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

[Dan Tenenbaum]

----- Original Message -----
> From: "Hervé Pagès" <hpages at fredhutch.org>
> To: "Philipp Angerer" <philipp.angerer at helmholtz-muenchen.de>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, October 4, 2016 9:23:29 AM
> Subject: Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

> 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/checkResults/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.
> 

Note that ipython/jupyter are requirements not of destiny but of the CRAN package nbconvertR, which does list those dependencies in its SystemDependencies field. https://cran.r-project.org/web/packages/nbconvertR/index.html
SystemRequirements:	pandoc, ipython (>= 3.0) or jupyter, ipython/jupyter notebook optional dependencies, pywin32 (on windows)

Dan


> Thanks,
> H.
> 
>>
>> Best, Philipp
>>
>>
>>
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> --
> Hervé Pagès
> 
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