[bug#30570] Patches submitted on behalf of Nextjournal

[bug#30570] Patches submitted on behalf of Nextjournal

[Leo Famulari]

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Hi,

I'm submitting these packages on behalf of Nextjournal
(https://nextjournal.com). I packaged them originally a few months ago
and recently updated them for submitting to GNU Guix.

gnu: Add flatbuffers.
gnu: Add python-plotly.
gnu: Add r-maps.
gnu: Add r-mapproj.
gnu: Add Rgooglemaps.
gnu: Add r-geosphere.
gnu: Add r-subplex.
gnu: Add r-desolve.
gnu: Add Diversitree.
gnu: Add r-jpeg.
gnu: Add r-ggmap.
gnu: Add r-feather.
gnu: Add google-brotli.
gnu: Add apache-arrow.
gnu: Add python-pyarrow.
gnu: Add python-feather-format.

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[bug#30570] [PATCH 01/16] gnu: Add flatbuffers.

[Leo Famulari]

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

diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 8df4841ea..ce389ca4a 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -9,6 +9,7 @@
 ;;; Copyright © 2017 Frederick M. Muriithi <fredmanglis@gmail.com>
 ;;; Copyright © 2017 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -409,3 +410,28 @@ JSON's ability, but serializes to a binary format which is smaller and faster
 to generate and parse.  The two primary functions are @code{cbor.loads} and
 @code{cbor.dumps}.")
     (license license:asl2.0)))
+
+(define-public flatbuffers
+  (package
+    (name "flatbuffers")
+    (version "1.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://github.com/google/flatbuffers/archive/v"
+                            version ".tar.gz"))
+        (sha256
+         (base32
+          "0blc978wc5h91662vai24xj92c3bx56y6hzid90qva7il302jl64"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:configure-flags
+       (list (string-append "-DCMAKE_INSTALL_LIBDIR="
+                            (assoc-ref %outputs "out") "/lib")
+             "-DCMAKE_BUILD_TYPE=Release")))
+    (home-page "https://google.github.io/flatbuffers/")
+    (synopsis "Memory-efficient serialization library")
+    (description "FlatBuffers is a cross platform serialization library for C++,
+C#, C, Go, Java, JavaScript, PHP, and Python.  It was originally created for
+game development and other performance-critical applications.")
+    (license license:asl2.0)))
-- 
2.16.1

[bug#30570] [PATCH 02/16] gnu: Add python-plotly.

[Leo Famulari]

* gnu/packages/graph.scm (python-plotly, python2-plotly): New variables.
---
 gnu/packages/graph.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 70df77b5d..e22b981ac 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,7 +33,10 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages statistics)
+  #:use-module (gnu packages time)
   #:use-module (gnu packages xml))
 
 (define-public igraph
@@ -172,3 +176,34 @@ model.")
      "This package interfaces R with the graphviz library for plotting R graph
 objects from the @code{graph} package.")
     (license license:epl1.0)))
+
+(define-public python-plotly
+  (package
+    (name "python-plotly")
+    (version "2.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "plotly" version))
+        (sha256
+         (base32
+          "0n18116jz6bl5n9cq23vabv1gcbh1x3yficdnfq55v0z4cwy0zlf"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:tests? #f)) ; The tests are not distributed in the release
+    (propagated-inputs
+     `(("python-decorator" ,python-decorator)
+       ("python-nbformat" ,python-nbformat)
+       ("python-pytz" ,python-pytz)
+       ("python-requests" ,python-requests)
+       ("python-six" ,python-six)))
+    (home-page "https://plot.ly/python/")
+    (synopsis "Interactive plotting library for Python")
+    (description "Plotly's Python graphing library makes interactive,
+publication-quality graphs online.  Examples of how to make line plots, scatter
+plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
+subplots, multiple-axes, polar charts, and bubble charts. ")
+    (license license:expat)))
+
+(define-public python2-plotly
+  (package-with-python2 python-plotly))
-- 
2.16.1

[bug#30570] [PATCH 03/16] gnu: Add r-maps.

