Paul Johnson
2004-Oct-11 18:08 UTC
[R] Diagnosing trouble with R-2.0, Fedora Core 2, and Rcmdf
Greetings, R-help! On 2 Fedora Core 2 Linux systems, i've completely erased the previous R and all packages and then installed R-2.0 and installed fresh packages. In using Rcmdr, I see some trouble and I wonder if other people see this and if it is due to the tcl/tk, or R, or Rcmdr. (If readers have not yet tried Rcmdr, I recommend it not just because of the GUI it provides, but also because Prof. Fox has created several very handy commands, like scatter3d, which make it possible to use advanced packages like rgl. Rcmdr provides several very handy wrapper commands that "just work" and users don't have to fuss over so many details! And, if you are new at R, you can use pull down menus and then Rcmdr displays the commands that correspond with those menu options. Very educational!) In no particular order, here are the issues I see with R-2.0 and Rcmdr 1. In the panel to select a dataset from a package (nenu: Data/Data in packages), I can type in the name of a dataset, but the GUI will not let me choose the name of a package from which to select a dataset. Nothing happens when I pick a package name. (With previous R/Rcmdr, I did not have this trouble). 2. When using Rcmdr, some of the output from commands shows in the Rcmdr bottom window, but some is sent to the xterm in which R was started. For example, with a scatter3d() command, if I add the option model.summary=T, the model summary shows in the xterm. But some other models show results in the bottom pane of Rcmdr. And, it seems to me, there are some commands in which I've noticed some of the output going to the Rcmdr bottom buffer and some to the xterm. 3. When I want to exit Rcmdr and choose the pull down "exit from Commander and R", I get a Segmentation Fault that closes Rcmdr and R. 4. 3d plots do not display on the screen until I click in the rgl window that displays the graph. This might be a video card/AGP driver problem, I suppose. These systems have the NVidia FX5200 cards and the NVidia proprietary X driver. If other users don't see the same on other kinds of systems, I guess that will tell me where the problem lies. 5. At random times, I get an error tcl/tk window popping up with a message about MASS and categorical variables. It says Error in data(package=parse(text=packageName)); 'MASS' must be character string or NULL It says that over and over, sometimes it has other package names, as in: Error in data(package=parse(text=packageName)); 'relimp' must be character string or NULL These seem to be harmless? -- Paul E. Johnson email: pauljohn at ku.edu Dept. of Political Science http://lark.cc.ku.edu/~pauljohn 1541 Lilac Lane, Rm 504 University of Kansas Office: (785) 864-9086 Lawrence, Kansas 66044-3177 FAX: (785) 864-5700
John Fox
2004-Oct-12 13:20 UTC
[R] Diagnosing trouble with R-2.0, Fedora Core 2, and Rcmdf
Dear Paul, I'm currently out of town, limiting a bit my ability to answer these questions definitively, but I'll give it a shot (hoping that my memory isn't faulty): On Mon, 11 Oct 2004 13:08:39 -0500 Paul Johnson <pauljohn at ku.edu> wrote:> Greetings, R-help! > > On 2 Fedora Core 2 Linux systems, i've completely erased the previous > R and all packages and then installed R-2.0 and installed fresh > packages. > > In using Rcmdr, I see some trouble and I wonder if other people see > this and if it is due to the tcl/tk, or R, or Rcmdr. (If readers > have not yet tried Rcmdr, I recommend it not just because of the GUI > it provides, but also because Prof. Fox has created several very > handy commands, like scatter3d, which make it possible to use > advanced packages like rgl. Rcmdr provides several very handy wrapper > commands that "just work" and users don't have to fuss over so many > details! And, if you are new at R, you can use pull down menus and > then Rcmdr displays the commands that correspond with those menu > options. Very educational!) > > In no particular order, here are the issues I see with R-2.0 and > Rcmdr > > 1. In the panel to select a dataset from a package (nenu: Data/Data > in packages), I can type in the name of a dataset, but the GUI will > not let me choose the name of a package from which to select a > dataset. Nothing happens when I pick a package name. (With previous > R/Rcmdr, I did not have this trouble). >The problem is that the Rcmdr code doesn't quote the name of the package. I believe that I've fixed this problem, but haven't posted the fixed version either to my web site or to CRAN.> 2. When using Rcmdr, some of the output from commands shows in the > Rcmdr bottom window, but some is sent to the xterm in which R was > started. For example, with a scatter3d() command, if I add the option > model.summary=T, the model summary shows in the xterm. But some > other models show results in the bottom pane of Rcmdr. And, it seems > to me, there are some commands in which I've noticed some of the > output going to the Rcmdr bottom buffer and some to the xterm. >As I recall, I've fixed this problem as well, but perhaps not in a completely general way. Again, I haven't yet released the fixed version.> 3. When I want to exit Rcmdr and choose the pull down "exit from > Commander and R", I get a Segmentation Fault that closes Rcmdr and R. >This I haven't seen before.> 4. 3d plots do not display on the screen until I click in the rgl > window that displays the graph. This might be a video card/AGP > driver problem, I suppose. These systems have the NVidia FX5200 > cards and the NVidia proprietary X driver. If other users don't see > the same on other kinds of systems, I guess that will tell me where > the problem lies. >I believe that I've noticed this problem on a Quantian system.