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

Hi Philipp,
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

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_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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
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

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 at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

--
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

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

----- 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)

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

--
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

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

----- 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

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

--
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

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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
----- Original Message -----
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.

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 at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

--
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

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
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
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
Hi Philipp,
    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

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