[Leo Famulari]

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

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index d75416415..367895018 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,6 +27,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
   #:use-module (guix build-system scons)
+  #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -378,3 +380,22 @@ development.")
     (synopsis "Python bindings for Mapnik")
     (description "This package provides Python bindings for Mapnik.")
     (license license:lgpl2.1+)))
+
+(define-public r-maps
+  (package
+   (name "r-maps")
+   (version "3.2.0")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "maps" version))
+       (sha256
+        (base32
+         "0577f3b5d3a7djl7r0miy9mzr6xq6jb32p8nyrma7m2azasbwyj3"))))
+   (build-system r-build-system)
+   (home-page "https://cran.r-project.org/web/packages/maps")
+   (synopsis "Draw Geographical Maps")
+   (description "This package provies an R module for display of maps.
+Projection code and larger maps are in separate packages ('mapproj' and
+'mapdata').")
+   (license license:gpl2)))
-- 
2.16.1

[bug#30570] [PATCH 04/16] gnu: Add r-mapproj.

[Leo Famulari]

* gnu/packages/geo.scm (r-mapproj): New variable.
---
 gnu/packages/geo.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 367895018..8e066197d 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -399,3 +399,25 @@ development.")
 Projection code and larger maps are in separate packages ('mapproj' and
 'mapdata').")
    (license license:gpl2)))
+
+(define-public r-mapproj
+  (package
+   (name "r-mapproj")
+   (version "1.2-5")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mapproj" version))
+       (sha256
+        (base32
+         "0rjz37r4rizk2c6jaf54f0kfb60dqv6b262cnhiwjl55d4x6l0pk"))))
+   (build-system r-build-system)
+   (propagated-inputs `(("r-maps" ,r-maps)))
+   (home-page "https://cran.r-project.org/web/packages/mapproj")
+   (synopsis "Map projection in R")
+   (description "This package converts latitude/longitude into projected
+coordinates.")
+   (license (list license:gpl2 ; The R interface
+                  (license:non-copyleft ; The C code
+                    "https://www.gnu.org/licenses/license-list.en.html#lucent102"
+                    "Lucent Public License Version 1.02")))))
-- 
2.16.1

[bug#30570] [PATCH 05/16] gnu: Add Rgooglemaps.

[Leo Famulari]

* gnu/packages/geo.scm (r-rgooglemaps): New variable.
---
 gnu/packages/geo.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 8e066197d..88a374fb4 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -421,3 +421,25 @@ coordinates.")
                   (license:non-copyleft ; The C code
                     "https://www.gnu.org/licenses/license-list.en.html#lucent102"
                     "Lucent Public License Version 1.02")))))
+
+(define-public r-rgooglemaps
+  (package
+   (name "r-rgooglemaps")
+   (version "1.4.1")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RgoogleMaps" version))
+       (sha256
+        (base32
+         "0fsmlnhl4kw2j4972kfanzw9njhnzk695gsyw8g6yppsmz2clcaq"))))
+   (properties `((upstream-name . "RgoogleMaps")))
+   (build-system r-build-system)
+   (propagated-inputs `(("r-png" ,r-png)))
+   (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
+   (synopsis "Use Google Maps in R")
+   (description "This package serves two purposes: (i) Provide a comfortable R
+interface to query the Google server for static maps, and (ii) Use the map as a
+background image to overlay plots within R.  This requires proper coordinate
+scaling.")
+   (license license:gpl2+)))
-- 
2.16.1

[bug#30570] [PATCH 06/16] gnu: Add r-geosphere.

[Leo Famulari]

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

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 88a374fb4..c937510be 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -37,6 +37,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages cran)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
@@ -443,3 +444,23 @@ interface to query the Google server for static maps, and (ii) Use the map as a
 background image to overlay plots within R.  This requires proper coordinate
 scaling.")
    (license license:gpl2+)))
+
+(define-public r-geosphere
+  (package
+   (name "r-geosphere")
+   (version "1.5-7")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "geosphere" version))
+       (sha256
+        (base32
+         "186qdm5niq7v3d4w4rngx71znsgi44hnam7698bsx9ar5mg5b6wx"))))
+   (build-system r-build-system)
+   (propagated-inputs `(("r-sp" ,r-sp)))
+   (home-page "https://cran.r-project.org/web/packages/geosphere")
+   (synopsis "Spherical Trigonometry")
+   (description "This package computes spherical trigonometry for geographic
+applications.  That is, compute distances and related measures for angular
+(longitude/latitude) locations.")
+   (license license:gpl3+)))
-- 
2.16.1

[bug#30570] [PATCH 07/16] gnu: Add r-subplex.

