[Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

[Andrzej Oleś]

Dear all,

linux builders have both IPython 3+ and Jupyter installed, see
https://github.com/Bioconductor/BBS-provision-cookbook/blob/master/recipes/default.rb#L256-L264

For consistency, maybe it would make sense to have them both on Windows too.

Cheers,
Andrzej

On Tue, Oct 4, 2016 at 6:23 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Philipp,
>
> On 10/04/2016 12:13 AM, Angerer, Philipp via Bioc-devel wrote:
>
>> Hi,
>>
>> Looking at my package’s build report, the devel version isn’t built
>> anymore on windows: http://bioconductor.org/checkR
>> esults/devel/bioc-LATEST/destiny/tokay1-buildsrc.html
>>
>> The release version is built just fine with moscato2:
>> http://bioconductor.org/checkResults/release/bioc-LATEST/
>> destiny/moscato2-buildsrc.html
>>
>> It would be really nice if this could be fixed. Usually running “jupyter
>> nbconvert --help” successfully means that nbconvertR will work.
>>
>
> The error says:
>
>   Either IPython 3+ or Jupyter has to be installed, but neither could
>   be called.
>
> But neither Jupyter or IPython 3+ is installed on tokay1 at the moment.
> Which one should we install?
>
> Note that packages with special requirements should list them in the
> SystemRequirements field of the DESCRIPTION file. Also it would be great
> if you could provide an INSTALL file in the top-level folder of the
> package where you explain the installation process of these
> requirements.
>
> Thanks,
> H.
>
>
>> Best, Philipp
>>
>>
>>
>>
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>>
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>>
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>>
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>>
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>>
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>>
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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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>
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>
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