[Bioc-devel] older packages - clippda

[Martin Morgan]

On 10/13/2011 10:08 AM, Martin Morgan wrote:
> 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

Actually here I see that you did update the version; the convention is 
that within a release the versions are incremented at the third position 
1.3.0, 1.3.1, 1.3.2 etc. Increments of the second position are meant to 
coincide with releases, with the use of an odd second position 1.2.x 
1.4.x reserved for the release branch; the Bioc release process manages 
the version bumps from odd to even (1.3.x --> 1.4.0) for the transition 
from devel to release, and from odd to odd (1.3.x --> 1.5.0) for the new 
devel branch.

Martin

> ------------------------------------------------------------------------
> 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
>
> http://bioconductor.org/developers/svnlog/
>
> which is updated every 10 (I think) minutes. A link available after
> clicking 'Developers' on the web site points to
>
> http://bioconductor.org/developers/source-control/
>
> 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
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/
>
> (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
>
> http://bioconductor.org/packages/2.9/bioc/html/clippda.html
>
> 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.
>
> Martin


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