Re: [R] plotmath overstrikes in output on a Linux system
On Tue, Apr 8, 2008 at 1:23 PM, Paul Johnson [EMAIL PROTECTED] wrote: On Tue, Apr 8, 2008 at 4:29 AM, Prof Brian Ripley [EMAIL PROTECTED] wrote: Looks likes the the laptop is using different fonts with incorrect font metrics. This could happen because it has a different screen resolution, or one of the systems is set to use scalable fonts or it is giving metrics for one fonts and using another or I found a fix for the funny font overlaps, and it was quite by accident. In case there are other Fedora users for whom this might appear, I would like to close the thread with this. In the livna repository, there is a package called freetype-freeworld-2.3.5-3.lvn8 After installing that, the fonts on screen are fine. I do not understand exactly why this works, or why freetype-freeworld is not in the freetype distribution all along. The package is described thusly, and you will notice it has the same magic words that Professor Ripley used--hints and glyphs: $ rpm -qi freetype-freeworld Name: freetype-freeworld Relocations: (not relocatable) Version : 2.3.5 Vendor: rpm.livna.org Release : 3.lvn8Build Date: Tue 18 Sep 2007 10:28:30 AM CDT Install Date: Sun 13 Apr 2008 11:16:45 PM CDT Build Host: plague-builder.livna.org Group : System Environment/Libraries Source RPM: freetype-freeworld-2.3.5-3.lvn8.src.rpm Size: 685309 License: FTL or GPLv2+ Signature : DSA/SHA1, Sat 22 Sep 2007 10:23:19 AM CDT, Key ID 71295441a109b1ec Packager: rpm.livna.org http://bugzilla.livna.org URL : http://www.freetype.org Summary : A free and portable font rendering engine Description : The FreeType engine is a free and portable font rendering engine, developed to provide advanced font support for a variety of platforms and environments. FreeType is a library which can open and manages font files as well as efficiently load, hint and render individual glyphs. FreeType is not a font server or a complete text-rendering library. This version is compiled with the patented bytecode interpreter and subpixel rendering enabled. It transparently overrides the system library using ld.so.conf.d. -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plotmath overstrikes in output on a Linux system
I've been testing plotmath. But I'm getting some funny output one one computer. The problem is that characters are 'jumbled' and overstrike when symbols are introduced. Sample code: mu - 440.0 sigma - 12.5 myx - seq( mu - 4*sigma, mu+ 4*sigma, length.out=500) myDensity - dnorm(myx,mean=mu,sd=sigma) # Here's one way to retrieve the values of mu and sigma and insert them into an expression t1t2 - bquote (paste(Normal(, mu== .(mu), ',', sigma== .(sigma),)) ) plot(myx, myDensity, type=l, xlab=X, ylab=Probability Density , main=t1t2) I have tested this code and it works on two desktop Fedora Linux 8 systems to make a nice figure, but on a Dell Laptop with Fedora Linux 8 and R 2.6.2, something funny happens: the characters overstrike each other. The Greek letter mu is printed several spaces to the left of the ( that it is supposed to follow. I made an itty bitty picture of the figure title to show you: http://pj.freefaculty.org/R/plotmath_problem.png I can force in spaces to re-arrange the symbols so they do not overstrike. The following looks fine in the output. t1t2 - bquote (paste(Normal ( , mu== .(mu), ' , ', sigma== .(sigma), )) ) ### Note spaces manually inserted above are needed, otherwise plotmath overlaps l of plot(myx, myDensity, type=l, xlab=X, ylab=Probability Density , main=t1t2) What do you suppose is wrong? The X configuration? -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotmath overstrikes in output on a Linux system
