[PATCH 09/19] gnu: Add r-markdown.

[PATCH 09/19] gnu: Add r-markdown.

[Vicente Vera]

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From 7e291c7f87498368be556941f6eb7315f94a7c74 Mon Sep 17 00:00:00 2001
From: Vicente Vera Parra <vicentemvp@gmail.com>
Date: Sun, 13 Sep 2015 13:17:39 -0300
Subject: [PATCH 09/19] gnu: Add r-markdown.

* gnu/packages/statistics.scm (r-markdown): 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 0019bbe..b3e9b2b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -657,3 +657,33 @@ package (http://www.andre-simon.de).")
      "Guesses the MIME type from a filename extension using the data
 derived from /etc/mime.types in UNIX-type systems.")
     (license license:gpl2)))
+
+(define-public r-markdown
+  (package
+    (name "r-markdown")
+    (version "0.7.7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://cran/src/contrib/markdown_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32 "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb"))))
+    (build-system r-build-system)
+    ;; Skip check phase because the tests require knitr to be
+    ;; installed. Since it won't (markdown is a dependency of the knitr
+    ;; package), installation will fail.
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'check))))
+    (propagated-inputs
+     `(("r-mime" ,r-mime)))
+    (home-page "https://github.com/rstudio/markdown")
+    (synopsis "'Markdown' Rendering for R")
+    (description
+     "Provides R bindings to the 'Sundown' 'Markdown' rendering
+library (https://github.com/vmg/sundown). 'Markdown' is a plain-text
+formatting syntax that can be converted to 'XHTML' or other formats.
+See http://en.wikipedia.org/wiki/Markdown for more information about
+'Markdown'.")
+    (license license:gpl2)))
-- 
2.5.1

Re: [PATCH 09/19] gnu: Add r-markdown.

[Ricardo Wurmus]

> From 7e291c7f87498368be556941f6eb7315f94a7c74 Mon Sep 17 00:00:00 2001
> From: Vicente Vera Parra <vicentemvp@gmail.com>
> Date: Sun, 13 Sep 2015 13:17:39 -0300
> Subject: [PATCH 09/19] gnu: Add r-markdown.

> * gnu/packages/statistics.scm (r-markdown): New variable.

[...]

> +    ;; Skip check phase because the tests require knitr to be
> +    ;; installed. Since it won't (markdown is a dependency of the knitr
> +    ;; package), installation will fail.
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (delete 'check))))

Two things: 1) the comment isn’t very clear.  “Since it won’t” what?  Maybe
you can rephrase.  2) Instead of deleting the “check” phase just write

    (arguments `(#:tests? #f))

> +    (propagated-inputs
> +     `(("r-mime" ,r-mime)))
> +    (home-page "https://github.com/rstudio/markdown")
> +    (synopsis "'Markdown' Rendering for R")

Quoting “Markdown” looks odd.  How about just

    “Markdown rendering library for R”

> +    (description
> +     "Provides R bindings to the 'Sundown' 'Markdown' rendering
> +library (https://github.com/vmg/sundown). 'Markdown' is a plain-text
> +formatting syntax that can be converted to 'XHTML' or other formats.
> +See http://en.wikipedia.org/wiki/Markdown for more information about
> +'Markdown'.")

The quoting looks very odd.  Does this mean that “Sundown” must be
available at runtime in order to use the “r-markdown” package?  If this
is so, shouldn’t a “sundown” package be among the inputs of this
package?

> +    (license license:gpl2)))

This appears to be correct.  The license headers of the files in the “R”
directory only explicitly mention “version 2”, there is no “or later”
clause.  I just wonder what this means for libraries using
“r-markdown”, such as “r-knitr”, which according to your next patch is
supposedly released under “GPLv3+”.  IIUC this cannot be the case.

~~ Ricardo

Re: [PATCH 09/19] gnu: Add r-markdown.

[Vicente Vera]

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Hello Ricardo,

Both the code and the comment related to the check phase were changed.
Indeed, the comment was pretty much unreadable. Hope the new one is
better.

New patch attached.

