On Fri, 27 Apr 2007, Matthew Neilson wrote: > Hey again, > > Just to let you know that I managed to test out R-2.5.0, and the transparency > glitch has thankfully disappeared. I apologise for wasting your time with > this. > > One final question, though. Did you mean to say that the known transparency > bug was fixed in version 2.5.0? Or was it fixed in a patched version of > R-2.4.0? Only asking because, if the final Panther binary (version 2.4.0) > available on CRAN doesn't fix the bug, there's no point in me installing this > on top of my happily working (and otherwise fully functional) version of R.
I meant to say '2.4.0 patched', which became 2.4.1. The release of 2.4.0 has the bug: NEWS says o A request for an opaque colour in the pdf() device after a translucent one did not set the transparency back to opaque in 2.4.0. Semi-transparent background colours were not being plotted on the pdf() device. > > Many thanks, > > > -Matt > > > > On 27 Apr 2007, at 13:35, Matthew Neilson wrote: > >> Hi Brian, >> >> Terribly sorry if I accidentally broke a rule. sessionInfo() produces the >> following: >> >>> sessionInfo() >> R version 2.2.1, 2005-12-20, powerpc-apple-darwin7.9.0 >> >> attached base packages: >> [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" >> [7] "base" >> >> I cannot upgrade to the latest version of R, since I'm using OS X 10.3.9 >> (Panther) and the latest builds require 10.4.4 (Tiger) or greater. It's >> interesting to know that R version 2.4.0 >> contains a transparency bug, though - I'll ask IT Services to install the >> latest version of R on the G5 and see if that helps. >> >> Many thanks for all your help, >> >> >> -Matt >> >> >> >> On Fri Apr 27 12:58 , Prof Brian Ripley <[EMAIL PROTECTED]> sent: >> >>> The posting guide says >>> >>> For questions about unexpected behavior or a possible bug, you should, >>> at a minimum, copy and paste the output from sessionInfo() into your >>> message. >>> >>> If you are using an old version of R and think it does not work >>> properly, upgrade to the latest version and try that, before posting. >>> >>> [There is a known bug in 2.4.0 related to semi-transparency, fixed in >>> 2.4.0. I would not have attempted to answer a question about 2.1.1, and >>> we do rely on people seeking free technical assistance doing their bit.] >>> >>> >>> On Fri, 27 Apr 2007, Matthew Neilson wrote: >>> >>>> Thanks for your fast response. >>>> >>>> I'm using R version 2.1.1 on OS X 10.3.9 to create the pdfs. I have tried >>>> viewing the pdf output in both Acrobat 6 and 7 (both display a white >>>> border around each polygon) as well >> as >>>> Preview (displays fine). I have emailed the pdf file to some >>>> correspondents running Windows, and they also see white borders when >>>> viewing with Acrobat (version unspecified). >>>> >>>> I have tried using R version 2.4.0 on a G5 machine (which I can access >>>> remotely) running OS X 10.4.8, but the resulting pdf renders incorrectly >>>> (i.e. with a white border around >> each >>>> polygon) in both Acrobat *and* Preview. So it would appear that the >>>> combination of R 2.1.1 and OS X 10.3.9 gives slightly better results - >>>> although plots still appear incorrect >> when >>>> printed or viewed in Acrobat. >>>> >>>> Unfortunately, I don't have access to a Windows machine to test this out. >>>> Even if I did, many of my scripts include various Unix system calls so I >>>> don't think that would be a viable >>>> solution. Could this be a bug in the OS X pdf driver? >>> >>> The R pdf() device is the same on all platforms. >>> >>>> Many thanks, >>>> >>>> >>>> -Matt >>>> >>>> >>>> >>>> On 27 Apr 2007, at 06:42, Prof Brian Ripley wrote: >>>> >>>>> What version of R, what OS, what version of Acrobat? >>>>> >>>>> I don't see this in 2.5.0 on Windows (using Acrobat 7: Acrobat does not >>>>> exist on Linux, AFAIK). And reading the PDF produced shows no sign of >>>>> an >>>>> extra object for the border. >>>>> >>>>> On Fri, 27 Apr 2007, Matthew Neilson wrote: >>>>> >>>>>> Hey all, >>>>>> >>>>>> I'm trying to create a plot of two semi-transparent regions. The reason >>>>>> they need to be partially transparent is so that I can see if there's >>>>>> any overlap. Here's some example >> code: >>>>>> >>>>>> # BEGIN >>>>>> >>>>>> pdf(file="test.pdf",version="1.4") >>>>>> plot(0,0,type="l",ylim=range(-3,3),xlim=range(-1,5)) >>>>>> polygon(c(0,1,2,3,4,3,2,1,0), c(0,1,2,1,0,-1,-2,-1,0), >>>>>> col=rgb(1,0,0,0.5), >>>>>> border=NA) >>>>>> polygon(c(1,2,3,4,5,4,3,2,1), c(0,1,2,1,0,-1,-2,-1,0), >>>>>> col=rgb(0,0,1,0.5), >>>>>> border=NA) >>>>>> dev.off() >>>>>> >>>>>> # END >>>>>> >>>>>> The problem with this is that, despite setting "border = NA", I get a >>>>>> big white border surrounding each polygon!! Funnily enough, setting the >>>>>> alpha channel equal to 1 (as opposed to 0.5) *doesn't* give the border, >>>>>> but an alpha channel of 1 produces an opaque polygon! :S >>>>>> >>>>>> I have read the FAQ, and (unfortunately) turning off line-art smoothing >>>>>> does not give the desired effect. Furthermore, my pdfs print with a >>>>>> white border surrounding each transparent polygon. >>>>>> >>>>>> Now, here comes the really bizarre part. Whilst Adobe Acrobat displays >>>>>> the unwanted white border, Apple Preview respects the "border=NA" >>>>>> argument and shows the two diamonds as they are intended. However, >>>>>> opening up the pdf in Illustrator CS reveals that there is in fact a >>>>>> transparent (according to Illustrator) border *on top* of each diamond. >>>>>> Deleting these two borders (one for each polygon) and re-saving the pdf >>>>>> appears to correct the issue. So the obvious question is: how did the >>>>>> surrounding borders get there in the first place? A bug in the polygon >>>>>> function, perhaps? >>>>>> >>>>>> Does anyone have any ideas for preventing these unwanted borders around >>>>>> semi-transparent polygons (without having to resort to Illustrator)? >>>>>> Has >>>>>> anyone else even come across this problem? >>>>>> >>>>>> Many thanks, >>>>>> >>>>>> >>>>>> -Matt >>>>>> >>>>> >>>>> -- >>>>> 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, UK Fax: +44 1865 272595 >>>> >>>> ______________________________________________ >>>> R-help@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 >>>> and provide commented, minimal, self-contained, reproducible code. >>>> >>> >>> -- >>> 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, UK Fax: +44 1865 272595 >> >> ______________________________________________ >> R-help@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 >> and provide commented, minimal, self-contained, reproducible code. >> >> > > -- > ************************************ > Matthew Neilson > University of Strathclyde > Department of Mathematics > Livingstone Tower > 26 Richmond Street > Glasgow G1 1XH > > Tel : + 44(0)141 548 4559 > e-mail : [EMAIL PROTECTED] > ************************************ > -- 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, UK Fax: +44 1865 272595 ______________________________________________ R-help@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 and provide commented, minimal, self-contained, reproducible code.