[R] [R-pkgs] New Quantian releases with almost all of CRAN / BioC

Dirk Eddelbuettel 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())[1] 
  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 [1] below regarding recipients for this posting. Thanks!)

Executive Summary: 

    Quantian 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 ships as one compressed iso file of 2.7gb that is
    Relative to the previous release, 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

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

    o Some highlights in 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
        and more.

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

V   Bugs fixed from

    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 because of C++ library conflicts
      (celestia, gdal) are now included.

VI  Known Bugs in

    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.

VIII 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.

Best regards,  Dirk

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

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