[R-pkgs] New Quantian releases with almost all of CRAN / BioC
edd at debian.org
Thu Mar 2 04:16:00 CET 2006
[ I hope this is not considered off-topic for the list:
A new Quantian release was just announced, and it contains even more R.
As before, we have R (now 2.2.1), ESS, Ggobi, Rpy, several BioInfo tools
-- but now we also have RSPerl, JGR, rJava and more. A full sync to CRAN
and BioC as of Feb 25, 2006 now yields dim(installed.packages())
of 877. Feedback welcome, but preferably on the quantian-general
lists (which requires subscriptions to keep the spammers out).
The original announcement is below. I also welcome careful forwarding
to other audiences or communities I may not reach.
-- Thanks, Dirk ]
(Please see note  below regarding recipients for this posting. Thanks!)
Quantian 0.7.9.2 is the second Quantian release based on Knoppix 4.0.2.
Quantian adds hundreds of scientific / numeric packages, as well as the
an openMosix enabled 2.4.27 kernel, to the cdrom version of Knoppix.
Version 0.7.9.2 ships as one compressed iso file of 2.7gb that is
Relative to the previous release 0.7.9.1, several small bugs have been
fixed, Sun's Java 1.5.0 SDK has been added along with several Java-based
applications (ImageJ, Weka, JGR, Mondrian), several other applications
have been added, yet more R packages from CRAN and BioC are included and
a few other packages have been updated.
Quantian now contains over 2550 Debian packages, over 870 packages
for R and a few extra applications.
Quantian comes as one bootable dvd iso of 2.85 gb (compressed) with
over 7.6 gb (uncompressed) of software of interest to quantitative
analysists, scientists, researchers or students.
Announcing Quantian release 0.7.9.2
I What is it?
Quantian is a remastering of Knoppix, the self-configuring and directly
bootable cdrom/dvd that turns any pc or laptop into a full-featured Linux
workstation, and (parts of) clusterKnoppix, which adds support for
openMosix-based cluster computing. However, Quantian differs from
Knoppix by having a particular focus on quantitative, numerical or
scientific applications, and hence adds a very large set of programs of
interest to applied or theoretical workers in quantitative or data-driven
fields to the solid base provided by Knoppix..
See http://dirk.eddelbuettel.com/quantian.html for more details.
II What Quantian highlights should I care about ?
o Second release based on Knoppix 4.0.2: Derived from the cdrom version of
Knoppix, Quantian utilises the unionfs setup of Knoppix to combine two
compressed loop images for a total of 2.85 gb (from two files of 1.66 gb
and 1.19 gb) corresponding to over 7.6 gb of software.
o KDE 3.4/3.5, Kernel 2.6.12; added backport of kernel 2.4.27 with
openMosix patch for continued openMosix support including unionfs
support (that was missing in 0.7.9.1)
o Some highlights in 0.7.9.2 are
- Java support via the 'Java 1.5.0' SDK from Sun, installed via
the packages from www.debian-unofficial.org; this allowed us to
add ImageJ, Weka, Mondrian and JGR.
- some other packages that were added: celestia, cervisia, gcj,
gnuhtml2latex, inkscape, octplot, oprofile, prospect, praat, rserve,
wxmaxima, xalan, (x)orsa as well as many library additions/upgrades
- even more complete R support with 877 packages (25 from 'core R',
another 76 from Debian packages, and 779 directly installed from CRAN
and BioConductor, covering over 99% of all packages at CRAN and
BioConductor [ not counting a handful of windows-only CRAN packages]
for complete coverage as of 25 Feb 2006), ESS editing in Emacs /
XEmacs, GGobi visualization, Rpad webinterface, the award winning JGR
'Java GUI for R', RSPerl, Rserve, an early release of the RKward GUI
- continued strong bioinformatics/biology support:
BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade,
bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki,
mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview,
t-coffee, textopo, ImageJ, and more;
- continued strong mathematics / computational algrebra support: axiom,
blacs, calc, euler, gap, giac, mathomatic, maxima, pari, scalapack,
scilab, texmacs, yacas, yorick;
- continued strong visualization / graphics support: dx, garlic, gdpc,
gnuplot, grace, grass, gri, illuminator, kst, labplot, mayavi,
matplot, proj, plplot, plotmtv, rasmol, starplot, vtk, xd3d, xgraph,
- large number of programming and scripting languages, editors,
debuggers and libraries;
- excellent latex support with auctex, lyx, kile, texmacs interface,
as well as numerous macro packages, bibtex tools;
- office support via openoffice and koffice suites, abiword, gnumeric
and other applications;
- plus all the tools and toys from the current Knoppix relase.
