[Bioc-devel] Your bioc package has R_PROFILE.R

Yu Chuan Tai yuchuan at stat.Berkeley.EDU
Fri Feb 3 18:53:21 CET 2006

Hi Seth,

Thanks for your clarifications. I will follow your instructions and let 
you know if I have more questions.

Yu Chuan

On Fri, 3 Feb 2006, Seth Falcon wrote:

> Hi Yu Chuan,
> I'm cc'ing bioc-devel because I suspect there are others with similar
> questions, it will be useful to have the answer in the archives, and
> I'd like to encourage using bioc-devel for developer questions :-)
> On  3 Feb 2006, yuchuan at stat.berkeley.edu wrote:
>> Thanks for your notifications. I do have R_PROFILE.R in my source
>> directory, how should I remove this file from SVN?
> With svn, everything happens in two steps.  The first step is to
> "schedule" something to happen and the second step is to "commit" the
> something to the repository.  More specifically, the "schedule" step
> is what you do in your working copy on your system.  The "commit" step
> is when you run 'svn commit' in your working copy to send changes to
> the repository.
> So to remove a file:
> svn rm filefoo.txt
> svn status  ## will show that filefoo.txt is schedule for removal
> svn commit
>> And how to use Depends to load dependencies?
> In your package code, you do not need to call library() or require().
> Instead, simply list the packages that your package depends on in the
> 'Depends' field of the DESCRIPTION file.
> If you have a NAMESPACE file for your package (recommended), then when
> you are using functions from another package that also has a
> namespace, you have a choice of using the Depends field and the
> Imports field, in which case you use import directives in the
> NAMESPACE file.  This latter approach is, IMO, more elegant.
>> A more general question, I made some changes to the package which
>> will be included in the next release of bioC, how can I update the
>> whole package on SVN?
> 1. checkout a working copy of your package using svn.
> 2. Make the edits.  If you already have the edits, copy the changed
>   files over the files that come from the checkout.
> 3. Run svn status to verify changes.
> 4. Test, test, test
> 5. svn commit.
> Further questions NAMESPACE files, Depends, Imports, and even svn
> usage are fair game for this list.
> Best,
> + seth

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