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[R-pkg-devel] recommendation: codetoolsBioC

7 messages · Kasper Daniel Hansen, John C Nash, Duncan Murdoch +3 more

Original
Kasper Daniel Hansen
# 
With the new NAMESPACE requirements of importing everything in the bundled
packages I would like to recommend using
  writeNamespaceImports
from codetoolsBioC.  This analyzes your code and produces a NAMESPACE file
with all imports.  Of course, you might benefit from checking it manually.

This package is from Bioconductor, but you need to check it out from svn
(it was never officially released).

svn co
https://hedgehog.fhcrc.org/gentleman/bioconductor/trunk/madman/Rpacks/codetoolsBioC


Perhaps similar tools exists elsewhere now; this package has been around
for quite a while.

Best,
Kasper
8 days later
John C Nash
# 
There has been some disagreement on where it is appropriate to post
questions about package checking procedures, including the building of
the environment e.g., R-devel under Linux Mint.

In looking at https://www.r-project.org/mail.html, it seems to me that
the procedures belong with r-package-devel, but there doesn't seem to be
a good home for the consequent need to build R-devel to do this. Have I
missed the appropriate list?

It seems to me that the volume of queries of this sort, and the success
of WinBuilder, suggest we could seriously use similar a Linbuilder and
MacBuilder (and possibly others). There's a lot of duplicated effort
being wasted on the R-devel side in particular.

Is there sufficient interest to
- make the effort to emulate Winbuilder for Linux and/or Mac
- coordinate the volunteer effort
- fund/support the necessary infrastructure (it could be worth a modest
contribution to save effort)?

For the record, I'm willing to participate. I've managed to set up Linux
Mint VirtualBox instances that run R current and R devel for testing,
though I find I must do more work than I'd like to maintain things,
likely as a result of my own limited skills.

JN
Duncan Murdoch
#
On 21/07/2015 9:01 AM, ProfJCNash wrote:
That sounds like the sort of project the R Consortium would support.
They are just getting started, but soon they will have a committee set
up to decide on projects, and presumably soon after that will have a
process in place to solicit them.

Duncan Murdoch
Mauricio Zambrano Bigiarini
#
On 21 July 2015 at 11:46, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
In my humble opinion, such a project could be of great utility to
several people that is starting to migrate to GNU/Linux, or to people
willing to test their packages with the latest development version of
R but without all the knowledge to properly set up the environment on
their local machines.

If I can contribute to a "LinBuilder" (e.g., testing), I would be
willing to do it.

Kind regards,


Mauricio Zambrano-Bigiarini, PhD

=====================================
Dept. of Civil Engineering
Faculty of Engineering and Sciences
Universidad de La Frontera
PO Box 54-D, Temuco, Chile
=====================================
mailto     : mauricio.zambrano at ufrontera.cl
work-phone : +56 45 259 2812
http://ingenieriacivil.ufro.cl/
=====================================
"When the pupil is ready, the master arrives."
(Zen proverb)
=====================================
Linux user #454569 -- Linux Mint user
Gavin Simpson
# 
Perhaps I have missed some detail, but would Gabor Csardi's r-builder code
not provide this (or something close to it) for Linux at least? See:
https://github.com/metacran/r-builder

This builds on the R support for Travis CI, and allows for testing against
R-release and R-devel (plus R-oldrelease IIRC)

It's pretty trivial to set-up but you do need your code in a github repo
(for the Travis deployment - I don't know anything about Semaphore, the
other option r-builder allows for).

G

On 21 July 2015 at 09:04, MAURICIO ZAMBRANO BIGIARINI <
mauricio.zambrano at ufrontera.cl> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Gábor Csárdi
    

    

      
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On Tue, Jul 21, 2015 at 2:35 PM, Gavin Simpson <ucfagls at gmail.com> wrote:

            

      
      
      
    

        
It does, although it only does Ubuntu 12.04 if you use Travis, because
that's what Travis has. IMHO this does not really matter for 95% of
the packages, and having R-devel in addition to R-release and R-oldrel
is more important.

            

      
      
      
    

        
It actually does not build on R support for Travis CI. Since it needs
its own R installations, it does not make much sense to use the
built-in R support.

            

      
      
      
    

        
Yeah, it needs to be on GitHub.

Gabor

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Mauricio Zambrano Bigiarini
    

    

      
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Probably I'm too distrustful, but yesterday I tried to use Travis CI
and at the end I didn't do it, because of the permissions you're
requested to give to the application:

Review permissions:

Personal user data                         : Email addresses (read-only)
Repository webhooks and services: Read and write access
Commit statuses                             : Read and write access
Deployments                                   : Manage deployments and
deployment status
Organizations and teams                : Read-only access


Mauricio

=====================================
"When the pupil is ready, the master arrives."
(Zen proverb)
=====================================
Linux user #454569 -- Linux Mint user

        
On 21 July 2015 at 15:45, G?bor Cs?rdi <csardi.gabor at gmail.com> wrote: