Source Control

The Bioconductor project is maintained in a Subversion source control system.

Subversion Resources

• The Subversion Book is a key reference; start with the guided tour.
• Visit the Subversion home page.

• Read-only access to our svn repository is available with

  • user name: readonly
  • password: readonly

Software Packages

To check out (co) all packages in the software repository (~3 GB) use:

svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks Rpacks-devel

This creates a copy of all packages on your local machine. Specify a name other than "Rpacks-devel" if you want a top-level directory with different name.

To check out the code for the Biobase package use:

svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase

The check out command uses the directory name in the repository if the destination name is not specified.

Experiment Data Packages

The root of the Bioconductor experiment data svn repository is https://hedgehog.fhcrc.org/bioc-data/trunk/experiment. Experiment data packages are divided into two components: pkgs (containing all but the data files) and data_store (containing the data files). To obtain a specific experiment data package first check out the package infrastructure then fold the data in using the Python script https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/add_data.py on the exported package. Here are the commands to check out the affydata package:

svn export https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/add_data.py
svn co https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/affydata
./add_data.py affydata

Basic svn Operations

Primary commands:

• svn update will update your check out from the server to get any new changes.
• svn add foo will add foo to the repository (note that unlike CVS this is a recursive add. Use the -N switch if you don't want this behavior).
• svn delete foo will delete foo. If foo is a file it is removed from your local copy as well. If it is a directory it is not but is scheduled for deletion.
• svn copy foo bar will make a copy of foo named bar and copy the history.
• svn move foo bar is the same as copy except foo gets deleted.
• svn commit commits your changes. Much like CVS you can choose to specify a file (or files) or leave it blank and it will commit everything.

Some other commands:

• svn status foo will show you information about the file, particularly changes that you've made.
• svn diff foo will show you the exact diff of your changes to the server
• svn revert foo will bring you back to the server copy.
• svn log foo will show the log history for that file.

Many of these commands have additional arguments. Get help on diff, for example, like this:

svn help diff

The Subversion Book has more complete documentation and examples for all the commands and options.

Committing Changes to the Release Branch

If you wish to have a change made in the devel branch (aka the trunk) also available in the current release branch, you first need to take note of the revision number from your commit, for example,

$ svn commit -m"Sample commit"
Adding         Rpacks\Biobase\DESCRIPTION
Sending        Rpacks\Biobase\DESCRIPTION
Transmitting file data ..
Committed revision 140.

was revision 140. The changeset you want is -r 139:140, i.e. the changes between r139 and r140.

You'll need to have checked out the branches subdirectory, which is separate from trunk. If you have only checked out the madman subdirectory previously, you'll need to also check out the appropriate branch subdirectory:

svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks

Merge your changes from the trunk to the release branch, check and fix any conflicts, and commit. So, from your release branch directory (e.g. RELEASE_2_6/madman/Rpacks):

svn merge -r 139:140 https://hedgehog.fhcrc.org/gentleman/bioconductor/trunk/madman/Rpacks
svn status   # Look for C, indicating a conflict
             # fix conflicts... (remember to use svn resolve for each)
svn commit -m "merged -r139:140 from trunk"

Having Problems?

Here is a list of possible issues:

• Unrecognized URL scheme: If you see "unrecognized URL scheme" when trying to access the repository, it may indicate that your svn client does not support HTTPS. You can verify the supported "modes" by examining the output of svn --version. If you do not see support for HTTPS, you will need to upgrade your client.

• Username or password not recognized: Most usernames we issue are in the form of an email address. It may help to quote the user name: svn co --username="bob@internet.net". Try double and single quotes.

• Need help arranging access to your package? Use contact information for new package submission.

• Still unresolved? Ask on the bioc-devel mailing list.