "r-snakecase")

From ffdeda3ce06ada0f50455e1bf70c9a2329f2d660 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 12 Nov 2018 16:22:37 +0100
Subject: [PATCH 170/181] gnu: Add r-acd.

* gnu/packages/cran.scm (r-acd): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 446062cce6..a5cdbe31b6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4853,6 +4853,26 @@ network models for a given data set, where these models are used to identify
 statistical dependencies in messy, complex data.")
     (license license:gpl2+)))
 
+(define-public r-acd
+  (package
+    (name "r-acd")
+    (version "1.5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACD" version))
+       (sha256
+        (base32
+         "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
+    (properties `((upstream-name . "ACD")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/ACD/")
+    (synopsis "Categorical data analysis with complete or missing responses")
+    (description
+     "This package provides tools for categorical data analysis with complete
+or missing responses.")
+    (license license:gpl2+)))
+
 (define-public r-snakecase
   (package
     (name "r-snakecase")

From acbf23da447d7f0f7acec4eeef83db9bac800b03 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 12 Nov 2018 16:22:46 +0100
Subject: [PATCH 171/181] gnu: Add r-acdm.

* gnu/packages/cran.scm (r-acdm): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a5cdbe31b6..d7b331f674 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4873,6 +4873,34 @@ statistical dependencies in messy, complex data.")
 or missing responses.")
     (license license:gpl2+)))
 
+(define-public r-acdm
+  (package
+    (name "r-acdm")
+    (version "1.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACDm" version))
+       (sha256
+        (base32
+         "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
+    (properties `((upstream-name . "ACDm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-plyr" ,r-plyr)
+       ("r-rsolnp" ,r-rsolnp)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://cran.r-project.org/web/packages/ACDm/")
+    (synopsis "Tools for Autoregressive Conditional Duration Models")
+    (description
+     "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
+and Russell, 1998) models.  It creates trade, price or volume durations from
+transactions (tic) data, performs diurnal adjustments, fits various ACD models
+and tests them.")
+    (license license:gpl2+)))
+
 (define-public r-snakecase
   (package
     (name "r-snakecase")

From 08bf097a0bdd60042195abe89d361b8b664f5a94 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 12 Nov 2018 16:22:54 +0100
Subject: [PATCH 172/181] gnu: Add r-overlap.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d7b331f674..b7b1100423 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4901,6 +4901,27 @@ transactions (tic) data, performs diurnal adjustments, fits various ACD models
 and tests them.")
     (license license:gpl2+)))
 
+(define-public r-overlap
+  (package
+    (name "r-overlap")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "overlap" version))
+       (sha256
+        (base32
+         "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/overlap/")
+    (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
+    (description
+     "This package provides functions to fit kernel density functions to data
+on temporal activity patterns of animals; estimate coefficients of overlapping
+of densities for two species; and calculate bootstrap estimates of confidence
+intervals.")
+    (license license:gpl3+)))
+
 (define-public r-snakecase
   (package
     (name "r-snakecase")

From 3cef715a46c1f74e478e3c672e3e587cef3c18bb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 12 Nov 2018 16:23:04 +0100
Subject: [PATCH 173/181] gnu: Add r-circular.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b7b1100423..73ad9a8bda 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7683,3 +7683,28 @@ features (e.g. local modes).")
 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
 University Press, 2007.")
     (license license:gpl3+)))
+
+(define-public r-circular
+  (package
+    (name "r-circular")
+    (version "0.4-93")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "circular" version))
+       (sha256
+        (base32
+         "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-boot" ,r-boot)
+       ("r-mvtnorm" ,r-mvtnorm)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/circular/")
+    (synopsis "Circular statistics")
+    (description
+     "This package provides tools for circular statistics, from \"Topics in
+circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
+Scientific.")
+    (license license:gpl2+)))

From 10483a64eebf753ae17695d3c027e5fefa0df644 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 12 Nov 2018 16:23:16 +0100
Subject: [PATCH 174/181] gnu: Add r-activity.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 73ad9a8bda..8513dff4f5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7708,3 +7708,29 @@ University Press, 2007.")
 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
 Scientific.")
     (license license:gpl2+)))
+
+(define-public r-activity
+  (package
+    (name "r-activity")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "activity" version))
+       (sha256
+        (base32
+         "1lqajgxfps2h6amz1791vp3f52rs9ghmanq1nqfxqd2jmk3idkrx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-circular" ,r-circular)
+       ("r-overlap" ,r-overlap)
+       ("r-pbapply" ,r-pbapply)))
+    (home-page "https://cran.r-project.org/web/packages/activity/")
+    (synopsis "Animal activity statistics")
+    (description
+     "This package provides functions to fit kernel density functions to
+animal activity time data; plot activity distributions; quantify overall
+levels of activity; statistically compare activity metrics through
+bootstrapping; and evaluate variation in linear variables with time (or other
+circular variables).")
+    (license license:gpl3)))

From e4f4a04a51c657fd9cedcc8c08e8fad858533777 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 12 Nov 2018 16:23:26 +0100
Subject: [PATCH 175/181] gnu: Add r-ouch.

