Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine
Hi Philipp, On 10/05/2016 12:09 AM, Angerer, Philipp wrote: 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 Haha, yeah. Thanks, Dan! I’m already in the process of submitting nbconvertR 1.1, which only uses jupyter (Using ipython nbconvert is deprecated). That nbconvertR version also clarifies that the nbconvert python package (which depends on jupyter) needs to be installed, and contains install instructions in README.md. In the mean time can you please send me (off-list) that file so I can proceed on tokay1? 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 -- 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
Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine
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 Haha, yeah. Thanks, Dan! I’m already in the process of submitting nbconvertR 1.1, which only uses jupyter (Using ipython nbconvert is deprecated). That nbconvertR version also clarifies that the nbconvert python package (which depends on jupyter) needs to be installed, and contains install instructions in README.md. 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
Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine
- 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
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. 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
Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine
- 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) 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine
Dear all, linux builders have both IPython 3+ and Jupyter installed, see https://github.com/Bioconductor/BBS-provision-cookbook/blob/master/recipes/default.rb#L256-L264 For consistency, maybe it would make sense to have them both on Windows too. Cheers, Andrzej On Tue, Oct 4, 2016 at 6:23 PM, Hervé Pagèswrote: > 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/checkR >> esults/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. > > 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 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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. 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