Bioconductor changelog

The Bioconductor changelog is based on the blosxom blogging software, which allows us to have a single page that contains all the current posts for all packages, as well as individual pages for each package. In addition, blosxom creates an RSS feed that you can subscribe to, so you will be informed of any changes without having to actually go to the website.

There are many different ways to view the changelog:

• Point your browser to the main page, for the last 40 posts.
• See the last 40 posts for a particular package by clicking the package name in the blue bar on the left of the main page.
• See the posts for a particular year by appending the year onto the main page URI. For instance, adding 2007 to the end of the URI will show just the posts from 2007.
• See the posts for a particular month by appending the year followed by the month to the URI (e.g., adding 2007/10, will show just the posts from October 2007).
• See the posts for a particular day by appending the year, month, and day to the URI (e.g., 2007/10/27 will give just the posts for that day).
• The year/month/day trick also works for particular packages, so adding limma/2007/10/27 to the URI will do what you should expect by now.
• Adding index.rss to the end of any particular URI will give you the RSS feed, to which you can then subscribe (assuming your browser is compliant, which IE6 is not). For instance, if you are interested in changes to Biobase, you can subscribe by adding Biobase/index.rss will give you the RSS feed, from which you can subscribe if you are using an RSS compliant browser.
• Alternatively, you can subscribe to a particular feed using an RSS reader (such as Google Reader, Thunderbird, etc.) by inputting the correct URI, with the index.rss at the end.

Developers

The changelog is produced by automatically parsing the SVN logs, so there is a simple rule in place that determines what will or won't be published here. In general, whatever you put in your commit message will show up unless you:

• Don't use a commit message (e.g., svn commit -m ""), which is not the ideal thing to do.
• Prepend a # to the beginning of any line that you don't want published.

Please consider two things when making commits.

1. This changelog is intended to allow either end-users or fellow developers to know what changes have been made to your package. It is difficult for you to know if a change is important to somebody else, so more information is always better than less.
2. Bioconductor is both Open Source as well as open development. This implies that both the software and the development of the software are supposed to be freely available to all, with the intention that this openness will allow us as a group to produce world class software. Using useful commit messages and limiting the self-censorship that is possible here are both consistent with the goals of this project.

There has been some confusion about what constitutes a line, and how many #'s are required to comment out a commit message. In Python, (which is what is used to parse the SVN logs) and AFAIK all other computer languages, a line is ended with a newline character '\n', which when you are typing is created by hitting the return key. Therefore, you can have a complete paragraph commented out by doing something like this:

This is the beginning of a commit message and will end up in the changelog.

# This is part of the commit message that might not be interesting to others. There are several sentences here, but since I never hit the return button, Python will just think it is a single line. Therefore the whole thing will be scrubbed, even if it was line-wrapped when you wrote it.

You might however want to add something else that you would like to end up in the changelog. If you don't prepend a # to that line (like this one here), it will end up in the changelog.