Hi, Sage is a great tool. I've been waiting for R/rpy integration and I see that recent versions have R/rpy bundled. One problem I've encountered is that basic plotting with rpy in sage doesn't seem to work -- however, I've got a simple workaround which might be worth posting somewhere.
Here's the machine & version info: [balajis:~]$uname -a Darwin Macintosh-8.local 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 i386 MacBookPro1,1 Darwin [balajis:~]$sage -v | SAGE Version 3.1.1, Release Date: 2008-08-17 And here's the example bug: *No output is generated when I run r.hist(r.rnorm(20))*. [balajis:~]$sage ---------------------------------------------------------------------- | SAGE Version 3.1.1, Release Date: 2008-08-17 | | Type notebook() for the GUI, and license() for information. | ---------------------------------------------------------------------- sage: r.rnorm(20) [1] -0.49087837 -1.94011412 1.71741910 -0.89248178 0.73915490 -0.46471049 -0.42553938 0.46196391 [9] 0.33025458 1.02435878 -1.12997555 -0.08253489 -1.59833466 1.32528999 -0.32348019 2.29304930 [17] -0.54705933 0.10793088 1.28371034 0.36289179 sage: r.hist(r.rnorm(20),xlab="",ylab="",main="") [1] 20 This *should* be generating a plot and a histogram object, but it's just returning the number of arguments. Here's a workaround which does what I want -- note that I call it "rr" so it doesn't overlap with the built-in r. [balajis:~]$sage ---------------------------------------------------------------------- | SAGE Version 3.1.1, Release Date: 2008-08-17 | | Type notebook() for the GUI, and license() for information. | ---------------------------------------------------------------------- sage: from rpy import r as rr sage: rr.rnorm(10) [-0.58609553556082361, -0.075660923360481733, -0.69609524980131876, 1.7004392323744253, -1.5274655764987806, -1.6461045004296775, -0.6132766826900824, 0.0019692315208043763, 1.309716715308654, -1.1077072723136909] sage: rr.hist(rr.rnorm(10),xlab="",ylab="",main="") {'breaks': [-1.5, -1.0, -0.5, 0.0, 0.5, 1.0], 'counts': [2, 2, 1, 2, 3], 'density': [0.39999992000001605, 0.40000000000000008, 0.20000000000000001, 0.40000000000000002, 0.60000000000000009], 'equidist': True, 'intensities': [0.39999992000001605, 0.40000000000000008, 0.20000000000000001, 0.40000000000000002, 0.60000000000000009], 'mids': [-1.25, -0.75, -0.25, 0.25, 0.75], 'xname': 'c(0.98537142230916, -0.748763617907383, -0.527738177570716, -0.186196733768228, 0.911294217964427, -1.45795735527173, 0.343719696116503, 0.0333727688883639, -1.06629162286718, 0.932158759550036)'} A plot is also displayed, though it's an X11 plot generated by the rpy module rather than one of sage's pngs. This is a hack but a decent one, which allows integration of existing R/rpy code with sage libraries. One important caveat: moving around the X11 window or doing anything which causes a refresh can result in "bus errors" like the following. This seems particularly frequent when calling rpy without the xlab="",ylab="",main="" keyword arguments for the plot, as then there's a lot of cruft all over the X11 window. sage: rr.hist(rr.rnorm(100)) {'breaks': [-3.0, -2.5, -2.0, ... -1.84307690299984, 0.145126483019115)'} #UP to this point, normal output of hist sage: Error during wrapup: #<---- Now the errors start *** caught bus error *** *** caught bus error *** *** caught bus error *** *** caught bus error *** #<--- several Ctrl-C's required to get to this point Fatal Python error: GC object already tracked *** caught bus error *** address 0x2c, cause 'non-existent physical address' Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: /Applications/sage/local/bin/sage-sage: line 216: 2535 Abort trap sage-ipython "$@" -c "$SAGE_STARTUP_COMMAND;" [balajis:~]$ #<-------- Eventually dumps me to the prompt Any ideas on how to fix this? R has a lot of powerful visualization capabilities and it'd be great to call it from within sage without problems... --B -- Balaji S. Srinivasan, Ph.D. Stanford University Visiting Scholar, Depts. of Statistics and Computer Science 318 Campus Drive, Clark Center S251 (650) 380-0695 [EMAIL PROTECTED] http://jinome.stanford.edu --~--~---------~--~----~------------~-------~--~----~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~----------~----~----~----~------~----~------~--~---