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sas

R has been upgraded to version 2.13.1 on the ms workstations and compute servers.

All previously requested packages for R and BioConductor should be available in this newest build; please let us know if you find any problems.

I've installed Firefox 4.0 on the ms workstations but I have not made it the default since this is a .0 release and so a little bit suspect; the Firefox icon will still bring up version 3.5.

But you can try Firefox 4 with the command firefox4 (at a command prompt or via Alt-F2).

SAS 9.2 is now installed on bayes, which is far more capable machine the redpine.

Firefox and Thunderbird have been updated on the ms workstations; you will see a message the next time you start these apps. R 2.12.2 has been installed on the ms workstations, other linux workstatiosn and on the compute servers.

Firefox 3.6.13 and Thunderbird 3.1.7 have been installed on the linux workstations. You will see a slightly confusing question about making these new versions your default when you next run them.

SAS is unavailable temporarily because the only Sun Solaris system, redpine, has crashed. I am working to bring redpine back on-line. The department is reconsidering a linux license for SAS in the event that redpine isn't repairable (the cost for the linux version something line twenty times that of our current Solaris license, thus the reluctance to retire venerable redpine).

The plan, at present, is for the department to make SAS available one way or another.

The problems with the installation of R 2.12.1 on the ms workstations has been corrected.

My R upgrade broke when I propagated it to the ms workstations. For now, the command R will bring up R 2.11.0 instead of 2.12.1.

R 2.12.1 has been installed on the ms workstations, compute servers and other RHPCS-managed linux workstations. BioConductor and previously requested packages have been installed with 2.12.1.

Let us know if any packages are missing or if find any other problems.

Maple 14 has been installed (or is being installed) on all RHPCS-managed workstations and compute servers for which is is licensed. The license server is not responding properly to Maple 13 license requests right now; fixing it will be a low-priority task unless I hear that someone really needs that version.

Firefox, Thunderbird and Adobe Reader have been upgraded on the ms workstations. Things may be a little weird until you restart these applications.

We might have missed installing your favourite application during the workstations upgrade. If you can't find something you need or if something appears to be not working right, please email sysadmin@math.mcmaster.ca.

Thunderbird on the ms workstations has been updated; this is a minor stability/security upgrade. You should close and restart Thunderbird if your session predates this message.

Firefox on the ms workstations was updated on Friday (to ver. 3.6.7) and again today (to ver. 3.6.8); the Adobe Acrobat plugin was also updated. With each update, you will see a "welcome to the new version" message from Firefox and may be asked to select this latest version as your default browser.

R 2.11.0 has been installed on the ms workstations and compute servers.

MATLAB R2010a has been installed on the ms workstations and will be available on the compute servers shortly. The commands matlab (graphical) and matlab-console (text-only) will bring up this latest version; use matlab-r2009a to run the previous release.

R 2.10.1 has been installed on the ms workstations and compute servers and is now the default version. To run the previous version, use the command R-2.9.2.

Firefox on the standard ms workstations has been upgraded from 3.5.4 to 3.5.7; you will see upgrade and default browser notices the next time you start Firefox.

We ran into more problems with the new MATLAB license server. We've gone back to the previous configuration and so this morning's MATLAB problems are resolved.

I will be removing some of the older versions Maple (ver. <= 11), MATLAB (ver. <= 2007b) and R (ver. < 2.9.2) from the compute servers and linux workstations next week; let me know if you need one of these old versions for specific research or instructional reasons. I will be installing R 2.10.0 and MATLAB 2009b at the same time.

We are making changes to the campus MATLAB license server which led to some problems with MATLAB timing out or not starting. Those problems are fixed.

Firefox has been updated to version 3.5.4; the next tim you start firefox, you may see a message about the upgrade and a request to make this update your default browser.

MATLAB wasn't working for half an hour this morning due to a problem with the license server but is now working again. This was unrelated to the upgrades to MATLAB itself.

MATLAB has been upgraded to the latest version (2009a) on the ms workstations and the compute servers. Use matlab to run the graphical version or matlab-console to run the console/text version.

Maple has been upgraded to the latest version (13) on the ms workstations and the compute servers. Use the comand maple for the console/text version and xmaple for the graphical version.

R has been upgraded to the latest version (2.9.2) on the ms workstations and the compute servers.

Earlier this week, I changed the default desktop interface on the ms workstations from KDE to Gnome. I expected this to affect only new users, but it affected everyone who had never changed from the previous default.

