[PATCH] gnu: Add r-limma.

[PATCH] gnu: Add r-limma.

[Roel Janssen]

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(+)

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")
-- 
2.7.4

Re: [PATCH] gnu: Add r-limma.

[Ricardo Wurmus]

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

Re: [PATCH] gnu: Add r-limma.

[Roel Janssen]

Dear Ricardo,

Thanks for your quick response.

Ricardo Wurmus writes:

> 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.

Ok.  I removed it from the second version of this patch.

>> +    (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.

Great, I adapted the text from the website.
Here's the new version of the patch:


From a56362450a085d0b5d2730c52f4fed9200a24fb9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 3 May 2016 12:22:50 +0200
Subject: [PATCH] gnu: Add r-limma.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 079fd46..d6da0ac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4171,6 +4171,26 @@ 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"))))
+    (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 can be used for the analysis of gene expression
+studies, especially the use of linear models for analysing designed experiments
+and the assessment of differential expression.  The analysis methods apply to
+many different technologies, including microarrays, RNA-seq, quantitative PCR
+and many protein technologies.")
+    (license license:gpl2+)))
+
 (define-public r-xvector
   (package
     (name "r-xvector")
-- 
2.7.4