[Bioc-devel] Bioconductor code search (beta)

[Hervé Pagès]

On 06/06/2012 07:13 AM, Michael Lawrence wrote:
> Hi Itoshi,
>
> This is a cool idea. I'm wondering if it would be easier to implement if
> you just used the R parser to do the tokenization. A Lucene analyzer for R
> code would be generally useful.
>
> Does anyone know if there are tools similar to "sonar" for Java that
> produce code quality metrics, etc? That would be fun to run over
> Bioconductor.

See the Ohloh fiasco for tools that produce code quality metrics:

   http://www.ohloh.net/p/6293

Maybe they've run the tool on itself and it produced fantastic
results but...

OK maybe it's more challenging with code written in R than with code
written in another language. There doesn't even seem to be a consensual
well established good programming style in R. Naming of
functions/arguments/classes/variables, indentation, format
and location of comments, etc, is a big zoo with lots of exotic
species. Let alone a consensual well established good programming
style for code that makes heavy use of the S4 class system.

H.

>
> Michael
>
> On Tue, Jun 5, 2012 at 11:06 AM, Itoshi NIKAIDO<dritoshi at gmail.com>  wrote:
>
>> Hi Martin
>>
>> Thank you for your quick response. Now, i am improving a tokenizer
>> to optimize index of database.
>>
>> Itoshi
>>
>> Itoshi NIKAIDO, Ph.D.
>> FF20 8296 ED6F D9E5 7D05  8A0F 65D8 C2F5 C8D7 2CE2
>>
>>
>> On Wed, Jun 6, 2012 at 2:36 AM, Martin Morgan<mtmorgan at fhcrc.org>  wrote:
>>> On 6/5/2012 10:33 AM, Itoshi NIKAIDO wrote:
>>>>
>>>> Dear bioconductor developers
>>>>
>>>> I'm Itoshi Nikaido, developer of BrainStars package and maintainer of
>>>> Japan mirror of Bioconductor.
>>>>
>>>> http://www.bioconductor.org/packages/release/bioc/html/BrainStars.html
>>>> http://bioconductor.jp/
>>>>
>>>> Today, I am happy to announce of opening a full code search engine for
>>>> all bioconductor package (only devel version).  The site has following
>>>> features:
>>>>
>>>> - fast full text search
>>>> - code highlighting
>>>> - facet search by package name
>>>>
>>>> This site is beta version. I have some plans to improve and add
>> functions.
>>>>
>>>> - Optimization of tokenizer
>>>> - Query keyword highlighting
>>>> - Linking to official SVN site in each code
>>>> - Permalink have to be change nonsense code id to package file path
>>>>
>>>> and so on.
>>>>
>>>> Bioconductor Code Search
>>>> http://search.bioconductor.jp/
>>>>
>>>> If you have idea for improving the site, Please comment to me.
>>>
>>>
>>> neat; I searched for
>>>
>>> trimLRPatterns
>>>
>>> and got hits in ShortRead but not Biostrings (where it is defined).
>>>
>>> Martin
>>>>
>>>>
>>>> Thanks
>>>>
>>>> --
>>>> Itoshi NIKAIDO, Ph.D.
>>>> RIKEN Center for Developmental Biology
>>>> D-E203, 2-2-3, Minatojima-minamimachi, Chuo-ku,
>>>> Kobe, Hyogo 650-0047, Japan
>>>> http://www.hackingisbelieving.org/
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>>
>>> --
>>> Dr. Martin Morgan, PhD
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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