* gnu/packages/cran.scm (r-ouch): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8513dff4f5..6ce9bdd16f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7734,3 +7734,23 @@ levels of activity; statistically compare activity metrics through
 bootstrapping; and evaluate variation in linear variables with time (or other
 circular variables).")
     (license license:gpl3)))
+
+(define-public r-ouch
+  (package
+    (name "r-ouch")
+    (version "2.11-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ouch" version))
+       (sha256
+        (base32
+         "0xkwwi62vdahlcg3k32zb1nfwsx87zdssk79mvcxgfsw9bw4gahx"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-subplex" ,r-subplex)))
+    (home-page "http://kingaa.github.io/ouch/")
+    (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
+    (description
+     "This package provides tools to fit and compare Ornstein-Uhlenbeck models
+for evolution along a phylogenetic tree.")
+    (license license:gpl2+)))

From ee66a13563dc0ca03865ec3d3d36f8c55e885ac0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 14 Nov 2018 13:56:54 +0100
Subject: [PATCH 176/181] gnu: Add jamm.

* gnu/packages/bioinformatics.scm (jamm): New variable.
---
 gnu/packages/bioinformatics.scm | 79 +++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 674bbb107d..58cee5cbbe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14118,6 +14118,85 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
 absolute GSEA.")
     (license license:gpl2)))
 
+(define-public jamm
+  (package
+    (name "jamm")
+    (version "1.0.7.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/mahmoudibrahim/JAMM.git")
+             (commit (string-append "JAMMv" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are none
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'build
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (substitute* "JAMM.sh"
+               (("^sPath=.*")
+                (string-append "")))
+             #t))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (libexec (string-append out "/libexec/jamm"))
+                    (bin (string-append out "/bin")))
+               (substitute* '("JAMM.sh"
+                              "SignalGenerator.sh")
+                 (("^sPath=.*")
+                  (string-append "sPath=\"" libexec "\"\n")))
+               (for-each (lambda (file)
+                           (install-file file libexec))
+                         (list "bincalculator.r"
+                               "peakfinder.r"
+                               "peakhelper.r"
+                               "signalmaker.r"
+                               "xcorr.r"
+                               "xcorrhelper.r"
+                               ;; Perl scripts
+                               "peakfilter.pl"
+                               "readshifter.pl"))
+
+               (for-each
+                (lambda (script)
+                  (chmod script #o555)
+                  (install-file script bin)
+                  (wrap-program (string-append bin "/" script)
+                    `("PATH" ":" prefix
+                      (,(string-append (assoc-ref inputs "coreutils") "/bin")
+                       ,(string-append (assoc-ref inputs "gawk") "/bin")
+                       ,(string-append (assoc-ref inputs "perl") "/bin")
+                       ,(string-append (assoc-ref inputs "r-minimal") "/bin")))
+                    `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
+                    `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
+                (list "JAMM.sh" "SignalGenerator.sh")))
+             #t)))))
+    (inputs
+     `(("bash" ,bash)
+       ("coreutils" ,coreutils)
+       ("gawk" ,gawk)
+       ("perl" ,perl)
+       ("r-minimal" ,r-minimal)
+       ;;("r-parallel" ,r-parallel)
+       ("r-signal" ,r-signal)
+       ("r-mclust" ,r-mclust)))
+    (home-page "https://github.com/mahmoudibrahim/JAMM")
+    (synopsis "Peak finder for NGS datasets")
+    (description
+     "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq,
+ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak
+boundaries accurately.  JAMM is applicable to both broad and narrow
+datasets.")
+    (license license:gpl3+)))
+
 (define-public ngless
   (package
     (name "ngless")

From bac2974e8600c1a9b22f17d8b1cd75340731347f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 14 Nov 2018 15:40:19 +0100
Subject: [PATCH 177/181] gnu: feh: Update to 3.0.