[Leo Famulari]

gnu/packages/maths.scm (r-subplex): New variable.
---
 gnu/packages/maths.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 6be4c6959..d4e60d447 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -23,6 +23,7 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
 ;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3729,3 +3730,25 @@ specifications.  Also, state spaces can be manipulated, visualised and
 analysed.")
     (home-page "http://mcrl2.org")
     (license license:boost1.0)))
+
+(define-public r-subplex
+  (package
+    (name "r-subplex")
+    (version "1.5-2")
+    (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "subplex" version))
+      (sha256
+       (base32
+        "1v9xrnkapnq7v1jbhlg32ignklzf2vn8rqpayc8pzk8wvz53r33g"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/subplex")
+    (synopsis "Unconstrained Optimization using the Subplex Algorithm")
+    (description "This package implements the Subplex optimization algorithm.
+It solves unconstrained optimization problems using a simplex method on
+subspaces.  The method is well suited for optimizing objective functions that
+are noisy or are discontinuous at the solution.")
+    (license license:gpl3+)))
-- 
2.16.1

[bug#30570] [PATCH 08/16] gnu: Add r-desolve.

[Leo Famulari]

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

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d4e60d447..4dee4d3bd 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3752,3 +3752,32 @@ It solves unconstrained optimization problems using a simplex method on
 subspaces.  The method is well suited for optimizing objective functions that
 are noisy or are discontinuous at the solution.")
     (license license:gpl3+)))
+
+(define-public r-desolve
+  (package
+    (name "r-desolve")
+    (version "1.20")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "deSolve" version))
+        (sha256
+         (base32
+          "18nx3maww979a8p8ly4hv63y65mnjx8vbj2fpipd6rhcbf1lbsan"))))
+    (properties `((upstream-name . "deSolve")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://desolve.r-forge.r-project.org/")
+    (synopsis "Solvers for Initial Value Problems of Differential Equations")
+    (description "This package provides functions that solve initial
+value problems of a system of first-order ordinary differential equations (ODE),
+of partial differential equations (PDE), of differential algebraic equations
+(DAE), and of delay differential equations.  The functions provide an interface
+to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
+to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
+the Runge-Kutta family with fixed or variable time steps.  The package contains
+routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
+differential equations (PDE) that have been converted to ODEs by numerical
+differencing.")
+    (license license:gpl2+)))
-- 
2.16.1

[bug#30570] [PATCH 09/16] gnu: Add Diversitree.

[Leo Famulari]

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 820bd84d6..3353565cf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9,6 +9,7 @@
 ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -11886,3 +11887,34 @@ variable number of row and column annotations.  Loom also supports sparse
 graphs.  This library makes it easy to work with @file{.loom} files for
 single-cell RNA-seq data.")
     (license license:bsd-3)))
+
+(define-public r-diversitree
+  (package
+    (name "r-diversitree")
+    (version "0.9-10")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "diversitree" version))
+        (sha256
+         (base32
+          "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-desolve" ,r-desolve)
+       ("r-rcpp" ,r-rcpp)
+       ("r-suplex" ,r-subplex)))
+    (home-page "https://www.zoology.ubc.ca/prog/diversitree")
+    (synopsis "Comparative 'Phylogenetic' Analyses of Diversification")
+    (description "This package contains a number of comparative \"phylogenetic\"
+methods, mostly focusing on analysing diversification and character evolution.
+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
+include Markov models of discrete and continuous trait evolution and constant
+rate speciation and extinction.")
+    (license license:gpl2+)))
-- 
2.16.1

[bug#30570] [PATCH 10/16] gnu: Add r-jpeg.