You can revert to KDE if you wish by selecting it from the Session menu on the login screen.

The ms workstations (and most other linux gs/pdf/visitor workstations) are running the latest versions of Firefox and Thunderbird as of this afternoon. You may see slight inconsistencies until you close and re-open all Firefox and Thunderbird windows.

Snow Leopard should be available from Titles later this week. By early next week I should have had a chance to investigate incompatibilities and try an upgrade myself.

Thunderbird has been upgraded on the ms workstations. This is a minor update but you will still see a notice re. add-on updates.

Firefox on the ms workstations has been upgraded to version 3.5; see the release notes and tips and tricks pages for details of improvements and new features. You may see some stability problems until close all firefox windows and reopen the browser.

Firefox 3.0.11 has been installed on the ms workstations. This fixes a security flaw publicized yesterday.

Adobe Reader (acroread) has been updated to version 9.1.1 on the ms workstations. This version - just released - protects against a potential exploit in malacious PDF files. There are new versions for OS X and Windows, too.

See the CERT alert for details.

The latest version of R - 2.9.0 - has been installed on the ms workstations and the compute server. To run this version, use the command /usr/local/R/2.9.0/bin/R. The will become the default version started by the command R on May 25th.

Firefox has been updated again due to some stability problems in the previous release. Fingers crossed.

Firefox on the ms workstations has been updated 3.0.9; I hope that this will fix some stability issues with 3.0.8.

Firefox on the ms workstations has been upgraded to version 3.0.8 and this version (not version 2) is now the default. Use the command "firefox2" if you want to run the old version. Note that this version does not have the problem with the new Hotmail that early releases of Firefox 3 did.

Maple was not working on most servers and workstations due to a problem with the license server; the problem has been corrected and Maple works again.

A few people have encountered problems with Firefox 3 so I have rolled back to version 2. You can still use version 3 with the command firefox3 (from the command line or from Alt-F2).

One ms-workstation user has complained that firefox 3 seems slower than firefox 2; I am investigating. If you wish to use the previous version, you can run the command firefox2 from the command line or Alt-F2.

I've upgraded Firefox 3 on the ms workstations from 3.0.3 to 3.0.4, so you may see an upgrade notice again and be asked about your default browser choice.

The latest version of Thunderbird has been installed on the ms workstations. You should notice no changes other than Thunderbird prompting you for add-on upgrades.

The latest version of Firefox has been installed on the ms workstations; this version (3.0.3) is now the default. The problems that arose with the late October Hotmail upgrade appear to be resolved with this new version.

The latest version of Adobe Flash Player (10) has also been installed.

Maple 12 has been installed on the standard linux workstations and is now the default version; use the commands maple and xmaple to run version12. To run version 11, use maple11 and xmaple11.

Maple 11 is now available on the standard linux workstations. Use the command maple or xmaple to run.

R has been upgraded to version 2.7.2 on the ms workstations and compute servers. BioConductor and requested packages are up to date as well.

R 2.7.0 is now installed on the compute servers (bayes, bluespruce, etc.) and the ms workstations.

BioConductor and the previously requested packages have been installed in this latest version.

The Numerical Recipes plug-in for Adobe Reader 8 isn't working properly on the msprime linux workstations. In order to read an NR pdf file, save the file and then open in with acroread7*.

* Either run the command acroread7 from a terminal or right-click a PDF file, select "Open with" and then type in acroead7.

I upgraded the Adobe Reader plugin for firefox on the msprime systems late Wednesday afternoon. You may find that firefox is unstable or behaves oddly until you restart the program (by closing all windows).

In some circumstances, the linux workstations are bringing still opening Acrobat Reader ver. 7 rather than ver. 8 when double-clicking files. You can for the system to use the new version by right-clicking a PDF file, selecting "Open with" and then specifying "acroread8" (this will work in KDE and Gnome).

R has been upgraded to version 2.6.2 on the compute servers and msprime workstations; the latest BioConductor has also beeninstalled. You can still run the previous version on the compute servers with R-2.5. Let me know if any packages are missing in the new version.

I've upgraded Adobe (Acrobat) Reader on the msprime workstations from version 7 to version 8. The primary reason was to resolve a printing problem, but you will also notice that the printing controls are much improved you will no longer need (or be able to use, in fact) 'kprinter -c' to get printer options.

