[Bioc-devel] downloads number status shields for packages

[Hervé Pagès]

Hi Wolfgang,

Yep. All good suggestions. Thanks!

H.

On 05/08/2016 12:52 AM, Wolfgang Huber wrote:
> Hervé
>
> Thank you, looks great. Regarding files like https://bioconductor.org/packages/new-stats/bioc/Biobase/Biobase_2016_stats: woudln’t it be good to
> - provide column headers
> - give the file a reasonable extension reminding of its format
> - format it such that it can be read with default parameters e.g. by read.csv or readr::read_csv?
> - include package name and year among the columns, to allow easy rbind-ing of several of such files
> - also useful might be such a file with just all the packages and years in it.
>
> Best wishes
> 	Wolfgang
>
>> On May 5, 2016, at 21:03 GMT+2, Hervé Pagès <hpages at fredhutch.org> wrote:
>>
>> Hi,
>>
>> The download report is actually about to change. See:
>>
>>   https://bioconductor.org/packages/new-stats/bioc/Biobase/
>>
>> for how the new stats are going to look. This is work in progress (ETA
>> is next week) but an important change is that you'll be able to get the
>> numbers from tabulated files (e.g. the Biobase_<year>_stats files in the
>> case of Biobase) so parsing HTML won't be necessary.
>>
>> Cheers,
>> H.
>>
>> On 05/05/2016 11:51 AM, Lori Shepherd wrote:
>>> Hi Marcin,
>>>
>>> Here is a link to how Bioconductor creates it's badges:
>>> https://github.com/Bioconductor/bioconductor.org/blob/master/Rakefile#L648
>>>
>>> If you would like to create a badge for raw counts the following might
>>> be of use to you. Please also see help on XML Path Language:
>>> https://www.w3.org/TR/xpath/#path-abbrev
>>>
>>>
>>>
>>> library(xml2)
>>> url = "http://bioconductor.org/packages/stats/bioc/RTCGA.html"
>>> doc = read_html(url)
>>> rtcga = xml_find_all(doc, "//table[@class='stats']/tr/td[2]/text()")
>>> %>% as.character %>% as.integer
>>>
>>> url2 = "http://bioconductor.org/packages/stats/index.html"
>>> doc2 = read_html(url2)
>>> all = xml_find_all(doc2, "//table[@class='stats']/tr/td[2]/text()")
>>> %>% as.character %>% as.integer
>>>
>>>
>>>
>>> On Wed, May 4, 2016 at 3:43 PM, Marcin Kosiński <m.p.kosinski at gmail.com> wrote:
>>>> Hi Robert,
>>>>
>>>> Thanks for reply.
>>>>
>>>> What if I am interested in both showing raw counts and percentiles?
>>>> If this is not created and no one is willing to create sush shields, then I
>>>> can volounteer for that.
>>>> It'll be great to have some examples on how the percentile badges were
>>>> created.
>>>>
>>>> Best,
>>>> Marcin
>>>>
>>>>
>>>> 2016-05-04 17:22 GMT+02:00 Dan Tenenbaum <dtenenba at fredhutch.org>:
>>>>
>>>>> That's correct.
>>>>> Dan
>>>>>
>>>>>
>>>>> ----- Original Message -----
>>>>>> From: "Andrzej Oleś" <andrzej.oles at gmail.com>
>>>>>> To: "Robert M. Flight" <rflight79 at gmail.com>
>>>>>> Cc: "Marcin Kosiński" <m.p.kosinski at gmail.com>, "bioc-devel" <
>>>>> bioc-devel at r-project.org>, "Dan Tenenbaum"
>>>>>> <dtenenba at fredhutch.org>
>>>>>> Sent: Wednesday, May 4, 2016 8:15:36 AM
>>>>>> Subject: Re: [Bioc-devel] downloads number status shields for packages
>>>>>
>>>>>> Hi Marcin, Robert,
>>>>>>
>>>>>> I think one problem with raw counts is that these reflect only downloads
>>>>>> from BioC servers and not from the mirrors - is that correct @Dan?
>>>>>>
>>>>>> Cheers,
>>>>>> Andrzej
>>>>>>
>>>>>> On Wed, May 4, 2016 at 5:11 PM, Robert M. Flight <rflight79 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Those numbers are used to calculate the percentile download stat that is
>>>>>>> already on a given bioconductor package landing page. See
>>>>>>> http://bioconductor.org/packages/release/bioc/html/RTCGA.html
>>>>>>>
>>>>>>> I believe this was the way the Bioc admins went instead of just raw
>>>>>>> downloads.
>>>>>>>
>>>>>>> -Robert
>>>>>>>
>>>>>>> On Wed, May 4, 2016 at 10:58 AM Marcin Kosiński <m.p.kosinski at gmail.com
>>>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> Have anyone considered creating shields (http://shields.io/) with the
>>>>>>>> status of total downloads number for packages held on bioc? This
>>>>> already
>>>>>>>> works for CRAN packages http://cranlogs.r-pkg.org/
>>>>>>>>
>>>>>>>> It could take total `Nb of downloads` from the right table like here
>>>>>>>> http://bioconductor.org/packages/stats/bioc/RTCGA.html
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Marcin
>>>>>>>>
>>>>>>>>          [[alternative HTML version deleted]]
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>
>>>>>>>
>>>>>>>          [[alternative HTML version deleted]]
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>
>>>>          [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
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>>>
>>> _______________________________________________
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>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> Wolfgang
>
> Wolfgang Huber
> Principal Investigator, EMBL Senior Scientist
> Genome Biology Unit
> European Molecular Biology Laboratory (EMBL)
> Heidelberg, Germany
>
> wolfgang.huber at embl.de
> http://www.huber.embl.de
>
>
>
>
>
>
>
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319