[Bioc-devel] How to check package changes?

Hi,
I am putting this on the development list as I think it is most appropriate
for discussion here.

This is a general question: Is there any way to quickly find out how a
package has evolved though version development? -Some sort of change log
additional to the versioning information available. For example, as the R
software evolves we can see changes in the base packages at
http://cran.r-project.org/src/base/NEWS

  

The motivation for this is to quickly see what changes have occurred between
stable and development package releases.

Trolling through some R/bioC base and contributed packages installed on my
system I cannot see anything obvious. I guess this depends on the package
author, for example in the limma package an output from a written log file
is available using changeLog().

Maybe subversion is the best way of getting this sort of information from
packages although less people are familiar with svn.
  

Hi,
I am putting this on the development list as I think it is most  
appropriate
for discussion here.

This is a general question: Is there any way to quickly find out how a
package has evolved though version development? -Some sort of  
change log
additional to the versioning information available. For example, as  
the R
software evolves we can see changes in the base packages at
http://cran.r-project.org/src/base/NEWS

The motivation for this is to quickly see what changes have  
occurred between
stable and development package releases.

Trolling through some R/bioC base and contributed packages  
installed on my
system I cannot see anything obvious. I guess this depends on the  
package
author, for example in the limma package an output from a written  
log file
is available using changeLog().

Maybe subversion is the best way of getting this sort of  
information from
packages although less people are familiar with svn.

Marcus

I use personally think Trac is a great way to monitor changes to
packages in an svn repository:

http://trac.edgewall.org/

In addition to having a very nice looking interface, it makes it easy
to monitor change logs on a directory by directory basis. For example:

http://trac.edgewall.org/log/trunk/contrib
http://trac.edgewall.org/log/trunk/trac

(Please pardon the ads, they would not be there if we installed it
ourselves.)

I use Trac all the time on another project and I'd love to see it set
up for Bioconductor. I really miss the web based interface that went
away with CVS.

For xcms, I keep a separate change log that's more intended for user
consumption:

https://readonly:readonly at hedgehog.fhcrc.org/bioconductor/trunk/
madman/Rpacks/xcms/CHANGELOG

-Colin

On Apr 3, 2007, at 14:00 , Marcus Davy wrote:

Hi,
I am putting this on the development list as I think it is most
appropriate
for discussion here.

This is a general question: Is there any way to quickly find out how a
package has evolved though version development? -Some sort of
change log
additional to the versioning information available. For example, as
the R
software evolves we can see changes in the base packages at
http://cran.r-project.org/src/base/NEWS

The motivation for this is to quickly see what changes have
occurred between
stable and development package releases.

Trolling through some R/bioC base and contributed packages
installed on my
system I cannot see anything obvious. I guess this depends on the
package
author, for example in the limma package an output from a written
log file
is available using changeLog().

Maybe subversion is the best way of getting this sort of
information from
packages although less people are familiar with svn.

Marcus

Thanks to Colin Smith and Sean Davis for their comments.

The BioC monthly news report;

March-http://www.bioconductor.org/News/2007-04-04

is useful but summarizes changes for all packages by month. For others not
particular familiar with svn, a history log for any particular package is
available with;

svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/[Package]
/tmp/[Package] # continued line

svn log /tmp/[Package]

Marcus Davy <mdavy at hortresearch.co.nz> writes:

Thanks to Colin Smith and Sean Davis for their comments.

The BioC monthly news report;

March-http://www.bioconductor.org/News/2007-04-04

is useful but summarizes changes for all packages by month. For others
not particular familiar with svn, a history log for any particular
package is available with;

svn co
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/[Package]
/tmp/[Package] # continued line

svn log /tmp/[Package]

Actually, you don't need a working copy to get a log.  So you can ask
for the log of any svn URL:

svn log -v
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/[Package]