diff mbox

gnu: Add r-limma.

Message ID 87mvo761cn.fsf@gnu.org
State Dropped
Headers show

Commit Message

Roel Janssen May 3, 2016, 7:35 a.m. UTC
Dear Guix,

I have two R packages I would like to add.  The other package 'r-edger'
depends on this one.  This is the first time I'm attempting an inline
patch, so I hope this works out well.

Kind regards,
Roel Janssen

>From 565fa10f9896e1143419b2a2c6496b91a135a930 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 3 May 2016 09:30:14 +0200
Subject: [PATCH] gnu: Add r-limma.

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

Comments

Ricardo Wurmus May 3, 2016, 9:31 a.m. UTC | #1
Roel Janssen <roel@gnu.org> writes:

> Dear Guix,
>
> I have two R packages I would like to add.  The other package 'r-edger'
> depends on this one.  This is the first time I'm attempting an inline
> patch, so I hope this works out well.

Thanks for the patch.  It worked!

>>From 565fa10f9896e1143419b2a2c6496b91a135a930 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Tue, 3 May 2016 09:30:14 +0200
> Subject: [PATCH] gnu: Add r-limma.
>
> * gnu/packages/bioinformatics.scm (r-limma): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 18 ++++++++++++++++++
>  1 file changed, 18 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 079fd46..3dfb55e 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -4171,6 +4171,24 @@ names in their natural, rather than lexicographic, order.")
>  coding changes and predict coding outcomes.")
>      (license license:artistic2.0)))
>  
> +(define-public r-limma
> +  (package
> +    (name "r-limma")
> +    (version "3.26.9")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (bioconductor-uri "limma" version))
> +              (sha256
> +               (base32
> +                "0mj72zsj1awjf3i2y9x8m7ih4sx9qrs1rlrck9l7mn5afxqsfrsm"))))
> +    (properties `((upstream-name . "limma")))

I don’t think we need this as the name is all lowercase, as expected.
We only set the “upstream-name” property when the name contains special
characters or uppercase letters.

> +    (build-system r-build-system)
> +    (home-page "http://bioinf.wehi.edu.au/limma")
> +    (synopsis "This package provides linear models for microarray data")
> +    (description "This package provides linear models and differential
> +expression for microarray data analysis.")

The description could be improved.  There’s a better description on the
home page.  You might be able to adapt it.

> +    (license license:gpl2+)))
> +
>  (define-public r-xvector
>    (package
>      (name "r-xvector")

~~ Ricardo
diff mbox

Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 079fd46..3dfb55e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4171,6 +4171,24 @@  names in their natural, rather than lexicographic, order.")
 coding changes and predict coding outcomes.")
     (license license:artistic2.0)))
 
+(define-public r-limma
+  (package
+    (name "r-limma")
+    (version "3.26.9")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "limma" version))
+              (sha256
+               (base32
+                "0mj72zsj1awjf3i2y9x8m7ih4sx9qrs1rlrck9l7mn5afxqsfrsm"))))
+    (properties `((upstream-name . "limma")))
+    (build-system r-build-system)
+    (home-page "http://bioinf.wehi.edu.au/limma")
+    (synopsis "This package provides linear models for microarray data")
+    (description "This package provides linear models and differential
+expression for microarray data analysis.")
+    (license license:gpl2+)))
+
 (define-public r-xvector
   (package
     (name "r-xvector")