[PATCH] Add Rmarkdown.

[PATCH] Add Rmarkdown.

[Ricardo Wurmus]

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These three patches add Rmarkdown and dependencies.

The last patch that adds the “r-rmarkdown” package also changes the
import of “(gnu packages xml)” in haskell.scm to be less specific.  The
“#:select” phrase triggered an error due to circular package module
dependencies.  I hope it’s okay to put these two things in the same
patch?


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From 88bfcae0b05ef504455fe6ad3aca98d845d6dea4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 15 Dec 2015 12:11:02 +0100
Subject: [PATCH 1/3] gnu: Add r-bitops.

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0ffd495..e7d6ca4 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1342,3 +1342,22 @@ 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+)))
+
+(define-public r-bitops
+  (package
+    (name "r-bitops")
+    (version "1.0-6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "bitops" version))
+              (sha256
+               (base32
+                "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/bitops")
+    (synopsis "Bitwise operations")
+    (description
+     "This package provides functions for bitwise operations on integer
+vectors.")
+    (license license:gpl2+)))
+
-- 
2.1.0


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From 06c0b4ed3e046b033b71eaf26ff69198eebeeb08 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 15 Dec 2015 12:11:39 +0100
Subject: [PATCH 2/3] gnu: Add r-catools.

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e7d6ca4..d0cbb01 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1361,3 +1361,26 @@ also flexible enough to handle most nonstandard requirements.")
 vectors.")
     (license license:gpl2+)))
 
+(define-public r-catools
+  (package
+    (name "r-catools")
+    (version "1.17.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "caTools" version))
+              (sha256
+               (base32
+                "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
+    (properties `((upstream-name . "caTools")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bitops" ,r-bitops)))
+    (home-page "http://cran.r-project.org/web/packages/caTools")
+    (synopsis "Various tools including functions for moving window statistics")
+    (description
+     "This package contains several basic utility functions including:
+moving (rolling, running) window statistic functions, read/write for GIF and
+ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
+encoder/decoder, round-off-error-free sum and cumsum, etc.")
+    (license license:gpl3+)))
+
-- 
2.1.0


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From 9dd97f3c9d09d7eea05cb2e3046ae71e3d4712c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 15 Dec 2015 12:14:01 +0100
Subject: [PATCH 3/3] gnu: Add r-rmarkdown.

* gnu/packages/statistics.scm (r-rmarkdown): New variable.
* gnu/packages/haskell.scm: Do not select libxml2 from the xml module to
  prevent circular package module imports.
---
 gnu/packages/haskell.scm    |  2 +-
 gnu/packages/statistics.scm | 27 +++++++++++++++++++++++++++
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 277bdeb..a193e96 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -47,7 +47,7 @@
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages python)
   #:use-module (gnu packages pcre)
-  #:use-module ((gnu packages xml) #:select (libxml2))
+  #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg))
 
 (define ghc-bootstrap-x86_64-7.8.4
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d0cbb01..95176aa 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -29,6 +29,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages haskell)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages java)
@@ -1384,3 +1385,29 @@ ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
 encoder/decoder, round-off-error-free sum and cumsum, etc.")
     (license license:gpl3+)))
 
+(define-public r-rmarkdown
+  (package
+    (name "r-rmarkdown")
+    (version "0.8.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "rmarkdown" version))
+        (sha256
+          (base32
+            "07q5g9dvac5j3vnf4sjc60mnkij1k6y7vnzjz6anf499rwdwbxza"))))
+    (properties `((upstream-name . "rmarkdown")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-catools" ,r-catools)
+       ("r-htmltools" ,r-htmltools)
+       ("r-knitr" ,r-knitr)
+       ("r-yaml" ,r-yaml)
+       ("ghc-pandoc" ,ghc-pandoc)))
+    (home-page "http://rmarkdown.rstudio.com")
+    (synopsis "Convert R Markdown documents into a variety of formats")
+    (description
+     "This package provides tools to convert R Markdown documents into a
+variety of formats.")
+    (license license:gpl3+)))
+
-- 
2.1.0

Re: [PATCH] Add Rmarkdown.

[Ricardo Wurmus]

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

> These three patches add Rmarkdown and dependencies.
>
> The last patch that adds the “r-rmarkdown” package also changes the
> import of “(gnu packages xml)” in haskell.scm to be less specific.  The
> “#:select” phrase triggered an error due to circular package module
> dependencies.  I hope it’s okay to put these two things in the same
> patch?

I’d like to push these three patches in the next couple of hours.  Do
you have any objections?

~~ Ricardo