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

[Dan Tenenbaum]

----- Original Message -----
> From: "Hervé Pagès" <hpages at fredhutch.org>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Philipp Angerer" <philipp.angerer at helmholtz-muenchen.de>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, October 4, 2016 10:16:34 AM
> Subject: Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

> On 10/04/2016 09:56 AM, Dan Tenenbaum wrote:
>>
>>
>> ----- 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)
> 
> Good to know, thanks Dan! That makes testing on tokay1 easier:
> 
>   > library(nbconvertR)
>   > path <- system.file('doc', 'test-vignette.ipynbmeta',
> package='nbconvertR')
>   > nbconvert(path, 'pdf')
>   Error in get.binary() :
>     Either IPython 3+ or Jupyter has to be installed, but neither could
> be called.
> 
> I'll work on this.
> 
> @Philipp: no need to add anything to SystemRequirements or to add an
> INSTALL file to your package. I take this back.
> 

Although, since you (Philipp) are the maintainer of the nbconvertR package, you may want to create an INSTALL file in that package. It's up to you.

Dan



> Cheers,
> H.
> 
>>
>> Dan
>>
>>
>>> 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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>>>>
>>>> 	[[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>> --
>>> 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
> 
> --
> 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