> 5. At random times, I get an error tcl/tk window popping up with a > message about MASS and categorical variables. It says >This reflects the first problem, and is produced by the way that the Rcmdr initially suppresses and then reports warnings. I'll check further when I return home. Sorry for the problems. John> Error in data(package=parse(text=packageName)); > 'MASS' must be character string or NULL > > It says that over and over, sometimes it has other package names, as > in: > > Error in data(package=parse(text=packageName)); > 'relimp' must be character string or NULL > > These seem to be harmless? > -- > Paul E. Johnson email: pauljohn at ku.edu > Dept. of Political Science http://lark.cc.ku.edu/~pauljohn > 1541 Lilac Lane, Rm 504 > University of Kansas Office: (785) 864-9086 > Lawrence, Kansas 66044-3177 FAX: (785) 864-5700 > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html-------------------------------- John Fox Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/
John Fox
2004-Oct-13 00:23 UTC
[R] Diagnosing trouble with R-2.0, Fedora Core 2, and Rcmdf
Dear Paul, I've now had a chance to check into these problems further:> -----Original Message----- > From: r-help-bounces at stat.math.ethz.ch > [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Paul Johnson > Sent: Monday, October 11, 2004 1:09 PM > To: r help > Subject: [R] Diagnosing trouble with R-2.0, Fedora Core 2, and Rcmdf > > Greetings, R-help! > > On 2 Fedora Core 2 Linux systems, i've completely erased the > previous R and all packages and then installed R-2.0 and > installed fresh packages. > > In using Rcmdr, I see some trouble and I wonder if other > people see this and if it is due to the tcl/tk, or R, or > Rcmdr. (If readers have not yet tried Rcmdr, I recommend it > not just because of the GUI it provides, but also because > Prof. Fox has created several very handy commands, like > scatter3d, which make it possible to use advanced packages like rgl. > Rcmdr provides several very handy wrapper commands that "just > work" and users don't have to fuss over so many details! And, > if you are new at R, you can use pull down menus and then > Rcmdr displays the commands that correspond with those menu > options. Very educational!) > > In no particular order, here are the issues I see with R-2.0 and Rcmdr > > 1. In the panel to select a dataset from a package (nenu: > Data/Data in packages), I can type in the name of a dataset, > but the GUI will not let me choose the name of a package from > which to select a dataset. Nothing happens when I pick a > package name. (With previous R/Rcmdr, I did not have this trouble). >I had in fact fixed this in the development version of the package (Rcmdr 0.9-12). I've now posted that to my web site, at <http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/index.html>. I'd like to do some more testing before sending this version to CRAN.> 2. When using Rcmdr, some of the output from commands shows > in the Rcmdr bottom window, but some is sent to the xterm in > which R was started. For example, with a scatter3d() command, > if I add the option model.summary=T, the model summary shows > in the xterm. But some other models show results in the > bottom pane of Rcmdr. And, it seems to me, there are some > commands in which I've noticed some of the output going to > the Rcmdr bottom buffer and some to the xterm. >I did in fact try to deal with this problem. The solution that I employed didn't work for scatter3d() with model.summary=TRUE, since the printed summaries were produced as side effects by scatter3d(). That's a bad practice, and I've fixed it; now scatter3d() returns a list of summaries, and the Rcmdr can cope with that. (As you know, it's not my intention that model.summary=TRUE be set from the Rcmdr GUI, but it's better to have it work if you enter this from the script editor.) You imply, however, that there are other cases of this problem. It would help to know what they are -- assuming that they're not fixed in the development version now on my web site.> 3. When I want to exit Rcmdr and choose the pull down "exit > from Commander and R", I get a Segmentation Fault that closes > Rcmdr and R. >I haven't been able to duplicate this problem, to this point testing only under Windows XP. Does this occur only when an rgl graphics device is open? (The Rcmdr should close the rgl device before it exits.)> 4. 3d plots do not display on the screen until I click in the > rgl window that displays the graph. This might be a video > card/AGP driver problem, I suppose. These systems have the > NVidia FX5200 cards and the NVidia proprietary X driver. If > other users don't see the same on other kinds of systems, I > guess that will tell me where the problem lies. >As I said, I believe that I've seen this problem before under Quantian. It would help to know whether it's peculiar to the Rcmdr, scatter3d(), or rgl.> 5. At random times, I get an error tcl/tk window popping up > with a message about MASS and categorical variables. It says > > Error in data(package=parse(text=packageName)); > 'MASS' must be character string or NULL > > It says that over and over, sometimes it has other package > names, as in: > > Error in data(package=parse(text=packageName)); > 'relimp' must be character string or NULL > > These seem to be harmless?This should go away now that problem 1 is fixed. Regards, John> -- > Paul E. Johnson email: pauljohn at ku.edu > Dept. of Political Science http://lark.cc.ku.edu/~pauljohn > 1541 Lilac Lane, Rm 504 > University of Kansas Office: (785) 864-9086 > Lawrence, Kansas 66044-3177 FAX: (785) 864-5700 > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html