Please update to the latest version. Most importantly, this fixes a bug arising from a not-backward-compatible update to the igraph-package. It sounds like a needed change for that package, but results in most of the packages that use igraph to fail once the latest igraph version is installed.
This has been fixed for phyloseq. More details on the fix, and complete installation instructions can be found at the phyloseq installation instructions page.
Please feel free to post wiki suggestions for examples, new features, and definitely any issues or bugs! I aim to be very fast on responding to user requests, particularly in the cases if there are functional bugs, since I know this can slow down the already-difficult research everyone is doing.
Bugs, other issues, suggestions, and feature requests can all be posted at the phyloseq issues page. In principle you could also post requests for tutorials and examples on the wiki at this page as well, but an alternative might be to post those requests here on this blog, as an empty wiki page on the phyloseq wiki, or by simply sending me an email with specifics and any example code or other data that might help me turn-out a reproducible example as fast as possible.
Thanks!
joey
