[R] [R-pkgs] New Quantian release with over 800 CRAN/BioC packages

From: Dirk Eddelbuettel <edd_at_debian.org>
Date: Thu 15 Dec 2005 - 00:00:27 EST

[ Reposting this here as this Quantian release contains

(Please see note [1] below regarding recipients for this posting. Thanks!)

Executive Summary:

    Quantian is the first Quantian release based on Knoppix 4.0.2.     Quantian adds hundreds of scientific / numeric packages, as well as the     openMosix enabled 2.4.27 kernel, to the cdrom version of Knoppix.     

    Relative to the previous release, hundreds of applications have     been updated, and many new applications (such as polyxmass, scigraphica,     kst, octaviz, gromacs) have been added. Quantian now contains over 2400     Debian packages, and over 800 packages for R.

    Quantian comes as one bootable dvd iso of 2.5gb (compressed) with     almost 7 gb (uncompressed) of software of interest to quantitative     analysts, scientists, researchers or students.

Announcing Quantian release

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 First 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 2.5 gb (from two files of 2.0 gb
      and 425 mb) corresponding to almost 7 gb of software.

    o KDE 3.4, Kernel 2.6.12; added backport of kernel 2.4.27 with openMosix
      patch for continued openMosix support [ but note that openMosix and
      unionfs seem to conflict so kernel 2.4.27 only sees the first
      compressed loop image ]

    o Some highlights in are

- very complete R support with over 800 packages (28 from 'core R',
another 70 from Debian packages, and 724 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 ] ), ESS editing in Emacs/XEmacs, GGobi visualization, Rpad webinterface, and initial support for the RKward GUI;
- even stronger bioinformatics/biology support than before:
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, and more;
- continued strong mathematics / computational algrebra support: axiom,
blacs, calc, euler, gap, giac, mathomatic, maxima, pari, scalapack, scilab, texmacs, yacas, yorick;
- strong visualization / graphics support: dx, garlic, gdpc, gnuplot,
grace, grass, gri, illuminator, kst, labplot, mayavi, matplot, proj, plplot, plotmtv, rasmol, starplot, vtk, xd3d, xgraph, ygraph;
- 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 2.5 gb may upset web caching system such
      as squid. It may be best to rely on rsync or bittorrent instead
      of http.

    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

      available via


      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@lists.alioth.debian.org
      so that discussions can be continued on the list.

V Known Bugs in

    o Debian's current C++ transition affects the KDE packages. Several

      packages had to be installed from the stable relase, and a few
      (celestia, gdal) are currently uninstallable. This should should
      improve over the next few weeks/months.
    o Kdvi is broken. However, xdvi works as do the various pdf previewers
      so (PDF)LaTeX use is still possible.

    o As noticed above, when openMosix and kernel 2.4.27 are used, the
      second compressed loop image is not accessible implying that the 
      /opt, /usr/games, /usr/lib/j2se, /usr/share/doc, /usr/src, /usr/NX
      directories are not accessible.

VI 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 

      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.

VII Notes

    [1] 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. Otherwise, replies and
        follow-ups should go to   
	where posting may require an initial subscription.

Best regards, Dirk

Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison

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Received on Thu Dec 15 00:18:30 2005

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