Looks likes the the laptop is using different fonts with incorrect font metrics. This could happen because it has a different screen resolution, or one of the systems is set to use scalable fonts or it is giving metrics for one fonts and using another or BTW, this is probably nothing to do with plotmath per se -- the issue is most likely the device (presumably X11(), but you did not say) and its handling of font metric requests. It looks to me as if the widths of normal text strings (and not symbols) is the problem. I have seen something similar where there was a long-standing bug in plotmath (fixed in r44534), but this only manifested itself when text was kerned, which the X11() device in 2.6.2 does not ask for. My best guess is that the font selected is (to use the technical terms) returning glyph widths without left/right bearings. Please try 2.7.0 beta, which has a different X11() device (and the above bug fixed). That ought to solve the problem for you, but otherwise you'll need to debug what the X11 metricInfo callback is giving you. On Tue, 8 Apr 2008, Paul Johnson wrote: I've been testing plotmath. But I'm getting some funny output one one computer. The problem is that characters are 'jumbled' and overstrike when symbols are introduced. Sample code: mu - 440.0 sigma - 12.5 myx - seq( mu - 4*sigma, mu+ 4*sigma, length.out=500) myDensity - dnorm(myx,mean=mu,sd=sigma) # Here's one way to retrieve the values of mu and sigma and insert them into an expression t1t2 - bquote (paste(Normal(, mu== .(mu), ',', sigma== .(sigma),)) ) plot(myx, myDensity, type=l, xlab=X, ylab=Probability Density , main=t1t2) I have tested this code and it works on two desktop Fedora Linux 8 systems to make a nice figure, but on a Dell Laptop with Fedora Linux 8 and R 2.6.2, something funny happens: the characters overstrike each other. The Greek letter mu is printed several spaces to the left of the ( that it is supposed to follow. I made an itty bitty picture of the figure title to show you: http://pj.freefaculty.org/R/plotmath_problem.png I can force in spaces to re-arrange the symbols so they do not overstrike. The following looks fine in the output. t1t2 - bquote (paste(Normal ( , mu== .(mu), ' , ', sigma== .(sigma), )) ) ### Note spaces manually inserted above are needed, otherwise plotmath overlaps l of plot(myx, myDensity, type=l, xlab=X, ylab=Probability Density , main=t1t2) What do you suppose is wrong? The X configuration? -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotmath overstrikes in output on a Linux system
Paul Johnson wrote: I've been testing plotmath. But I'm getting some funny output one one computer. The problem is that characters are 'jumbled' and overstrike when symbols are introduced. Sample code: mu - 440.0 sigma - 12.5 myx - seq( mu - 4*sigma, mu+ 4*sigma, length.out=500) myDensity - dnorm(myx,mean=mu,sd=sigma) # Here's one way to retrieve the values of mu and sigma and insert them into an expression t1t2 - bquote (paste(Normal(, mu== .(mu), ',', sigma== .(sigma),)) ) plot(myx, myDensity, type=l, xlab=X, ylab=Probability Density , main=t1t2) I have tested this code and it works on two desktop Fedora Linux 8 systems to make a nice figure, but on a Dell Laptop with Fedora Linux 8 and R 2.6.2, something funny happens: the characters overstrike each other. The Greek letter mu is printed several spaces to the left of the ( that it is supposed to follow. I made an itty bitty picture of the figure title to show you: http://pj.freefaculty.org/R/plotmath_problem.png I can force in spaces to re-arrange the symbols so they do not overstrike. The following looks fine in the output. t1t2 - bquote (paste(Normal ( , mu== .(mu), ' , ', sigma== .(sigma), )) ) ### Note spaces manually inserted above are needed, otherwise plotmath overlaps l of plot(myx, myDensity, type=l, xlab=X, ylab=Probability Density , main=t1t2) What do you suppose is wrong? The X configuration My guess would be that something is wrong with the font metrics on one system. If the length of Normal( is miscalculated, that would explain the rest. Do you see the same thing if you do something like plot(0, main=quote(paste(Lengthy string, A))) It could be related to dpi settings; I seem to recall that this can do weird things on wide-screen displays. Doex xdpyinfo provide any clues? Look for lines like this screen #0: dimensions:1024x768 pixels (260x195 millimeters) resolution:100x100 dots per inch You could also play with the pointsize argument to X11() and see if the problem disappears at different sizes. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotmath overstrikes in output on a Linux system
