[PATCH]: Five R packages.

[PATCH]: Five R packages.

[Ricardo Wurmus]

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From 9b319907000ad6b1796d1887cabcf010aa806d3e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 26 Nov 2015 16:59:08 +0100
Subject: [PATCH 1/5] gnu: Add r-data-table.

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 2af9de2..876a2b3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1264,3 +1264,25 @@ informative error messages when it's not available.")
     (description "The devtools package is a collection of package development
 tools to simplify the devolpment of R packages.")
     (license license:gpl2+)))
+
+(define-public r-data-table
+  (package
+    (name "r-data-table")
+    (version "1.9.6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "data.table" version))
+              (sha256
+               (base32
+                "0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-chron" ,r-chron)))
+    (home-page "https://github.com/Rdatatable/data.table/wiki")
+    (synopsis "Extension of data.frame")
+    (description
+     "@code{data.table} is an extension of @code{data.frame} providing fast
+aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast
+add/modify/delete of columns by group using no copies at all, list columns and
+a fast file reader (@code{fread}).")
+    (license license:gpl3+)))
-- 
2.1.0


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From a4d9def0f63e42d90517845b9013bb6a560a0b49 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 26 Nov 2015 16:59:29 +0100
Subject: [PATCH 2/5] gnu: Add r-readr.

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 876a2b3..0d8eb08 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1286,3 +1286,25 @@ aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast
 add/modify/delete of columns by group using no copies at all, list columns and
 a fast file reader (@code{fread}).")
     (license license:gpl3+)))
+
+(define-public r-readr
+  (package
+    (name "r-readr")
+    (version "0.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "readr" version))
+              (sha256
+               (base32
+                "156422xwvskynna5kjc8h1qqnn50kxgjrihl2h2b7vm9sxxdyr2m"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-curl" ,r-curl)
+       ("r-rcpp" ,r-rcpp)
+       ("r-bh" ,r-bh)))
+    (home-page "https://github.com/hadley/readr")
+    (synopsis "Read tabular data")
+    (description
+     "This package provides functions to read flat or tabular text files from
+disk (or a connection).")
+    (license license:gpl2+)))
-- 
2.1.0


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From 02e8f968f332a7be6da13bab7f0c4d96d828ade1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 26 Nov 2015 16:59:49 +0100
Subject: [PATCH 3/5] gnu: Add r-plotrix.

* gnu/packages/statistics.scm (r-plotrix): New variable.
---
 gnu/packages/statistics.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0d8eb08..b84e3f0 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1308,3 +1308,21 @@ a fast file reader (@code{fread}).")
      "This package provides functions to read flat or tabular text files from
 disk (or a connection).")
     (license license:gpl2+)))
+
+(define-public r-plotrix
+  (package
+    (name "r-plotrix")
+    (version "3.6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "plotrix" version))
+              (sha256
+               (base32
+                "0zn6k8azh40v0lg7q9yd4sy30a26bcc0fjvndn4z7k36avlw4i25"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/plotrix")
+    (synopsis "Various plotting functions")
+    (description
+     "This package provides lots of plotting, various labeling, axis and color
+scaling functions for R.")
+    (license license:gpl2+)))
-- 
2.1.0


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From d9e02e7197db16460c513b7ccc1155d85df7198e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 26 Nov 2015 17:00:08 +0100
Subject: [PATCH 4/5] gnu: Add r-gridbase.

* gnu/packages/statistics.scm (r-gridbase): New variable.
---
 gnu/packages/statistics.scm | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b84e3f0..279ae64 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1326,3 +1326,20 @@ disk (or a connection).")
      "This package provides lots of plotting, various labeling, axis and color
 scaling functions for R.")
     (license license:gpl2+)))
+
+(define-public r-gridbase
+  (package
+    (name "r-gridbase")
+    (version "0.4-7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "gridBase" version))
+              (sha256
+               (base32
+                "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/gridBase")
+    (synopsis "Integration of base and grid graphics")
+    (description
+     "This package provides an integration of base and grid graphics for R.")
+    (license license:gpl2+)))
-- 
2.1.0


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From 0e6557d12cba8e25aad9789b3fb4c454ce16c244 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 26 Nov 2015 17:00:26 +0100
Subject: [PATCH 5/5] gnu: Add r-lattice.

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 279ae64..0a4bd62 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1343,3 +1343,23 @@ scaling functions for R.")
     (description
      "This package provides an integration of base and grid graphics for R.")
     (license license:gpl2+)))
+
+(define-public r-lattice
+  (package
+    (name "r-lattice")
+    (version "0.20-33")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "lattice" version))
+              (sha256
+               (base32
+                "0car12x5vl9k180i9pc86lq3cvwqakdpqn3lgdf98k9n2h52cilg"))))
+    (build-system r-build-system)
+    (home-page "http://lattice.r-forge.r-project.org/")
+    (synopsis "High-level data visualization system")
+    (description
+     "The lattice package provides a powerful and elegant high-level data
+visualization system inspired by Trellis graphics, with an emphasis on
+multivariate data.  Lattice is sufficient for typical graphics needs, and is
+also flexible enough to handle most nonstandard requirements.")
+    (license license:gpl2+)))
-- 
2.1.0

Re: [PATCH]: Five R packages.

