[Bioc-devel] exp. data, updates

Hervé Pagès hpages at fhcrc.org
Wed Jul 10 22:12:37 CEST 2013

Hi Stephanie,

On 07/10/2013 12:51 PM, Stephanie M. Gogarten wrote:
> I had this issue with GWASTools/GWASdata at one point.  There is only
> one copy of an experiment data package, so if you change it, it will
> break the current release version of bsseq.

Yes there is only one copy of an experiment data package in svn.
But the package gets built twice: for BioC release and for BioC devel.
Then, it gets propagated twice: to the release repos and to the devel

If you make a change in svn that breaks the package in release, then
the modified package won't propagate to the release repos. So everything
is fine. The package looks broken in release if you look at the build
report, but the build report is for the modified package, not for the
package that is actually in the release repos.



>  The solution I came up with
> was to add new objects with different names to the data package, and
> change my examples in the devel version to use the new names.  You can
> delete the old objects after the next release cycle.
> Stephanie
> On 7/10/13 7:05 AM, Kasper Daniel Hansen wrote:
>> I have just changed the class definition for a core class in bsseq.  A
>> supporting experiment data package, bsseqData, contains two objects of
>> this
>> core class and now it needs to be updated (specifically because the
>> example() contains a command which prints the object and this printing
>> now
>> fails).
>> I can update the bsseqData package, but do I mess with earlier releases
>> when I do this? I am uncertain because the /data is stored in another
>> repository. How should I handle this?
>> Best,
>> Kasper
>>     [[alternative HTML version deleted]]
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioc-devel mailing list