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

From: "Herv? Pag?s" <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: "Herv? Pag?s" <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




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--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
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--
Herv? Pag?s

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