[Leo Famulari]

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

diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 9052a34e9..1fc1366e4 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -17,6 +17,7 @@
 ;;; Copyright © 2017 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1231,3 +1232,23 @@ medical image data, e.g. magnetic resonance image (MRI) and functional MRI
     (synopsis "Color picker")
     (description "Gpick is an advanced color picker and palette editing tool.")
     (license license:bsd-3)))
+
+(define-public r-jpeg
+  (package
+   (name "r-jpeg")
+   (version "0.1-8")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "jpeg" version))
+       (sha256
+        (base32
+         "05hawv5qcb82ljc1l2nchx1wah8mq2k2kfkhpzyww554ngzbwcnh"))))
+   (build-system r-build-system)
+   (inputs `(("libjpeg" ,libjpeg)))
+   (home-page "http://www.rforge.net/jpeg/")
+   (synopsis "Read and write JPEG images with R")
+   (description "This package provides a way to read, write and display bitmap
+images stored in the JPEG format with R.  It can read and write both files and
+in-memory raw vectors.")
+   (license license:gpl2+)))
-- 
2.16.1

[bug#30570] [PATCH 11/16] gnu: Add r-ggmap.

[Leo Famulari]

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

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index c937510be..bb1f64841 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -45,6 +45,8 @@
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages webkit)
   #:use-module (gnu packages xml))
 
@@ -464,3 +466,36 @@ scaling.")
 applications.  That is, compute distances and related measures for angular
 (longitude/latitude) locations.")
    (license license:gpl3+)))
+
+(define-public r-ggmap
+  (package
+   (name "r-ggmap")
+   (version "2.6.1")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggmap" version))
+       (sha256
+        (base32
+         "0mssb09w818jv58h7mly9y181pzv22sgcd4a079cfpq04bs0wigw"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-digest" ,r-digest)
+      ("r-geosphere" ,r-geosphere)
+      ("r-ggplot2" ,r-ggplot2)
+      ("r-jpeg" ,r-jpeg)
+      ("r-mapproj" ,r-mapproj)
+      ("r-plyr" ,r-plyr)
+      ("r-png" ,r-png)
+      ("r-proto" ,r-proto)
+      ("r-reshape2" ,r-reshape2)
+      ("r-rgooglemaps" ,r-rgooglemaps)
+      ("r-rjson" ,r-rjson)
+      ("r-scales" ,r-scales)))
+   (home-page "https://github.com/dkahle/ggmap")
+   (synopsis "Spatial Visualization with ggplot2")
+   (description "This package provides a collection of functions to visualize
+spatial data and models on top of static maps from various online sources (e.g
+Google Maps and Stamen Maps).  It includes tools common to those tasks,
+including functions for geolocation and routing.")
+   (license license:gpl2)))
-- 
2.16.1

[bug#30570] [PATCH 12/16] gnu: Add r-feather.

[Leo Famulari]

* gnu/packages/serialization.scm (r-feather): New variable.
---
 gnu/packages/serialization.scm | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index ce389ca4a..58ff2a1c0 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -33,17 +33,20 @@
   #:use-module (guix utils)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
+  #:use-module (guix build-system r)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cran)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages perl)
-  #:use-module (guix build-system python))
+  #:use-module (gnu packages statistics))
 
 (define-public cereal
   (package
@@ -435,3 +438,25 @@ to generate and parse.  The two primary functions are @code{cbor.loads} and
 C#, C, Go, Java, JavaScript, PHP, and Python.  It was originally created for
 game development and other performance-critical applications.")
     (license license:asl2.0)))
+
+(define-public r-feather
+  (package
+    (name "r-feather")
+    (version "0.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "feather" version))
+        (sha256
+         (base32
+          "1q6dbkfnkpnabq8lb6bm9ma44cfcghx2lm23pyk3vg7943wrn1pi"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-hms" ,r-hms)
+       ("r-rcpp" ,r-rcpp)
+       ("r-tibble" ,r-tibble)))
+    (home-page "https://github.com/wesm/feather")
+    (synopsis "R Bindings to the Feather API")
+    (description "Read and write feather files, a lightweight binary columnar
+daa store designed for maximum speed.")
+    (license license:asl2.0)))
-- 
2.16.1

[bug#30570] [PATCH 13/16] gnu: Add google-brotli.