On Tue, Apr 8, 2008 at 4:29 AM, Prof Brian Ripley [EMAIL PROTECTED] wrote: Looks likes the the laptop is using different fonts with incorrect font metrics. This could happen because it has a different screen resolution, or one of the systems is set to use scalable fonts or it is giving metrics for one fonts and using another or BTW, this is probably nothing to do with plotmath per se -- the issue is most likely the device (presumably X11(), but you did not say) and its handling of font metric requests. It looks to me as if the widths of normal text strings (and not symbols) is the problem. I have seen something similar where there was a long-standing bug in plotmath (fixed in r44534), but this only manifested itself when text was kerned, which the X11() device in 2.6.2 does not ask for. My best guess is that the font selected is (to use the technical terms) returning glyph widths without left/right bearings. Please try 2.7.0 beta, which has a different X11() device (and the above bug fixed). That ought to solve the problem for you, but otherwise you'll need to debug what the X11 metricInfo callback is giving you. I installed R-latest from the beta directory. Following your leads, I've got some information that may help you see if this is purely an isolated X11 problem on my computer or something you might fix in R. On screen, I see this bad looking plot: http://pj.freefaculty.org/R/png-screenshot-notOK.png Using a png device to write the graph to file, either with dev.copy(png ... ) or png (file = ) plot ( ) dev.off() The saved file is GOOD: http://pj.freefaculty.org/R/png-output-OK.png http://pj.freefaculty.org/R/png_dev_copy_OK.png More details about this laptop. The display has a native resolution of 1680x1050, and IF I put the X11 display at that resolution, then the on-screen X11 display of that particular graph is fine. However, if I change the display to another value, the one I prefer is 1400x1050, and re-start, then I see the bad on-screen display. In both cases, however, I have confirmed that the DPI settings in xdpyinfo are correctly representing pixels/inches. That leads me back to Prof. Ripley's suggestion that I've got a mismatch in fonts between what X11 really wants and what it gets. The font configuration on these systems is becoming so complicated I'm completely bewildered, as Fedora has both traditional linux font server and xft fonts and pango/cairo and freetype and apparently anything else they can think of. I'm going to keep studying the R admin guide to see how to debug it. off topic Finally, something came up that I don't want to forget. It is an RPM building question for R fans. This concerns my experience with R-beta-20080407.r45159. R built installed without any apparent trouble, and I decided to try to make an RPM package of it so other Fedora people can test. I took the spec file from the existing Fedora 8 updates R package, and made a few changes to suit the new file name for R, and I built RPMS. The build proceeds without noticeable trouble, but when I try to install the RPM, I get this error $ sudo rpm -ivh R-2.7.20080407.r45159-1fc8.1.i386.rpm Password: error: Failed dependencies: perl(R::Dcf) is needed by R-2.7.20080407.r45159-1fc8.1.i386 perl(R::Logfile) is needed by R-2.7.20080407.r45159-1fc8.1.i386 perl(R::Rd) is needed by R-2.7.20080407.r45159-1fc8.1.i386 perl(R::Rdconv) is needed by R-2.7.20080407.r45159-1fc8.1.i386 perl(R::Rdtools) is needed by R-2.7.20080407.r45159-1fc8.1.i386 perl(R::Utils) is needed by R-2.7.20080407.r45159-1fc8.1.i386 perl(R::Vars) is needed by R-2.7.20080407.r45159-1fc8.1.i386 As you can see, the package does have the perl modules, but something has gone wrong in the scripting process that takes note of them: $ rpm -qilp R-2.7.20080407.r45159-1fc8.1.i386.rpm | grep perl /usr/share/R/perl /usr/share/R/perl/File /usr/share/R/perl/File/Copy /usr/share/R/perl/File/Copy/Recursive.pm /usr/share/R/perl/R /usr/share/R/perl/R/Dcf.pm /usr/share/R/perl/R/Logfile.pm /usr/share/R/perl/R/Rd.pm /usr/share/R/perl/R/Rdconv.pm /usr/share/R/perl/R/Rdlists.pm /usr/share/R/perl/R/Rdtools.pm /usr/share/R/perl/R/Utils.pm /usr/share/R/perl/R/Vars.pm /usr/share/R/perl/Text /usr/share/R/perl/Text/DelimMatch.pm /usr/share/R/perl/build-help-windows.pl /usr/share/R/perl/build-help.pl /usr/share/R/perl/massage-Examples.pl I'm contacting the RPM maintainer from redhat to see if he knows. But if you know, please let me know. -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