o See http://dirk.eddelbuettel.com/quantian/changelog.html for details.
o See http://dirk.eddelbuettel.com/quantian/howto.html for several
short HOWTOs on booting Quantian from hd on either Windows or Linux,
booting via a bootcd (such as clusterKnoppix), or botting from a
USB memory device. Contributions, corrections, and feedback on these
HOWTOs is always appreciated.
III Where do I get it?
o Downloads are available from the main host at Seattle at FHCRC:
and at the East Coast at
The most recent release is also available at
Note that file size of 2.75 gb may upset web caching system such
as squid. It may be prudent to rely on rsync or bittorrent instead
o Bittorrents should be available shortly at
o The main European mirrors should catch up shortly:
o CD/DVD vendors will probably update their offerings soon as well.
See the Quantian site for a list.
IV Mailing lists
o Two mailing lists exist for Quantian
quantian-announce for announcements, intended to be low volume
quantian-general for general discussions about Quantian
for subscription info etc., and start using the quantian-general lists
for general questions, comments, suggestions or discussions about
Quantian-general is subscribed to quantian-announce, so you only need
to subscribe to one (but can of course subscribe to both). Posting to
quantian-general requires a subscription.
Reply-To: for this message is quantian-general at lists.alioth.debian.org
so that discussions can be continued on the list.
V Bugs fixed from 0.7.9.1
o The missing default boot option for isolinux has been added, simply
pressing return at the boot prompt (or waiting) now yields kernel 2.6.
o Marco Caliari figured out how to add unionfs support to Kernel 2.4.27,
so we now have openMosix support with the full 7.5 gb of software!
o Progress from Debian's C++ transition allowed us to update many KDE
packages, including kdvi. KDE is in parts updates to release 3.5, some
applications are still from release 3.4. Several other applications
that were uninstallable in 0.7.9.1 because of C++ library conflicts
(celestia, gdal) are now included.
VI Known Bugs in 0.7.9.2
o Only under kernel 2.4.27, kdesktop comes up with an error message
that needs to be acknowledged. Konsole then has a broken color schema.
Simply selecting a working schema, and manually running kdesktop fixes
o No other issue as of 28 Feb 2006. Please report anything you notice
to the quantian-general mailing list.
VII Other items
o Feedback / poll on package additions or removal
As always, I welcome comments and suggestions about programs to be
added or removed. Existing Debian packages, and possibly existing
rpm packages, typically get inserted quite readily.
Please send feedback, questions, comments, ... to the
quantian-general at lists.alioth.debian.org
list to maximise the number of eyes glancing at any one question.
Notice that a subscription to the list is needed in order to post.
o Feedback would also be appreciated on ways to better communicate with
difference scientific communities that could be interested in Quantian.
 This email is sent via the quantian-announce mailing list. I have
subscribed those whose email addresses are in my quantian mail folder
due to prior emails. The quantian-announce mailing list only sends
moderator-approved posts -- so there should be no spam whatsoever.
Anybody who considers this unwanted is kindly asked to send me
a private mail to get unsubscribed immediately.
Best regards, Dirk
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
More information about the R-packages