[Leo Famulari]

* gnu/packages/compression.scm (google-brotli): New variable.
---
 gnu/packages/compression.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index f25c4bba3..f4a3a610c 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -21,6 +21,7 @@
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2101,3 +2102,46 @@ single-member files which can't be decompressed in parallel.")
    (description "innoextract allows extracting Inno Setup installers under
 non-Windows systems without running the actual installer using wine.")
    (license license:zlib)))
+
+(define-public google-brotli
+  (package
+    (name "google-brotli")
+    (version "1.0.2")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/google/brotli/archive/v"
+                                 version ".tar.gz"))
+             (sha256
+              (base32
+               "08kl9gww2058p1p7j9xqmcmrabcfihhj3fq984d7fi3bchb2mky2"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'rename-static-libraries
+           ;; The build tools put a 'static' suffix on the static libraries, but
+           ;; other applications don't know how to find these.
+           (let ((lib (string-append (assoc-ref %outputs "out") "/lib/")))
+             (lambda _
+               (rename-file (string-append lib "libbrotlicommon-static.a")
+                            (string-append lib "libbrotlicommon.a"))
+               (rename-file (string-append lib "libbrotlidec-static.a")
+                            (string-append lib "libbrotlidec.a"))
+               (rename-file (string-append lib "libbrotlienc-static.a")
+                            (string-append lib "libbrotlienc.a"))
+               #t))))
+       #:configure-flags
+       (list ;; Defaults to "lib64" on 64-bit archs.
+             (string-append "-DCMAKE_INSTALL_LIBDIR="
+                            (assoc-ref %outputs "out") "/lib"))))
+    (home-page "https://github.com/google/brotli")
+    (synopsis "General-purpose lossless compression")
+    (description "This package provides the reference implementation of Brotli,
+a generic-purpose lossless compression algorithm that compresses data using a
+combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd
+order context modeling, with a compression ratio comparable to the best
+currently available general-purpose compression methods. It is similar in speed
+with @code{deflate} but offers more dense compression.
+
+The specification of the Brotli Compressed Data Format is defined in RFC 7932.")
+    (license license:expat)))
-- 
2.16.1

[bug#30570] [PATCH 14/16] gnu: Add apache-arrow.

[Leo Famulari]

* gnu/packages/databases.scm (apache-arrow): New variable.
---
 gnu/packages/databases.scm | 74 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 29b6ca169..8de274ab2 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -31,6 +31,7 @@
 ;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Kristofer Buffington <kristoferbuffington@gmail.com>
 ;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -58,6 +59,7 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages curl)
@@ -92,6 +94,7 @@
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages valgrind)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -2717,3 +2720,74 @@ Replay oplog entries between MongoDB servers
 Monitor read/write activity on a mongo server
 @end table")
     (license license:asl2.0)))
+
+(define-public apache-arrow
+  (package
+    (name "apache-arrow")
+    (version "0.7.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/apache/arrow")
+               (commit (string-append "apache-arrow-" version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32
+            "1x7sdd8lbs3nfqjql1pcgbkjc19bls56zmgjayshkmablvlc4dy3"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'enter-source-directory
+           (lambda _ (chdir "cpp") #t))
+         (add-after 'unpack 'set-env
+           (lambda _
+             (setenv "BOOST_ROOT" (assoc-ref %build-inputs "boost"))
+             (setenv "BROTLI_HOME" (assoc-ref %build-inputs "brotli"))
+             (setenv "FLATBUFFERS_HOME" (assoc-ref %build-inputs "flatbuffers"))
+             (setenv "JEMALLOC_HOME" (assoc-ref %build-inputs "jemalloc"))
+             (setenv "RAPIDJSON_HOME" (assoc-ref %build-inputs "rapidjson"))
+             #t)))
+       #:configure-flags
+       (list "-DCMAKE_BUILD_TYPE=Release"
+             "-DARROW_PYTHON=ON"
+
+             ;; Install to PREFIX/lib (the default is
+             ;; PREFIX/lib64).
+             (string-append "-DCMAKE_INSTALL_LIBDIR="
+                            (assoc-ref %outputs "out")
+                            "/lib")
+
+             ;; XXX These Guix package offer static
+             ;; libraries that are not position independent,
+             ;; and ld fails to link them into the arrow .so
+             "-DARROW_WITH_SNAPPY=OFF"
+             "-DARROW_WITH_ZLIB=OFF"
+             "-DARROW_WITH_ZSTD=OFF"
+             "-DARROW_WITH_LZ4=OFF"
+
+             ;; Building the tests forces on all the
+             ;; optional features and the use of static
+             ;; libraries.
+             "-DARROW_BUILD_TESTS=OFF"
+             "-DARROW_BUILD_STATIC=OFF")))
+    (inputs
+     `(("boost" ,boost)
+       ("rapidjson" ,rapidjson)
+       ("brotli" ,google-brotli)
+       ("flatbuffers" ,flatbuffers)
+       ;; Arrow is not yet compatible with jemalloc >= 5:
+       ;; https://issues.apache.org/jira/browse/ARROW-1141
+       ("jemalloc" ,jemalloc-4.5.0)
+       ("python-3" ,python)
+       ("python-numpy" ,python-numpy)))
+    (home-page "https://arrow.apache.org/")
+    (synopsis "Columnar in-memory analytics")
+    (description "Apache Arrow is a columnar in-memory analytics layer
+designed to accelerate big data. It houses a set of canonical in-memory
+representations of flat and hierarchical data along with multiple
+language-bindings for structure manipulation. It also provides IPC and common
+algorithm implementations.")
+    (license license:asl2.0)))
-- 
2.16.1

