[Bioc-devel] Package Home Pages

[James W. MacDonald]

Laurent Gautier wrote:
> There seems to be at least one other issue with names:
> 
> http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/GSEA
> 
> returns information for all packages with a name starting with GSEA.
> Same story with affy.

Yes. Blosxom is just a simple set of Perl scripts that uses the 
directory structure of its home directory to decide what to put on 
screen. So if you did

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/G

you would get everything from all sub-directories that start with G. 
This is a feature of the software.

Best,

Jim



> 
> L.
> 
> 
> 2008/7/18 Diego Diez <diez at kuicr.kyoto-u.ac.jp>:
>> Hi, just noticed that this works:
>>
>> http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma
>>
>> i.e. without the ".light" and also in that page there is a strange
>> reference to a .light package:
>>
>> http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma/.light
>>
>> i guess there is some issue with the dot character.
>>
>> Diego
>>
>> On Fri, Jul 18, 2008 at 8:42 AM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:
>>> Henrik,
>>> I provided links to the existing Bioconductor changelog blosxom blog at the
>>> University of Michigan. With the Bioconductor manifest growing at such a
>>> rapid pace, my guess is that the newer packages haven't yet made the blog.
>>>
>>>
>>> Patrick
>>>
>>>
>>>
>>> Henrik Bengtsson wrote:
>>>> Thanks. Looks good.
>>>>
>>>> FYI, when I go to the package specifics for aroma.light
>>>> [http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma.light/] there is a
>>>> somewhat poetic message delivered in red:
>>>>
>>>> "Error: I'm afraid this is the first I've heard of a "light" flavoured
>>>> Blosxom. Try dropping the "/+light" bit from the end of the URL."
>>>>
>>>> /Henrik
>>>>
>>>>
>>>> On Thu, Jul 17, 2008 at 3:54 PM, Patrick Aboyoun <paboyoun at fhcrc.org>
>>>> wrote:
>>>>
>>>>> I just modified the build system to add "Bioconductor Changelog" links to
>>>>> the "Multiple platform build/check report" pages. To see an example of
>>>>> these
>>>>> links go to
>>>>>
>>>>> http://bioconductor.org/checkResults/2.2/bioc-LATEST/
>>>>>
>>>>> and look for the Bioconductor Changelog links. Similar links will be
>>>>> added
>>>>> to the BioC 2.3 report when it is created later tonight.
>>>>>
>>>>> Given that the changelog is geared towards developers, I did not include
>>>>> a
>>>>> link in the package home pages that Wolfgang referred to because it could
>>>>> fall into the category of too much information for a general user of the
>>>>> package. If the Bioconductor development community believes we should
>>>>> include a link on the package home pages as well, I will add them. It
>>>>> doesn't take much effort to change the infrastructure.
>>>>>
>>>>>
>>>>> Cheers,
>>>>> Patrick
>>>>>
>>>>>
>>>>>
>>>>> Patrick Aboyoun wrote:
>>>>>
>>>>>> Sean and Wolfgang,
>>>>>> I think these two enhancements to the bioconductor.org website would be
>>>>>> very useful and not too much work to implement. I'll add them on the
>>>>>> website
>>>>>> task list and send out a message to this group when they are
>>>>>> implemented. If
>>>>>> there are any other related ideas, keep them coming. It is easier to
>>>>>> implement them all at once, rather than one at a time.
>>>>>>
>>>>>>
>>>>>> Patrick
>>>>>>
>>>>>>
>>>>>> Sean Davis wrote:
>>>>>>
>>>>>>> On Fri, Jul 11, 2008 at 6:58 AM, Wolfgang Huber <huber at ebi.ac.uk>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I like the package overview pages, such as
>>>>>>>> http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html
>>>>>>>>
>>>>>>>> Would it be possible that they also link to the output of, for
>>>>>>>> example:
>>>>>>>>
>>>>>>>> svn log --username readonly --password readonly \
>>>>>>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma
>>>>>>>>
>>>>>>>> which any of our users can run (but I assume most wouldn't know how
>>>>>>>> to)?
>>>>>>>>
>>>>>>>> This additional service to our users may also encourage pkg developers
>>>>>>>> to be more precise in their svn log entries :)
>>>>>>>>
>>>>>>>>
>>>>>>> Hi, Wolfgang.  I agree this would be a simple and useful addition for
>>>>>>> the devel archives.  Since we already have the bioconductor change log
>>>>>>> in place, it would be trivial to change the HTML on the devel pages to
>>>>>>> include a link like:
>>>>>>>
>>>>>>> http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/cellHTS2
>>>>>>>
>>>>>>> Sean
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at stat.math.ethz.ch mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at stat.math.ethz.ch mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at stat.math.ethz.ch mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>> --
>> Diego Diez, Ph
>> Bioinformatics center,
>> Institute for Chemical Research,
>> Kyoto University.
>> Gokasho, Uji, Kyoto 611-0011 JAPAN
>> diez at kuicr.kyoto-u.ac.jp
>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
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