[PATCH 3/7] gnu: Add r-biocviews.

[PATCH 3/7] gnu: Add r-biocviews.

[Roel Janssen]

* gnu/packages/bioinformatics.scm (r-biocviews): New variable.
---
 gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3d607cc..fa32075 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5333,6 +5333,34 @@ CRAN, and (some) github packages.")
 the graph algorithms contained in the Boost library.")
     (license license:artistic2.0)))
 
+(define-public r-biocviews
+  (package
+    (name "r-biocviews")
+    (version "1.40.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "biocViews" version))
+              (sha256
+               (base32
+                "1d1g06zwx3xhc07mdhs5x31730xw08fg3x73xyfj0qdy2ykww3f9"))))
+    (properties
+     `((upstream-name . "biocViews")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-graph" ,r-graph)
+       ("r-rbgl" ,r-rbgl)
+       ("r-rcurl" ,r-rcurl)
+       ("r-xml" ,r-xml)
+       ("r-knitr" ,r-knitr)
+       ("r-runit" ,r-runit)))
+    (home-page "http://bioconductor.org/packages/Biocviews")
+    (synopsis "Bioconductor structures for vocabularies and narratives of 
+views")
+    (description "This package provides structures for vocabularies and
+narratives of views for Bioconductor packages.")
+    (license license:artistic2.0)))
+
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-- 
2.10.0

Re: [PATCH 3/7] gnu: Add r-biocviews.

[Ricardo Wurmus]

Roel Janssen <roel@gnu.org> writes:

> * gnu/packages/bioinformatics.scm (r-biocviews): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
>  1 file changed, 28 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 3d607cc..fa32075 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -5333,6 +5333,34 @@ CRAN, and (some) github packages.")
>  the graph algorithms contained in the Boost library.")
>      (license license:artistic2.0)))
>  
> +(define-public r-biocviews
> +  (package
> +    (name "r-biocviews")
> +    (version "1.40.1")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (bioconductor-uri "biocViews" version))
> +              (sha256
> +               (base32
> +                "1d1g06zwx3xhc07mdhs5x31730xw08fg3x73xyfj0qdy2ykww3f9"))))
> +    (properties
> +     `((upstream-name . "biocViews")))
> +    (build-system r-build-system)
> +    (propagated-inputs
> +     `(("r-biobase" ,r-biobase)
> +       ("r-graph" ,r-graph)
> +       ("r-rbgl" ,r-rbgl)
> +       ("r-rcurl" ,r-rcurl)
> +       ("r-xml" ,r-xml)
> +       ("r-knitr" ,r-knitr)
> +       ("r-runit" ,r-runit)))
> +    (home-page "http://bioconductor.org/packages/Biocviews")
> +    (synopsis "Bioconductor structures for vocabularies and narratives of 
> +views")

I don’t know what this means.  Does this mean “data structures”?  What
is a vocabulary or narrative in this case?

~~ Ricardo

Re: [PATCH 3/7] gnu: Add r-biocviews.

[Roel Janssen]

Ricardo Wurmus writes:

> Roel Janssen <roel@gnu.org> writes:
>
>> * gnu/packages/bioinformatics.scm (r-biocviews): New variable.
>> ---
>>  gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
>>  1 file changed, 28 insertions(+)
>>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 3d607cc..fa32075 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -5333,6 +5333,34 @@ CRAN, and (some) github packages.")
>>  the graph algorithms contained in the Boost library.")
>>      (license license:artistic2.0)))
>>  
>> +(define-public r-biocviews
>> +  (package
>> +    (name "r-biocviews")
>> +    (version "1.40.1")
>> +    (source (origin
>> +              (method url-fetch)
>> +              (uri (bioconductor-uri "biocViews" version))
>> +              (sha256
>> +               (base32
>> +                "1d1g06zwx3xhc07mdhs5x31730xw08fg3x73xyfj0qdy2ykww3f9"))))
>> +    (properties
>> +     `((upstream-name . "biocViews")))
>> +    (build-system r-build-system)
>> +    (propagated-inputs
>> +     `(("r-biobase" ,r-biobase)
>> +       ("r-graph" ,r-graph)
>> +       ("r-rbgl" ,r-rbgl)
>> +       ("r-rcurl" ,r-rcurl)
>> +       ("r-xml" ,r-xml)
>> +       ("r-knitr" ,r-knitr)
>> +       ("r-runit" ,r-runit)))
>> +    (home-page "http://bioconductor.org/packages/Biocviews")
>> +    (synopsis "Bioconductor structures for vocabularies and narratives of 
>> +views")
>
> I don’t know what this means.  Does this mean “data structures”?  What
> is a vocabulary or narrative in this case?

No, it means a structured way of describing things by keywords.  It is
an attempt at standardizing meta data to create a search function.  A
vocabulary is a stricter set of words to use for a purpose.  So, package
maintainers should use existing keywords when they reasonably fit
instead of creating new keywords who's meaning is almost identical to an
existing keyword.

Would the following synopsis and description be good?

>    (synopsis "Bioconductor package categorization helper")
>    (description "The purpose of biocViews is to create HTML pages that
> categorize packages in a Bioconductor package repository according to keywords,
> also known as views, in a controlled vocabulary.")

Thanks for your effort and time.

Kind regards,
Roel Janssen

Re: [PATCH 3/7] gnu: Add r-biocviews.

[Ricardo Wurmus]

Roel Janssen <roel@gnu.org> writes:

>>> +    (synopsis "Bioconductor structures for vocabularies and narratives of 
>>> +views")
>>
>> I don’t know what this means.  Does this mean “data structures”?  What
>> is a vocabulary or narrative in this case?
>
> No, it means a structured way of describing things by keywords.  It is
> an attempt at standardizing meta data to create a search function.  A
> vocabulary is a stricter set of words to use for a purpose.  So, package
> maintainers should use existing keywords when they reasonably fit
> instead of creating new keywords who's meaning is almost identical to an
> existing keyword.

Thanks for the explanation!

> Would the following synopsis and description be good?
>
>>    (synopsis "Bioconductor package categorization helper")
>>    (description "The purpose of biocViews is to create HTML pages that
>> categorize packages in a Bioconductor package repository according to keywords,
>> also known as views, in a controlled vocabulary.")

Yes, that’s much better.  Thank you!

~~ Ricardo

Re: [PATCH 3/7] gnu: Add r-biocviews.

[Roel Janssen]

Ricardo Wurmus writes:

> Roel Janssen <roel@gnu.org> writes:
>
>>>> +    (synopsis "Bioconductor structures for vocabularies and narratives of 
>>>> +views")
>>>
>>> I don’t know what this means.  Does this mean “data structures”?  What
>>> is a vocabulary or narrative in this case?
>>
>> No, it means a structured way of describing things by keywords.  It is
>> an attempt at standardizing meta data to create a search function.  A
>> vocabulary is a stricter set of words to use for a purpose.  So, package
>> maintainers should use existing keywords when they reasonably fit
>> instead of creating new keywords who's meaning is almost identical to an
>> existing keyword.
>
> Thanks for the explanation!
>
>> Would the following synopsis and description be good?
>>
>>>    (synopsis "Bioconductor package categorization helper")
>>>    (description "The purpose of biocViews is to create HTML pages that
>>> categorize packages in a Bioconductor package repository according to keywords,
>>> also known as views, in a controlled vocabulary.")
>
> Yes, that’s much better.  Thank you!

Thanks for the quick response!  I pushed it with these changes.

Kind regards,
Roel Janssen