[bug#30570] [PATCH 15/16] gnu: Add python-pyarrow.

[Leo Famulari]

* gnu/packages/databases.scm (python-pyarrow, python2-pyarrow): New variables.
---
 gnu/packages/databases.scm | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 8de274ab2..d7d005f84 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2791,3 +2791,49 @@ representations of flat and hierarchical data along with multiple
 language-bindings for structure manipulation. It also provides IPC and common
 algorithm implementations.")
     (license license:asl2.0)))
+
+(define-public python-pyarrow
+  (package
+    (name "python-pyarrow")
+    (version "0.7.0")
+    (source
+      (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/apache/arrow")
+             (commit (string-append "apache-arrow-" version))))
+       (file-name (git-file-name name version))
+       (sha256
+         (base32
+           "1x7sdd8lbs3nfqjql1pcgbkjc19bls56zmgjayshkmablvlc4dy3"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:tests? #f ; XXX Test failures related to missing libhdfs, libhdfs3,
+                   ; and "Unsupported numpy type 22".
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-source-directory
+           (lambda _ (chdir "python") #t))
+         (add-after 'unpack 'set-env
+           (lambda _
+             (setenv "ARROW_HOME" (assoc-ref %build-inputs "apache-arrow"))
+             #t)))))
+    (propagated-inputs
+     `(("apache-arrow" ,apache-arrow)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-six" ,python-six)))
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)
+       ("python-setuptools-scm" ,python-setuptools-scm)))
+    (home-page "https://arrow.apache.org/docs/python/")
+    (synopsis "Python library for Apache Arrow")
+    (description "This library provides a Pythonic API wrapper for the reference
+Arrow C++ implementation, along with tools for interoperability with pandas,
+NumPy, and other traditional Python scientific computing packages.")
+    (license license:asl2.0)))
+
+(define-public python2-pyarrow
+  (package-with-python2 python-pyarrow))
-- 
2.16.1

[bug#30570] [PATCH 16/16] gnu: Add python-feather-format.

[Leo Famulari]

* gnu/packages/serialization.scm (python-feather-format,
python2-feather-format): New variables.
---
 gnu/packages/serialization.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 58ff2a1c0..761b8c353 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -41,6 +41,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages pkg-config)
@@ -460,3 +461,27 @@ game development and other performance-critical applications.")
     (description "Read and write feather files, a lightweight binary columnar
 daa store designed for maximum speed.")
     (license license:asl2.0)))
+
+(define-public python-feather-format
+  (package
+    (name "python-feather-format")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "feather-format" version))
+        (sha256
+         (base32
+          "1adivm5w5ji4qv7hq7942vqlk8l2wgw87bdlsia771z14z3zp857"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-pandas" ,python-pandas)
+       ("python-pyarrow" ,python-pyarrow)))
+    (home-page "https://github.com/wesm/feather")
+    (synopsis "Python wrapper to the Feather file format")
+    (description "This package provides a Python wrapper library to the
+Apache Arrow-based Feather binary columnar serialization data frame format.")
+    (license license:asl2.0)))
+
+(define-public python2-feather-format
+  (package-with-python2 python-feather-format))
-- 
2.16.1

[bug#30570] [PATCH 01/16] gnu: Add flatbuffers.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/serialization.scm (flatbuffers): New variable.

