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

Seth Falcon sfalcon at fhcrc.org
Fri Feb 3 18:27:39 CET 2006

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.


+ seth

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