Re: [Bioc-devel] Registering native routines with Rcpp

[Vincent Carey]

some more news on registration

https://stat.ethz.ch/pipermail/r-devel/2017-February/073755.html

On Mon, Feb 6, 2017 at 12:08 PM, Kevin Ushey  wrote:

> For what it's worth, the Rcpp team is aware that CRAN will soon be emitting
> NOTEs for packages not registering native routines as well -- it's
> currently tracked at
>
> https://github.com/RcppCore/Rcpp/issues/636
>
> The main difficulty on the Rcpp side is ensuring that we play well with
> users who already have an 'R_init_*' function, although that case should be
> relatively rare.
>
> Best,
> Kevin
>
> On Mon, Feb 6, 2017 at 7:17 AM, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
>
> > Might be worth it to take this one over to Rcpp-devel and get some
> feedback
> > there?
> >
> > Best,
> > Kasper
> >
> > On Mon, Feb 6, 2017 at 5:22 AM, Aaron Taudt 
> wrote:
> >
> > > Dear all,
> > >
> > > I am trying to register the native routines in my package as
> recommended
> > by
> > > BiocCheck. I have done this previously for a package using C++ code.
> > > However, for this package I am using Rcpp and I cannot figure out how
> to
> > > register my native routines.
> > >
> > > My first problem is that I don't know which routines I actually have to
> > > register. Is it ithe ones in the auto-generated "RcppExports.cpp" file,
> > or
> > > the ones that the have the "// [[Rcpp::export]]" tag?
> > >
> > > I have tried the Rcpp.package.skeleton() function, but this package
> > doesn't
> > > have native routine registration.
> > >
> > > Thanks for your help.
> > >
> > > Aaron
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ___
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> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> >
> > [[alternative HTML version deleted]]
> >
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> >
>
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Re: [Bioc-devel] Problem on malbec2 server

[Hervé Pagès]

Hi Juan Pablo,

We just updated R on malbec2 a couple of hours ago and kintr
has not been re-installed yet.

Please make sure that your package suggests knitr otherwise the
Single Package Builder has no way to know that knitr needs to
be installed before trying to run 'R CMD build' or 'R CMD check'
on your package.

Thanks,
H.


On 02/14/2017 01:01 PM, Romero, Juan Pablo wrote:

Hi everyone,

I did a minor update to the package I'm currently developing and the build 
report shows an error on malbec2 server:

* checking for file EventPointer/DESCRIPTION ... OK
* preparing EventPointer:
* checking DESCRIPTION meta-information ... OK
Error in loadVignetteBuilder(pkgdir, TRUE) :
  vignette builder 'knitr' not found
Execution halted

Could this be related with a problem in the server? A few hours ago I did a 
build and it completed without errors and warnings so,
I doubt that the version bump (Updated a link on the package vignette) caused 
this problem.

Thank you.

Juan Pablo



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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] Problem on malbec2 server

[Romero, Juan Pablo]

Hi everyone,

I did a minor update to the package I'm currently developing and the build 
report shows an error on malbec2 server:

* checking for file EventPointer/DESCRIPTION ... OK
* preparing EventPointer:
* checking DESCRIPTION meta-information ... OK
Error in loadVignetteBuilder(pkgdir, TRUE) :
  vignette builder 'knitr' not found
Execution halted

Could this be related with a problem in the server? A few hours ago I did a 
build and it completed without errors and warnings so,
I doubt that the version bump (Updated a link on the package vignette) caused 
this problem.

Thank you.

Juan Pablo



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