The old version is still available via the command acroread7.

R 2.5 is now installed on bayues and bluespruce; BioConductor and required packages are being installed today.

As announced earlier this month, MATLAB 2007b has been made the default version; you can run older versions with matlab2007a, matlab2006b, etc (likewise for mex and mbuild).

MATLAB 2007b has been installed on the msprime workstations and the compute servers (bluespruce, bayes, etc.). Use the command matlab2007b to run this new version; matlab2007a and matlab2006a will remain available.

As for December 10th, the command matlab will run version 2007b; until then, the command matlab will continue to run version 2006a.

OS X 10.5 has been commercially available for two weeks now. I have been using it on my PowerBook for one week have have installed it on two other systems (a PPC Power Mac and an Intel Mac Pro). Most people will find the upgrade process painless and useful; some should wait for updates.

If you make use of X11 you should most certainly wait to upgrade: X11 (a new port based on x11.org instead of xfree86) has serious problems.

As always, I recommend either a clean install (after copying your /Users folder and any application folders to another disk or parition) instead of an upgrade: it's more work, but you start from a clean, defined point. Alternatively, you can use the "archive and install" option for a similar result.

When Tiger came out, we had access to $40 copies though a bulk purchase arranged by Wilfrid Laurier University; there is no such deal available to us for Leopard. The OS costs $115 at Titles. The Family Pack costs $199 and can be use for five systems, but I'm afraid that research groups do not count as families as far as Apple is concerned.

We now have a wiki server. If you'd like a mediawiki (i.e. wikipedia) wiki for your research group or project, just email me.

Maple 9 has been removed from bluespruce and bayes; the commands maple and xmaple will now invoke Maple 10. Due to new university licensing policy, the department won't be able to upgrade from Maple 9 on the desktop linux workstations.

Maxima, an open-source symbolic algebra package, has been installed on bluespruce and the msprime workstations. Maxima is the descendant of Macsyma, a program upon which Maple was based - Maxima may be considered a sort of "free Maple."
These screenshots give you a good idea of the functionality.

MATLAB 2007a is now available on bayes, bluespruce, freesurface and the msprime workstations. matlab2007a will run the new version; matlab will continue to run version 2006 until July 23rd.

OpenOffice is working again and has been upgraded from 2.0 to 2.2. If the icons in the KDE or Gnome menu don't work, trying logging out and back in to refresh them.

We are seeing problems with the OpenOffice suite on the msprime workstations. The OpenOffice applications (Writer, Calc, Draw and Present) will be unavailable for part of the day while I do some testing and sort things out. You can try KOffice or Abiword and Gnumeric as alternatives for now.

OpenOffice Calc (the OOo spreadsheet application) was not opening when one double-clicked on .xls or .ods files on the msprime workstations; this has been fixed.

It was pointed out to me today that for most people, click OpenOffice Calc, Math or Draw always brought up OpenOffice Write (the word processor); the same was true of the command-line shortcuts oocalc, oomath and oodraw. The icons and commands should now bring up the correct application.

The lab in question has ordered 100 new licences but they have not arrived yet and probably won't for a week or so. We are looking into an interim solution.

Some people have had trouble starting MATLAB today, receiving messages like this:

License Manager Error -4.
Maximum number of users for MATLAB reached.
Try again later.

The problem is that one lab on campus has processes claiming some 80% of the available licenses; we are investigating.

R 2.4.0 has been installed on bayes and the Mandriva 2006.0 msprime hosts. You can run R with the commands R-2.4.0, R-2.3.1, and R; R will continue to run 2.3.1 for the next week or so.

R 2.3.1 was installed along side R 2.1 in August. The command R now runs the newer version.

MATLAB 2006a is being replaced by MATLAB2006b on the servers and workstations. Version 2006b is primarily a bug-fix release and should have no effect on functionality.

Help now works in Maple 9.

Note that Maple 10 will not be available on graduate-student, post-doc or visitor workstations for licensing reasons; Maple 10 is, however. available on the compute servers.

When running MATLAB 2006 on a server(e.g. bayes, bluespruce), manipulating plots may cause a linux workstation to crash. Run this command at the start of a session or .m file in order to avoid the problem:
opengl software

This does not appear to be a problem when displaying back to OS X systems nor when running MATLAB 2006 locally.

MATLAB 2006a was installed in June along side MATLAB R14SP3; the former version is now the default.

