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

[Hervé Pagès]

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.

Cheers,
H.

>
> Dan
>
>
>> Thanks,
>> H.
>>
>>>
>>> Best, Philipp
>>>
>>>
>>>
>>>
>>> Helmholtz Zentrum Muenchen
>>>
>>> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
>>>
>>> Ingolstaedter Landstr. 1
>>>
>>> 85764 Neuherberg
>>>
>>> www.helmholtz-muenchen.de
>>>
>>> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
>>>
>>> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen
>>>
>>> Registergericht: Amtsgericht Muenchen HRB 6466
>>>
>>> USt-IdNr: DE 129521671
>>>
>>>
>>> 	[[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