[Bioc-devel] older packages - clippda

Martin Morgan mtmorgan at fhcrc.org
Thu Oct 13 19:08:32 CEST 2011

On 10/13/2011 09:47 AM, Stephen Nyangoma wrote:
> Martin, I recently used version control to update my package clippda,
> but I have not received any acknowledgement. Where am I supposed to
> get information on what to do next? When should the updates be
> available to the users? Kindest regards. Stephen

Hi Stephen --

Usually svn reports a successful commit immediately.

 From the command line (I'm not sure how you're interacting with svn? 
you can review changes with, e.g.,

   cd clippda
   svn log -v|less

which leads in your case to

r58290 | s.nyangoma | 2011-09-21 06:26:34 -0700 (Wed, 21 Sep 2011) | 1 line
Changed paths:
    M /trunk/madman/Rpacks/clippda/DESCRIPTION

updated the version to 1.3.0
r58289 | s.nyangoma | 2011-09-21 06:22:13 -0700 (Wed, 21 Sep 2011) | 1 line
Changed paths:
    M /trunk/madman/Rpacks/clippda/inst/doc/LittBib.bib

new reference added

and so on; if you're using a particular interface to svn please provide 
some addition info and we'll try to help. There is also log at


which is updated every 10 (I think) minutes. A link available after 
clicking 'Developers' on the web site points to


for a quick introduction, including a link to the Subversion book with 
additional details.

Usually, commits are made to the 'devel' branch (as above). All packages 
in the devel branch are built daily (modulo disaster) with results 
available at


(this link and links to daily builds of the release branch are also 
available on the 'Developer' page of the wiki. For clippda the build 
report says

Last Changed Rev: 58290 / Revision: 59104
Last Changed Date: 2011-09-21 06:26:34 -0700

The 'CHECK' column indicates that some warnings were generated by R CMD 
check on all platforms; click on the WARNINGS to see the output (looks 
like two man pages try to document the same function).

When a package is built and checked without errors (clippda satisfies 
this condition -- warnings are not errors) it is made available to 
biocLite when invoked from the appropriate platform. So from the build 
results page we can click to


and see that the version available via biocLite('clippda') for users of 
R-devel (actually, at this particular point in the release cycle R-2-14 
alpha and later) is 1.3.0.

This actually brings up a final point -- all changes to svn should be 
accompanied by a 'version bump' in the DESCRIPTION file -- users of 
clippda with version number 1.3.0 might have the version before your 
last commit or after, there's no way to tell!

So an excellent test of your knowledge is to

- edit DESCRIPTION to version 1.3.1
- check it in, review the svn log, etc. Try svn diff -rPREV:HEAD to see 
the most recent changes
- wait ten minutes and look on the svn log link above to see your 
changes broadcast to the world.
- wait for the build system to do another iteration (typically changes 
made by 6pm PST become available by 12pm the next day), visit the build 
/ check page to see how you did across all platforms.
- use R-2-14 or R-devel and try biocLite("clippda") to get the updated 
version of your package.

Computational Biology
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Telephone: 206 667-2793

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