----- Original Message ----- > From: "Hervé Pagès" <hpa...@fredhutch.org> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Philipp Angerer" <philipp.ange...@helmholtz-muenchen.de>, "bioc-devel" > <bioc-devel@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" <hpa...@fredhutch.org> >>> To: "Philipp Angerer" <philipp.ange...@helmholtz-muenchen.de>, "bioc-devel" >>> <bioc-devel@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 >>>> >>>> >>>> >>>> >>>> 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@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: hpa...@fredhutch.org >>> Phone: (206) 667-5791 >>> Fax: (206) 667-1319 >>> >>> _______________________________________________ >>> Bioc-devel@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
