[Bioc-devel] svn account information

Martin Morgan mtmorgan at fhcrc.org
Tue May 18 22:07:54 CEST 2010

On 05/18/2010 07:10 AM, Zhu, Julie wrote:
> Hi Nishant,
> With the new release, do I have to change the URLs using SVN to update the
> repository for both released and dev version? Thanks so much for your help!

Hi Julie --

The svn repository is 'branched' when a new release of Bioconductor is
created. The 'devel' versions of packages continue to have the same
location in the repository, e.g.,


whereas the release version is at


If you need to update the release version (only for bug fixes, and only
after carefully checking that the bug fix is correct), then you might
check out the 'release' branch into its own directory

  cd R-2-6-repository
  svn co

and make changes to it. When you commit your changes, they are committed
to the release branch.

See the instructions here


for more information.


> Best regards,
> Julie
> *******************************************
> Lihua Julie Zhu, Ph.D
> Research Associate Professor
> Program in Gene Function and Expression
> Program in Molecular Medicine
> University of Massachusetts Medical School
> 364 Plantation Street, Room 613
> Worcester, MA 01605
> 508-856-5256
> http://www.umassmed.edu/pgfe/faculty/zhu.cfm
> On 8/7/09 1:32 PM, "Nishant Gopalakrishnan" <ngopalak at fhcrc.org> wrote:
>> Hi Julie,
>> You have been given read/write access to the ChIPpeakAnno package:
>>   URL:
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAnno
>> The rest of this email contains the standard information sent to all new
>> Bioconductor official maintainers. Please read it carefully and let me know
>> if you have any question or problem with your svn access.
>> For more general questions or advice about the development/maintenance of
>> your package, please use the Bioc-devel mailing list (our primary channel
>> for communication between developers and for important announcements like
>> release schedules, build system news, etc...).
>> Thanks for participating,
>> Nishant
>> ==============================================================================
>> Subversion Quick Start
>> ----------------------
>> You will need the Subversion client (the 'svn' command) in order to
>> access our Subversion repository.  Typical use:
>>   o Check out your package with:
>>       svn co
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mypackage/
>>     This will create a working copy of the package source tree on
>>     your local disk.  You can edit the files, add new files (first
>>     create the new file, then put it under revision control with
>>     'svn add <newfile>'), delete files (with 'svn del <file>')
>>     and rename files (with 'svn rename <file>').
>>   o Once you are done, commit your changes with:
>>       cd top/directory/of/mypackage
>>       svn ci -m 'comment your changes here'
>>   o Next time you want to work again on the package, don't forget
>>     to 'svn update' first (no need to check out the whole source
>>     tree again):
>>       cd top/directory/of/your/mypackage
>>       svn up
>> You have global read access to the Bioconductor repository and
>> read/write access to your own package directory.
>> More about Subversion
>> ---------------------
>> - The Subversion command line client is available here:
>>     http://subversion.tigris.org/project_packages.html
>> - Windows users looking for a GUI interface should look at the
>>   TortoiseSVN project (http://tortoisesvn.tigris.org).
>> - If you plan to build the Subversion client from source, be sure to
>>   include support for HTTPS by adding "--with-ssl" to the configure
>>   line.
>> - Read _our_ SVN How To page at
>>     http://wiki.fhcrc.org/bioc/SvnHowTo
>> How we build, test and publish the Bioconductor packages
>> --------------------------------------------------------
>> Please, keep an eye on the build/check daily report for the
>> Bioconductor devel packages (currently BioC 2.5):
>>   http://bioconductor.org/checkResults/2.5/bioc-LATEST/
>> A package is made publicly available only if it passes the CHECK
>> test on lamb1 with no error (it can have warnings though). Then the
>> easiest (and recommended) way to install it is with biocLite():
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("mypackage")
>> However, if your package is already published and you make changes
>> to it, the new version will not replace the old version unless
>> you have bumped z in the version number x.y.z. DON'T FORGET TO
>> BUMP Z! or the last version of your package will not be pushed
>> to the public repository.
>> Mailing lists
>> -------------
>> Let me know or ask on the Bioc-devel mailing list
>> (bioc-devel at stat.math.ethz.ch) if you have any question.
>> Also, when your package will pass the CHECK test for the first time,
>> we strongly encourage you to send a note to Bioc-devel to announce
>> its public avaibility (with a short description) so other people
>> can start to test it.
>> Finally, if you have not already done so, we urge you to
>> subscribe to the Bioconductor mailing list so that you can
>> answer questions from users of your package and respond to bug
>> reports promptly. You can find the information about the mailing
>> lists here:
>>   http://bioconductor.org/docs/mailList.html
>> Thanks for contributing to the Bioconductor project!
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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