2015-09-14 8:10 GMT-03:00 Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>:
>
>> From 7e291c7f87498368be556941f6eb7315f94a7c74 Mon Sep 17 00:00:00 2001
>> From: Vicente Vera Parra <vicentemvp@gmail.com>
>> Date: Sun, 13 Sep 2015 13:17:39 -0300
>> Subject: [PATCH 09/19] gnu: Add r-markdown.
>
>> * gnu/packages/statistics.scm (r-markdown): New variable.
>
> [...]
>
>> +    ;; Skip check phase because the tests require knitr to be
>> +    ;; installed. Since it won't (markdown is a dependency of the knitr
>> +    ;; package), installation will fail.
>> +    (arguments
>> +     `(#:phases
>> +       (modify-phases %standard-phases
>> +         (delete 'check))))
>
> Two things: 1) the comment isn’t very clear.  “Since it won’t” what?  Maybe
> you can rephrase.  2) Instead of deleting the “check” phase just write
>
>     (arguments `(#:tests? #f))
>
>> +    (propagated-inputs
>> +     `(("r-mime" ,r-mime)))
>> +    (home-page "https://github.com/rstudio/markdown")
>> +    (synopsis "'Markdown' Rendering for R")
>
> Quoting “Markdown” looks odd.  How about just
>
>     “Markdown rendering library for R”
>
>> +    (description
>> +     "Provides R bindings to the 'Sundown' 'Markdown' rendering
>> +library (https://github.com/vmg/sundown). 'Markdown' is a plain-text
>> +formatting syntax that can be converted to 'XHTML' or other formats.
>> +See http://en.wikipedia.org/wiki/Markdown for more information about
>> +'Markdown'.")
>
> The quoting looks very odd.  Does this mean that “Sundown” must be
> available at runtime in order to use the “r-markdown” package?  If this
> is so, shouldn’t a “sundown” package be among the inputs of this
> package?
>
>> +    (license license:gpl2)))
>
> This appears to be correct.  The license headers of the files in the “R”
> directory only explicitly mention “version 2”, there is no “or later”
> clause.  I just wonder what this means for libraries using
> “r-markdown”, such as “r-knitr”, which according to your next patch is
> supposedly released under “GPLv3+”.  IIUC this cannot be the case.
>
> ~~ Ricardo

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From 8dd6af01cb39879ac1e5eaa01abde922f9cc7008 Mon Sep 17 00:00:00 2001
From: Vicente Vera Parra <vicentemvp@gmail.com>
Date: Mon, 14 Sep 2015 15:50:26 -0300
Subject: [PATCH 09/12] gnu: Add r-markdown.

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5ce03f4..588fd62 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -655,3 +655,30 @@ via Andre Simon's highlight package (http://www.andre-simon.de).")
      "This package guesses the MIME type from a filename extension using the
 data derived from /etc/mime.types in UNIX-type systems.")
     (license license:gpl2)))
+
+(define-public r-markdown
+  (package
+    (name "r-markdown")
+    (version "0.7.7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://cran/src/contrib/markdown_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32 "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb"))))
+    (build-system r-build-system)
+    ;; Skip check phase because the tests require the r-knitr package to be
+    ;; installed. This prevents installation failures. Knitr normally
+    ;; shouldn't be available since r-markdown is a dependency of the r-knitr
+    ;; package.
+    (arguments `(#:tests? #f))
+    (propagated-inputs
+     `(("r-mime" ,r-mime)))
+    (home-page "https://github.com/rstudio/markdown")
+    (synopsis "Markdown rendering for R")
+    (description
+     "This package provides R bindings to the Sundown Markdown rendering
+library (https://github.com/vmg/sundown).  Markdown is a plain-text formatting
+syntax that can be converted to XHTML or other formats.  See
+http://en.wikipedia.org/wiki/Markdown for more information about Markdown.")
+    (license license:gpl2)))
-- 
2.5.2

Re: [PATCH 09/19] gnu: Add r-markdown.

[Vicente Vera]

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Updated patch attached.