The commands matlab and mex will now invoke version 2006a. Use the commands matlab14sp3 and mex14sp3 to invoke the previous versions.

This applies to the Hamilton Hall msprime workstations and to the compute servers bayes, bluespruce and freesurface. Other systems will be updated in the coming week.

Intel Fortran and MKL have been upgraded on bluespruce and freesurface to versions 9.1.036 (from 9.0) and 8.1.1( from 8.0), respectively.

R 2.3.1 (released June 6th by the R Project) has been installed on bayes; use the command R-2.3.1 to run this new version. R 2.1.1 will remain the default version run by the command R until September 1st.

R 2.3.1 will be installed on the msprime workstations in Hamilton Hall and the T13-109 workstations this week.

The command splus on bayes will now invoke version 7.0 instead of version 6.2; use the command splus6 to run the older version.

Splus 6.2 is working on bayes again now that a license-manager problem has been fixed. Note that version 7.0 is now the default; use splus6 to run version 6.2.

OpenOffice was not working on a few of the msprime workstations late last week; it is working again. Please send email if you are still having problems.

MATLAB Release 2006a (version 7.2.0.294) has been installed on the shared compute servers and the network workstations in Hamilton Hall and T13-109; use the command matlab2006a to run this version. Please let me know if you encounter anything weird. I plan to make the version the default (currently R14SP3) come August.

See the Release Notes for more information.

The latest version of Firefox and Thunderbird have been installed on the msprime and T13-109 workstations. There are minor updates featuring security and stability patches; you may see an upgrade notice the next time you run the applications.

Maple 10 is now available on bluespruce, bayes and freesurface. Use the commands xmaple10 or maple10; maple and xmaple will continue to start Maple 9 until June 15th.

Maple 10 will not be available on the msprime workstations until some problems to do with licensing costs are resolved.

I end up mentioning the screen utility a few times each month, so I'm putting mention of it here, even though it's hardly computing news. screen is an invaluable but under-used utility. Very simply, it allows you to have detachable shell: you can work in the shell, close it down, and pick it up again with everything inside still running. For example:

From your office:

ssh bayes
screen -a
R
<crtl>-a d
logout

From home:

ssh mathserv
ssh bayes
screen -r

... and there you are back at the R prompt. If you had set an R command running, it will have continued running in the background.

The licensing problem has been sorted and S-Plus 6.2 is now available on bayes again. S-Plus 7.0 is now installed, too.

To run version 6.2:
splus6

To run version 7.0:
splus7

The command splus will continue to run version 6.2 until the end of May, 2006; as of June 1st, it will instead run version 7.0

GAP (Groups, Algorithms, Programming), a system for computational discrete algebra, has been installed on the msprime workstations and the two applied-group compute servers bluespruce and freesurface.

See the GAP site for documentation and examples.

I've upgraded firefox on the msprimefrom 1.5 to 1.5.0.1. Sounds fabulously uniteresting, but I'm hoping that this will resolve some stability problems we've been experienced, as promised in the release notes.

You can now ssh to mathserv even if all you have access to is a Web browser:
http://mathserv.mcmaster.ca/ssh

Having heard no objections, I have made MATLAB R14SP3 the default on the bayes, freesurface, bluespruce and the msprime systems (in place of R14SP2). That is, the command matlab will now invoke R14SP3.

MATLAB R14SP2 and R14SP3 may be invoked specifically via the commands matlab14sp2 and matlab14sp3.

I have also removed these versions (where present) from the msprime workstations and the compute servers: R13, R14, R14SP1.

Intel has announced that they will release (Intel) OS X versions of their c++ and Fortran 95 compilers and the Math Kernel Library. No release date was announced.

http://www.intel.com/cd/ids/developer/asmo-na/eng/227389.htm

The latest releases of versions 8 and 9 of the Intel Fortran compilers and versions 7 and 8 of the Math Kernel Libraries have been installed on freesurface, bayes and the msprime workstations.

Firefox and Thunderbird on the Hamilton Hall msprime and T13-109 workstations have been updated.

Intel Fortran 9.0 has been installed on bayes and the msprime workstations. Version 8 is still available and is still the default.

G95 - the free, open source Fortran 95 compiler and runtime libraries - has been installed on the msprime workstations and the statistical server, bayes.

Enter g95 to run and g95 --help for options. More information is available on the G95 project page.

R 2.1.1 has been installed on bayes and the msprime workstations.