LGTM!

[bug#30570] [PATCH 02/16] gnu: Add python-plotly.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/graph.scm (python-plotly, python2-plotly): New variables.

LGTM.

[bug#30570] [PATCH 03/16] gnu: Add r-maps.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/geo.scm (r-maps): New variable.

LGTM.

[bug#30570] [PATCH 10/16] gnu: Add r-jpeg.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/image.scm (r-jpeg): New variable.

LGTM.

[bug#30570] [PATCH 07/16] gnu: Add r-subplex.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> gnu/packages/maths.scm (r-subplex): New variable.

[...]

> +    (synopsis "Unconstrained Optimization using the Subplex Algorithm")

Nitpick: no need to use title case here.  (The other R packages in this
series have the same issue it seems.)

Otherwise LGTM.

[bug#30570] [PATCH 08/16] gnu: Add r-desolve.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/maths.scm (r-desolve): New variable.

OK (modulo synopsis title case.)

[bug#30570] [PATCH 09/16] gnu: Add Diversitree.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/bioinformatics.scm (r-diversitree): New variable.

OK.

[bug#30570] [PATCH 11/16] gnu: Add r-ggmap.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/geo.scm (r-ggmap): New variable.

OK.

[bug#30570] [PATCH 05/16] gnu: Add Rgooglemaps.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/geo.scm (r-rgooglemaps): New variable.

OK.

[bug#30570] [PATCH 06/16] gnu: Add r-geosphere.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> *  gnu/packages/geo.scm (r-geosphere): New variable.

OK.

[bug#30570] [PATCH 04/16] gnu: Add r-mapproj.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/geo.scm (r-mapproj): New variable.

OK.

[bug#30570] [PATCH 13/16] gnu: Add google-brotli.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/compression.scm (google-brotli): New variable.

[...]

> +         (add-after 'install 'rename-static-libraries
> +           ;; The build tools put a 'static' suffix on the static libraries, but
> +           ;; other applications don't know how to find these.
> +           (let ((lib (string-append (assoc-ref %outputs "out") "/lib/")))
> +             (lambda _

Rather: (lambda (#:key outputs #:allow-other-keys)
          (let ((lib (string-append (assoc-ref outputs "out") "/lib/")))
            ...))

> +    (home-page "https://github.com/google/brotli")
> +    (synopsis "General-purpose lossless compression")
> +    (description "This package provides the reference implementation of Brotli,
> +a generic-purpose lossless compression algorithm that compresses data using a
> +combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd
> +order context modeling, with a compression ratio comparable to the best
> +currently available general-purpose compression methods. It is similar in speed
                                                           ^
Missing space.  :-)

Otherwise LGTM.

[bug#30570] [PATCH 14/16] gnu: Add apache-arrow.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/databases.scm (apache-arrow): New variable.

OK.

[bug#30570] [PATCH 15/16] gnu: Add python-pyarrow.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/databases.scm (python-pyarrow, python2-pyarrow): New variables.

[...]

> +    (home-page "https://arrow.apache.org/docs/python/")
> +    (synopsis "Python library for Apache Arrow")

s/library/bindings/?

LGTM.

[bug#30570] [PATCH 16/16] gnu: Add python-feather-format.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> * gnu/packages/serialization.scm (python-feather-format,
> python2-feather-format): New variables.

OK.

Thanks to Joshua/Nextjournal and to you for the whole series!  I assume
they’re aware you’re submitting it for inclusion, right?

Thanks,
Ludo’.

bug#30570: [PATCH 16/16] gnu: Add python-feather-format.

[Leo Famulari]

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On Sat, Mar 03, 2018 at 10:50:26PM +0100, Ludovic Courtès wrote:
> Leo Famulari <leo@famulari.name> skribis:
> 
> > * gnu/packages/serialization.scm (python-feather-format,
> > python2-feather-format): New variables.
> 
> OK.
> 
> Thanks to Joshua/Nextjournal and to you for the whole series!  I assume
> they’re aware you’re submitting it for inclusion, right?

Yes, of course!

Thanks for your review. I made the requested changes and pushed as
8d4f34d6c9667c82f1dc136f54954fb4ccef81b1.

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