2015-09-14 16:59 GMT-03:00 Vicente Vera <vicentemvp@gmail.com>:
> Hello Ricardo,
>
> Both the code and the comment related to the check phase were changed.
> Indeed, the comment was pretty much unreadable. Hope the new one is
> better.
>
> New patch attached.
>
> 2015-09-14 8:10 GMT-03:00 Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>:
>>
>>> From 7e291c7f87498368be556941f6eb7315f94a7c74 Mon Sep 17 00:00:00 2001
>>> From: Vicente Vera Parra <vicentemvp@gmail.com>
>>> Date: Sun, 13 Sep 2015 13:17:39 -0300
>>> Subject: [PATCH 09/19] gnu: Add r-markdown.
>>
>>> * gnu/packages/statistics.scm (r-markdown): New variable.
>>
>> [...]
>>
>>> +    ;; Skip check phase because the tests require knitr to be
>>> +    ;; installed. Since it won't (markdown is a dependency of the knitr
>>> +    ;; package), installation will fail.
>>> +    (arguments
>>> +     `(#:phases
>>> +       (modify-phases %standard-phases
>>> +         (delete 'check))))
>>
>> Two things: 1) the comment isn’t very clear.  “Since it won’t” what?  Maybe
>> you can rephrase.  2) Instead of deleting the “check” phase just write
>>
>>     (arguments `(#:tests? #f))
>>
>>> +    (propagated-inputs
>>> +     `(("r-mime" ,r-mime)))
>>> +    (home-page "https://github.com/rstudio/markdown")
>>> +    (synopsis "'Markdown' Rendering for R")
>>
>> Quoting “Markdown” looks odd.  How about just
>>
>>     “Markdown rendering library for R”
>>
>>> +    (description
>>> +     "Provides R bindings to the 'Sundown' 'Markdown' rendering
>>> +library (https://github.com/vmg/sundown). 'Markdown' is a plain-text
>>> +formatting syntax that can be converted to 'XHTML' or other formats.
>>> +See http://en.wikipedia.org/wiki/Markdown for more information about
>>> +'Markdown'.")
>>
>> The quoting looks very odd.  Does this mean that “Sundown” must be
>> available at runtime in order to use the “r-markdown” package?  If this
>> is so, shouldn’t a “sundown” package be among the inputs of this
>> package?
>>
>>> +    (license license:gpl2)))
>>
>> This appears to be correct.  The license headers of the files in the “R”
>> directory only explicitly mention “version 2”, there is no “or later”
>> clause.  I just wonder what this means for libraries using
>> “r-markdown”, such as “r-knitr”, which according to your next patch is
>> supposedly released under “GPLv3+”.  IIUC this cannot be the case.
>>
>> ~~ Ricardo

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From 86ac946c2146919ad9f74cf5220609da009c30a9 Mon Sep 17 00:00:00 2001
From: Vicente Vera Parra <vicentemvp@gmail.com>
Date: Tue, 15 Sep 2015 14:18:58 -0300
Subject: [PATCH 09/19] gnu: Add r-markdown.

* gnu/packages/statistics.scm (r-markdown): 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 a1c2bff..4b4e839 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -680,3 +680,33 @@ via Andre Simon's highlight package (http://www.andre-simon.de).")
      "This package guesses the MIME type from a filename extension using the
 data derived from /etc/mime.types in UNIX-type systems.")
     (license license:gpl2)))
+
+(define-public r-markdown
+  (package
+    (name "r-markdown")
+    (version "0.7.7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://cran/src/contrib/markdown_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb"))))
+    (build-system r-build-system)
+    ;; Skip check phase because the tests require the r-knitr package to be
+    ;; installed. This prevents installation failures. Knitr normally
+    ;; shouldn't be available since r-markdown is a dependency of the r-knitr
+    ;; package.
+    (arguments `(#:tests? #f))
+    (propagated-inputs
+     `(("r-mime" ,r-mime)))
+    (home-page
+     "https://github.com/rstudio/markdown")
+    (synopsis
+     "Markdown rendering for R")
+    (description
+     "This package provides R bindings to the Sundown Markdown rendering
+library (https://github.com/vmg/sundown).  Markdown is a plain-text formatting
+syntax that can be converted to XHTML or other formats.  See
+http://en.wikipedia.org/wiki/Markdown for more information about Markdown.")
+    (license license:gpl2)))
-- 
2.5.2