Re: [Bioc-devel] Harman not building on Windows due to mzR
Hi, Jason, On Mi, 2016-10-05 at 03:40 +, jason.r...@csiro.au wrote: > > [...] > This is arising from the vignette and is due to the package msmsEDA > not being present. If I keep peeling the dependencies back, I get to > mzR, which has trouble loading the Windows dynamic link library. See: > http://bioconductor.org/checkResults/3.4/bioc-LATEST/mzR/tokay1- > install.html Together with the BioC team we're currently trying to find out what's going on there, we have the problem at least since the move to the new Tokay1 build host. Any help on the issue of "LoadLibrary failure: The specified module could not be found." is highly welcome. On Linux I'd have ideas how to dig into the problem, and I'd be happy to try suggestions what to try next to fix the windows build. Sorry for the hassle, yours, Steffen -- IPB HalleAG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Harman not building on Windows due to mzR
Hi there, I notice the Harman package which I maintain is not building on Windows. See: http://bioconductor.org/checkResults/3.4/bioc-LATEST/Harman/? This is arising from the vignette and is due to the package msmsEDA not being present. If I keep peeling the dependencies back, I get to mzR, which has trouble loading the Windows dynamic link library. See: http://bioconductor.org/checkResults/3.4/bioc-LATEST/mzR/tokay1-install.html How do I manage this with the 3.4 release deadline on Oct 7 of "...packages passing ''R CMD build'' and ''R CMD check'' without error"? Cheers, Jason ? [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?
- Original Message -
> From: "Martin Morgan"
> To: "McDavid, Andrew" , "bioc-devel"
>
> Sent: Tuesday, October 4, 2016 2:09:27 PM
> Subject: Re: [Bioc-devel] Why can't NAMESPACE be a strict subset of
> DESCRIPTION Imports?
> On 10/04/2016 05:07 PM, McDavid, Andrew wrote:
>> BiocCheck throws a warning when a package is listed as Imports: in
>> DESCRIPTION
>> but not used in the NAMESPACE. This may happen when a developer uses the
>> fully
>> qualified names of objects within a package. I am unclear as to the
>> rationale
>> for this warning.
>>
>
> agree it's wrong. can you point to an example? Martin
>
https://bioconductor.org/spb_reports/MAST_buildreport_20160929192258.html#zin1_check_anchor
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import parallel, reshape2 in NAMESPACE as well as
DESCRIPTION.
Dan
>> Per Hadley:
>>
>> It's common for packages to be listed in Imports in DESCRIPTION, but not in
>> NAMESPACE. In fact, this is what I recommend: list the package in DESCRIPTION
>> so that it's installed, then always refer to it explicitly with pkg::fun().
>> Unless there is a strong reason not to, it's better to be explicit. It's a
>> little more work to write, but a lot easier to read when you come back to the
>> code in the future.
>>
>> Per R extensions:
>>
>> If a package only needs a few objects from another package it can use a fully
>> qualified variable reference in the code instead of a formal import. A fully
>> qualified reference to the function f in package foo is of the form foo::f.
>>
>> -Andrew
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
> ___
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Re: [Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?
On 10/04/2016 05:07 PM, McDavid, Andrew wrote:
BiocCheck throws a warning when a package is listed as Imports: in DESCRIPTION
but not used in the NAMESPACE. This may happen when a developer uses the fully
qualified names of objects within a package. I am unclear as to the rationale
for this warning.
agree it's wrong. can you point to an example? Martin
Per Hadley:
It's common for packages to be listed in Imports in DESCRIPTION, but not in
NAMESPACE. In fact, this is what I recommend: list the package in DESCRIPTION
so that it's installed, then always refer to it explicitly with pkg::fun().
Unless there is a strong reason not to, it's better to be explicit. It's a
little more work to write, but a lot easier to read when you come back to the
code in the future.
Per R extensions:
If a package only needs a few objects from another package it can use a fully
qualified variable reference in the code instead of a formal import. A fully
qualified reference to the function f in package foo is of the form foo::f.
-Andrew
[[alternative HTML version deleted]]
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[Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?