* gnu/packages/image-viewers.scm (feh): Update to 3.0.
---
 gnu/packages/image-viewers.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index 518417707f..029d5b5443 100644
--- a/gnu/packages/image-viewers.scm
+++ b/gnu/packages/image-viewers.scm
@@ -60,7 +60,7 @@
 (define-public feh
   (package
     (name "feh")
-    (version "2.28.1")
+    (version "3.0")
     (home-page "https://feh.finalrewind.org/")
     (source (origin
               (method url-fetch)
@@ -68,7 +68,7 @@
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0wian0gnx0yfxf8x9b8wr57fjd6rnmi3y3xj83ni6x0xqrjnf1lp"))))
+                "00fwf8yz7k8vzd30ly5ndlj6ax9w85dkjzjnlk95vd0zdrf4wyxn"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))

From d63f58848601cf45f60c88d9bb0f789ac1aa8438 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 14 Nov 2018 19:32:41 +0100
Subject: [PATCH 178/181] gnu: sudo: Update to 1.8.26.

* gnu/packages/admin.scm (sudo): Update to 1.8.26.
---
 gnu/packages/admin.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index fa60cadd01..2247902898 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -979,7 +979,7 @@ system administrator.")
 (define-public sudo
   (package
     (name "sudo")
-    (version "1.8.25p1")
+    (version "1.8.26")
     (source (origin
               (method url-fetch)
               (uri
@@ -989,7 +989,7 @@ system administrator.")
                                     version ".tar.gz")))
               (sha256
                (base32
-                "0nqri46d4dpycj96zin2f2wszmhm7q9mr68hhj9sp81pgmx9rjcx"))
+                "1qpyyfga8rs02p3186sns8qvh2bzwa48ka845nrcqh83dyd23nj0"))
               (modules '((guix build utils)))
               (snippet
                '(begin

From 7939387da83437918b87d00b06b19b7c987ed171 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 14 Nov 2018 19:54:10 +0100
Subject: [PATCH 179/181] gnu: nano: Update to 3.2.

* gnu/packages/nano.scm (nano): Update to 3.2.
---
 gnu/packages/nano.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm
index 8f96b605a6..057e8c3bd9 100644
--- a/gnu/packages/nano.scm
+++ b/gnu/packages/nano.scm
@@ -30,7 +30,7 @@
 (define-public nano
   (package
     (name "nano")
-    (version "3.1")
+    (version "3.2")
     (source
      (origin
       (method url-fetch)
@@ -38,7 +38,7 @@
                           version ".tar.xz"))
       (sha256
        (base32
-        "17kinzyv6vwgyx2d0ym1kp65qbf7kxzwpyg21ic1rijv1aj2rh0l"))))
+        "0jb3zq0v84xb0chyynkcp2jhs9660wmpkic294p4p6c96npp69yi"))))
     (build-system gnu-build-system)
     (inputs
      `(("gettext" ,gettext-minimal)

From 24dd6ec38ae6b54d4b9dc91fc2fe1119816a0a90 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 14 Nov 2018 20:19:07 +0100
Subject: [PATCH 180/181] gnu: mtools: Update to 4.0.20.

* gnu/packages/mtools.scm (mtools): Update to 4.0.20.
[source](uri): Change to 'bz2' compressed tarball.
---
 gnu/packages/mtools.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/mtools.scm b/gnu/packages/mtools.scm
index e4750f579f..5e3c3dd378 100644
--- a/gnu/packages/mtools.scm
+++ b/gnu/packages/mtools.scm
@@ -28,15 +28,15 @@
 (define-public mtools
   (package
     (name "mtools")
-    (version "4.0.19")
+    (version "4.0.20")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnu/mtools/mtools-"
-                          version ".tar.gz"))
+                          version ".tar.bz2"))
       (sha256
        (base32
-        "003qnj4rs22v2sih3is55scvav8xq9p1dp5b7gnyl67a60ky516r"))))
+        "1vcahr9s6zv1hnrx2bgjnzcas2y951q90r1jvvv4q9v5kwfd6qb0"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/mtools/")
     (synopsis "Access MS-DOS disks without mounting")

From e921993c25626541385f191f0463cad8e5e5c5c7 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 14 Nov 2018 20:52:39 +0100
Subject: [PATCH 181/181] gnu: xf86-video-r128: Update to 6.12.0.

* gnu/packages/xorg.scm (xf86-video-r128): Update to 6.12.0.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 49baef5f04..19ec6f5370 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -3174,14 +3174,14 @@ This driver is intended for the spice qxl virtio device.")
 (define-public xf86-video-r128
   (package
     (name "xf86-video-r128")
-    (version "6.11.0")
+    (version "6.12.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://xorg/individual/driver/"
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0snvwmrh8dqyyaq7ggicym6yrsg4brygkx9156r0m095m7fp3rav"))))
+                "0mz0v5mqmmbncr2drd5zvia1fb7frz2xqwflhhqbnaxx5j48c740"))))
     (build-system gnu-build-system)
     (inputs `(("mesa" ,mesa)
               ("xorgproto" ,xorgproto)