Short report on Debian at UseR! 2007 conference at Iowa State Univ.
UseR! 2007 at Iowa State University, Ames, IA, August 8-10, 2007
Following two successful UseR! conferences in Vienna in 2004 and 2006, the
first North American UseR! was help last week at Iowa State. I presented two
papers of which one has specific Debian content (more on that one below).
I. General Debian / Ubuntu feedback
Having maintained R and related packages for a number of years, and having
gone to four R conferences, I am somewhat recognised as the R/Debian link.
There are a number of Debian users among the R users and developers, though
there may now be more Ubuntu users. One sees the odd Fedora Core machine,
but in general there is always a surprisingly large number of Macs and the
obvious wintel ones. People seem happy with Debian and Ubuntu, though still
too few R users and developers seem to know that there are 'backports' of the
current R release for testing and different Ubuntu releases on every CRAN
mirror below bin/linux/. [ I help in this backporting effort, as did Chris
Steigies in the past, but it is mostly non-DDs Johannes Ranke (for Debian
backports) and Vincent Goulet (for Ubuntu) ]. So I was asked a few questions
about how to get R 2.5.1 onto Ubuntu 6.06 LTS or 7.04 and it is really just
an apt-get update away.
I gave a talk on automated builds of CRAN/BioC package (see below) and at the
outset asked the audience how many actually ran Debian or Ubuntu and about a
fifth to a quarter raised their hand -- but that is of course a self-selected
We generally have a pretty decent reputation in this community. No other
distro had included R as early as 1997, and we have more add-ons and related
software than other distros. People acknowledge that Debian/Ubuntu 'just
work' and most are happy that this allows them to concentrate on their work.
Also, quite a few (if not most Linux machines) of the backends of CRAN, and
releated services, are using Debian.
II. Paper / presentation on 2000 new Debian packages --
"Would you like 2000 new Debian packages with that?"
Something we hadn't really reported back to Debian is the relative success
and current status of the 'pkg-bioc' project at Alioth.
It goes back to something that Matt Hope (aiming for BioConductor.org, an R
repository for bioinformatics) and I (aiming for CRAN, R's core repo) had
started sort-of at the same time around 2003 or 2004, then merged and which
puddled along somewhat slowly. Steffen Moeller, an Alioth guest-member for
years and a very recent new DD, and David Vernazobres, also an Alioth
guest-member, did A LOT of work over the last 12 to 18 months, and I started
to chip in little bits here or there too.
The big news is that we can now build most of the around two thousand source
packages [ around 900 from CRAN and 1100 from BioC, I concentrate more on
CRAN; Steffen focusses more on BioC, and David does everything ] for R from
the CRAN and BioConductor archives. That's what our paper that I presented
was about, as well as an earlier presentation / paper Steffen gave two months
ago in Italy .
This was well received at the conference. Among the self-selected crowd of
Debian (or Ubuntu) users, the upside of this was clear, and most seem to
agree with the reasons we give in the paper as motivation. (In a nutshell:
dependencies work, convenience of 'build one install often', quality control,
scalability, common platform, different architectures, large audience -- see
the paper for discussion).
The big question is what to do with these 2000 packages. The process is
still too manual and fragile to be called 'production class'. Eventually
this should move somewhere -- either CRAN itself, or, less likely, be part of
Debian. I do say less likely here because I don't hink that two-thousand
machine-generated packages could reach the Debian QA standards. They are
also, as a large class, too esoteric. CRAN, on the other hand, builds
binaries for Windows, so this could be a better fit. Someone suggested
R-Forge -- which is a rather recent 'SF / Alioth for R' based on Debian's
gforge packages. Also, one question had to do with how to avoid 'waits' for
new packages -- people wouldn't want to wait for packages to reach testing
when this can take months. So a distinct backport service may be the best
option. Manpower and mirrors may be the crux.
 Slides and papers are at http://dirk.eddelbuettel.com/presentations.html
but note that neither paper had a DD as the target audience
Comments especially on II would be welcome. Please CC me on replies as I am
no longer subscribed to debian-devel.
Three out of two people have difficulties with fractions.