BiocCheck throws a warning when a package is listed as Imports: in DESCRIPTION but not used in the NAMESPACE. This may happen when a developer uses the fully qualified names of objects within a package. I am unclear as to the rationale for this warning. Per Hadley: It's common for packages to be listed in Imports in DESCRIPTION, but not in NAMESPACE. In fact, this is what I recommend: list the package in DESCRIPTION so that it's installed, then always refer to it explicitly with pkg::fun(). Unless there is a strong reason not to, it's better to be explicit. It's a little more work to write, but a lot easier to read when you come back to the code in the future. Per R extensions: If a package only needs a few objects from another package it can use a fully qualified variable reference in the code instead of a formal import. A fully qualified reference to the function f in package foo is of the form foo::f. -Andrew [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] package submission from bitbucket
Hi Lori, Thank you for the information and for the quick response! Thanks! Lauren On Tue, Oct 4, 2016 at 1:01 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Lauren, > > > Thank you for your interest in submitting to Bioconductor. > > Currently we only support the use of github for package submission. After > the package has been accepted through the review process, it does not have > to remain in github. > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Bioc-devel on behalf of Lauren > McIver > *Sent:* Tuesday, October 4, 2016 2:51:08 PM > *To:* bioc-devel@r-project.org > *Subject:* [Bioc-devel] package submission from bitbucket > > Hello Bioconductor Core Team, > > We use bitbucket to host all our software repositories. Is there a way to > submit a bitbucket URL for a new bioconductor package or does it need to be > from github? If it has to be in github, do we need to maintain the original > repository that created the initial bioconductor package request or is it > possible to remove this repository and only use the forked bioconductor > github repository after a package is accepted? > > Any advice on using bitbucket repositories when submitting packages to > bioconductor would be greatly appreciated! > > Thank you, > Lauren McIver > > Senior Software Developer > The Huttenhower Lab > Department of Biostatistics > Harvard T.H. Chan School of Public Health > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] package submission from bitbucket
Lauren, Thank you for your interest in submitting to Bioconductor. Currently we only support the use of github for package submission. After the package has been accepted through the review process, it does not have to remain in github. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Lauren McIver Sent: Tuesday, October 4, 2016 2:51:08 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] package submission from bitbucket Hello Bioconductor Core Team, We use bitbucket to host all our software repositories. Is there a way to submit a bitbucket URL for a new bioconductor package or does it need to be from github? If it has to be in github, do we need to maintain the original repository that created the initial bioconductor package request or is it possible to remove this repository and only use the forked bioconductor github repository after a package is accepted? Any advice on using bitbucket repositories when submitting packages to bioconductor would be greatly appreciated! Thank you, Lauren McIver Senior Software Developer The Huttenhower Lab Department of Biostatistics Harvard T.H. Chan School of Public Health [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] package submission from bitbucket
Hello Bioconductor Core Team, We use bitbucket to host all our software repositories. Is there a way to submit a bitbucket URL for a new bioconductor package or does it need to be from github? If it has to be in github, do we need to maintain the original repository that created the initial bioconductor package request or is it possible to remove this repository and only use the forked bioconductor github repository after a package is accepted? Any advice on using bitbucket repositories when submitting packages to bioconductor would be greatly appreciated! Thank you, Lauren McIver Senior Software Developer The Huttenhower Lab Department of Biostatistics Harvard T.H. Chan School of Public Health [[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"
> To: "Dan Tenenbaum"
> Cc: "Philipp Angerer" , "bioc-devel"
>
> 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"
>>> To: "Philipp Angerer" , "bioc-devel"
>>>
>>> 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
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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
>>>
>>> ___
>>> 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
On 10/04/2016 09:56 AM, Dan Tenenbaum wrote:
- Original Message -
From: "Hervé Pagès"
To: "Philipp Angerer" , "bioc-devel"
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]]
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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
- Original Message - > From: "Hervé Pagès" > To: "Philipp Angerer" , "bioc-devel" > > 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 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 > [[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
[Bioc-devel] Statistical Scalability for Streaming Data - 1/2 day workshop in London
Perhaps interesting for some: http://www.turing-gateway.cam.ac.uk/tgmw39.shtml ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] PKG_LIBS in make child processes
Hi all,
I have a subtle question related to how R CMD SHLIB handles variables in
make child processes. In more detail: I am the maintainer of the 'msa'
package which has been in Bioconductor since April 2015. This package
integrates three open-source libraries for multiple sequence alignment.
This is organized in the following way: in src/, there are three
sub-directories, one for each of the libraries (plus another one for a
garbage collector library, but that is not relevant at this point).
src/Makevars is made such that the libraries are compiled individually
to static libraries in their respective sub-directory, then these static
libraries are copied to src/, and finally the static libraries are
integrated into msa.so. The Makevars file looks as follows:
PKG_LIBS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if
(Sys.info()['sysname'] == 'Darwin') cat('-Wl,-all_load ./libgc.a
./libClustalW.a ./libClustalOmega.a ./libMuscle.a') else
cat('-Wl,--whole-archive ./libgc.a ./libClustalW.a
./libClustalOmega.a ./libMuscle.a -Wl,--no-whole-archive')"`
PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src"
-I"./ClustalOmega/src"
.PHONY: all mylibs
all: $(SHLIB)
$(SHLIB): mylibs
mylibs: build_gc build_muscle build_clustalw build_clustalomega
build_gc:
make --file=msaMakefile --directory=gc-7.2
@echo ""
@echo "-- GC -"
@echo ""
@echo "- Compilation finished -"
@echo ""
build_muscle:
make --file=msaMakefile --directory=Muscle
@echo ""
@echo " MUSCLE "
@echo ""
@echo "- Compilation finished -"
@echo ""
build_clustalw:
make --file=msaMakefile --directory=ClustalW
@echo ""
@echo "--- ClustalW ---"
@echo ""
@echo "- Compilation finished -"
@echo ""
build_clustalomega:
make --file=msaMakefile --directory=ClustalOmega
@echo ""
@echo "- ClustalOmega -"
@echo ""
@echo "- Compilation finished -"
@echo ""
This has always worked on Linux and Mac OS so far. Now I have received
an error report from a user who cannot install the package on a 64-bit
openSUSE 13.1 system using R 3.3.1. It turned out that R CMD SHLIB as
called in the make child processes (make target 'build_muscle' above)
uses the value of PKG_LIBS defined in the first line of the top-level
Makevars file shown above (which of course does not work and makes no
sense), while this does not happen on any other Unix-like system I have
tried so far (Ubuntu, CentOS, Mac OS). Maybe somebody can shed some
light on how variables defined inside the Makevars file propagate to
child processes. Thanks so much in advance!
Best regards,
Ulrich
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[Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine
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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
