Dirk Eddelbuettel
2005-Dec-14 13:00 UTC
[R] [R-pkgs] New Quantian release with over 800 CRAN/BioC packages
[ Reposting this here as this Quantian release contains - all CRAN packages as of December 10, 2005 * except the Windows only ones (BRugs, mimR, rcom, RWinEdt) * and three that would not build (Rlsf, ROracle, rJava) for lack of Java, Oracle or rlsf - all BioC packages for release 1.8 * excecpt RMAGEML (needs Java) - for a total of over 800 R packages - a couple other R niceties: (X)Emacs + ESS, Ggobi, Rpad, RKward...) I hope this isn't considered off-topic here; if so please let me know in private mail and I will refrain from posting in the future. -- Dirk ] (Please see note [1] below regarding recipients for this posting. Thanks!) Executive Summary: Quantian 0.7.9.1 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 0.6.9.3, 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 0.7.9.1 ================================== 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 0.7.9.1 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: http://quantian.fhcrc.org/ rsync://quantian.fhcrc.org/quantian/ and at the East Coast at http://research.warnes.net/downloads/quantian/CURRENT/ ftp://research.warnes.net/users/edd/quantian/CURRENT/ The most recent release is also available at http://quantian.alioth.debian.org/ 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 http://www.tlm-project.org/public/distributions/quantian/ o The main European mirrors should catch up shortly: http://sunsite.rediris.es/mirror/quantian http://sunsite.informatik.rwth-aachen.de/ftp/pub/Linux/quantian 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 http://alioth.debian.org/mail/?group_id=30303 for subscription info etc., and start using the quantian-general lists for general questions, comments, suggestions or discussions about Quantian. 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 Known Bugs in 0.7.9.1 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 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. 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 quantian-general at lists.alioth.debian.org 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 _______________________________________________ R-packages mailing list R-packages at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-packages
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