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

2016-10-07 Thread Hervé Pagès 

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

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

2016-10-05 Thread Angerer, Philipp via Bioc-devel 



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


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

2016-10-04 Thread Dan Tenenbaum 


- 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

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

2016-10-04 Thread Hervé Pagès 



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


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--
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

___
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--
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

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

2016-10-04 Thread Dan Tenenbaum 


- 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

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

2016-10-04 Thread Andrzej Oleś 
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 Pagès  wrote:

> 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
>

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

2016-10-04 Thread Hervé Pagès 

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]]

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--
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

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

2016-10-04 Thread Angerer, Philipp via Bioc-devel 
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. 

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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