[Kyle Meyer]

Hello,

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

> From 9b319907000ad6b1796d1887cabcf010aa806d3e Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 26 Nov 2015 16:59:08 +0100
> Subject: [PATCH 1/5] gnu: Add r-data-table.
>
> * gnu/packages/statistics.scm (r-data-table): New variable.

It seems data.table was already packaged under a different name in
0e4e03f (2015-09-26).

> From 0e6557d12cba8e25aad9789b3fb4c454ce16c244 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 26 Nov 2015 17:00:26 +0100
> Subject: [PATCH 5/5] gnu: Add r-lattice.
>
> * gnu/packages/statistics.scm (r-lattice): New variable.

Isn't lattice already included with the main R build as a recommended
package?

-- 
Kyle

Re: [PATCH]: Five R packages.

[Ricardo Wurmus]

Hi Kyle,

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> From 9b319907000ad6b1796d1887cabcf010aa806d3e Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Thu, 26 Nov 2015 16:59:08 +0100
>> Subject: [PATCH 1/5] gnu: Add r-data-table.
>>
>> * gnu/packages/statistics.scm (r-data-table): New variable.
>
> It seems data.table was already packaged under a different name in
> 0e4e03f (2015-09-26).

You are right!  I should update “r-data.table” because the license
seems to be GPL3+ not GPL2+.  

>> From 0e6557d12cba8e25aad9789b3fb4c454ce16c244 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Thu, 26 Nov 2015 17:00:26 +0100
>> Subject: [PATCH 5/5] gnu: Add r-lattice.
>>
>> * gnu/packages/statistics.scm (r-lattice): New variable.
>
> Isn't lattice already included with the main R build as a recommended
> package?

You’re right again.

Is there ever a reason to upgrade the included recommended packages?  I
know that when installing some bioconductor packages R asks whether to
upgrade some included packages, such as MASS.  I’m not sure if it makes
sense to offer separate packages for the latest versions of these
modules.

What do you think?  I’m not much of an R-user myself.

~~ Ricardo

Re: [PATCH]: Five R packages.

[Kyle Meyer]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

>> Isn't lattice already included with the main R build as a recommended
>> package?
>
> You’re right again.
>
> Is there ever a reason to upgrade the included recommended packages?  I
> know that when installing some bioconductor packages R asks whether to
> upgrade some included packages, such as MASS.  I’m not sure if it makes
> sense to offer separate packages for the latest versions of these
> modules.
>
> What do you think?  I’m not much of an R-user myself.

Hmm... I also don't spend much time in R.  I'd guess that the
recommended packages are quite stable, so the only advantage I see of
running a version of a package newer than the one included with R is
that you get rid of the prompt when using install.packages or
bioconductor.  I've always answered no to these prompts and haven't
noticed any issues (but my use of R is fairly limited, so that may not
be worth much).

In any case, I don't see these prompts as much of an issue because I'd
prefer to just use Guix for all R packages.  Why not manage bioconductor
packages with Guix as well?

-- 
Kyle

Re: [PATCH]: Five R packages.

[Ricardo Wurmus]

Kyle Meyer <kyle@kyleam.com> writes:

> In any case, I don't see these prompts as much of an issue because I'd
> prefer to just use Guix for all R packages.  Why not manage bioconductor
> packages with Guix as well?

I’m working on it already.  Currently, we cannot easily import
bioconductor packages, but I’m planning to rewrite the CRAN importer
such that it works on the DESCRIPTION file in the tarball rather than
the CRAN HTML page.  Once that’s done I’ll try to package much of
bioconductor 3.2 for Guix.

~~ Ricardo

Re: [PATCH]: Five R packages.

[Kyle Meyer]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

> Kyle Meyer <kyle@kyleam.com> writes:
>
>> In any case, I don't see these prompts as much of an issue because I'd
>> prefer to just use Guix for all R packages.  Why not manage bioconductor
>> packages with Guix as well?
>
> I’m working on it already.  Currently, we cannot easily import
> bioconductor packages, but I’m planning to rewrite the CRAN importer
> such that it works on the DESCRIPTION file in the tarball rather than
> the CRAN HTML page.  Once that’s done I’ll try to package much of
> bioconductor 3.2 for Guix.

That's great.  Thank you!

--
Kyle

Re: [PATCH]: Five R packages.

[Andreas Enge]

On Thu, Nov 26, 2015 at 04:46:40PM -0500, Kyle Meyer wrote:
> > * gnu/packages/statistics.scm (r-data-table): New variable.
> It seems data.table was already packaged under a different name in
> 0e4e03f (2015-09-26).

Normally we replace non-alphanumeric characters by "-". So the new name
would be the correct one. If you could modify the package, that would
be nice.

Andreas

Re: [PATCH]: Five R packages.

[Ricardo Wurmus]

Andreas Enge <andreas@enge.fr> writes:

> On Thu, Nov 26, 2015 at 04:46:40PM -0500, Kyle Meyer wrote:
>> > * gnu/packages/statistics.scm (r-data-table): New variable.
>> It seems data.table was already packaged under a different name in
>> 0e4e03f (2015-09-26).
>
> Normally we replace non-alphanumeric characters by "-". So the new name
> would be the correct one. If you could modify the package, that would
> be nice.

I have renamed the package and updated the description and license
(gpl3+ rather than gpl2+).

I also pushed the other packages; this includes “r-lattice”, which a
user may want to update even though it’s one of the default packages
coming with R.

~~ Ricardo