[R-SIG-Mac] Bug Report

[Byron Ellis]

Fortunately, this problem goes away in R-devel. You can also output
directly to a file (or the clipboard) as a pixel-identical TIFF (or
other supported format, including PDF (but not EPS, you can output
Photoshop though...)

On Fri, Feb 15, 2008 at 3:03 PM, Daschbach, John L
<John.Daschbach at pnl.gov> wrote:
> Richard,
>     This problem has been around for a while.  Based on an earlier reply
>  from Simon on this I find the following has always worked.
>
>  quartz.save('tmp.pdf',type='pdf')
>  Sys.sleep(4)
>  quartz.save('fig4.pdf',type='pdf')
>
>     I recall that plotting twice rather than just the delay helps, but I
>  don't have notes on that.
>
>     As far as machine speed is concerned I don't think it is necessarily due
>  to slow machines.  I had the problem on a slow box (G4 2 procs) and also on
>  my new box (PowerMac 2.6 GHz, 4 cores, with only idle and system programs
>  running other than R).
>
>     The Quartz output is really nice looking, but many of the journals we
>  publish in want eps or tiff for final figures.  Also, if your co-authors use
>  Word and not LaTeX then the pdf figures in the manuscript don't look so
>  great either.  The ghostscript conversion usually works, but the quality is
>  lower than the original pdf.  We have found converting to a high resolution
>  tiff (very large files) is the most reliable way to get figures in journals
>  without problems.
>
>  -John
>
>
>  On 2/13/08 5:53 AM, "Simon Urbanek" <simon.urbanek at r-project.org> wrote:
>
>  > Richard,
>  >
>  > thanks for the report. The issue is known and the only (known) cure
>  > lies in R-devel's new Quartz.
>  > It seems to be triggered by concurrency - e.g. on my machine your
>  > example produces five equal and correct PDF plots without problems -
>  > hence it occurs more often on slower machines. You may find several
>  > post about this bug on this mailing list and some suggestions on how
>  > to deal with it (adding delays before saving, preventing output and
>  > probably in your case not starting new devices each time).
>  >
>  > Cheers,
>  > Simon
>  >
>  > On Feb 13, 2008, at 7:40 AM, Richard Martin wrote:
>  >
>  >> Good Morning,
>  >>
>  >> I believe I have found a bug within R.app. It's a problem with
>  >> quartz.save() which _seems_ to manifest itself when using par(mfcol)
>  >> to create multi-window graphs (and hence affects topology plots etc).
>  >>
>  >> I have created a script which will repeat the bug _most_ of the time.
>  >>
>  >> for(i in 1:5) {
>  >>
>  >> quartz()
>  >> par(mfcol=c(2,2))
>  >> plot(1:10, type="b")
>  >> plot(1:10, type="b")
>  >> plot(1:10, type="b")
>  >> plot(1:10, type="b")
>  >> quartz.save(paste(i, ".pdf"), type="pdf")
>  >>
>  >> }
>  >>
>  >> EXPECTED OUTCOME: 5 files, named 1.pdf to 5.pdf, containing 4 graphs.
>  >> Each pdf should be identical.
>  >> ACTUAL OUTCOME: The pdf files are most often not equal. Sometimes
>  >> individual plots are left off the graphs (such that 1.pdf contains
>  >> only 2 or 3 plots, for example). More seriously, in some instances
>  >> console text is superimposed in a translated manner over the graphs
>  >> themselves. This can be seen in the attached pdf.
>  >>
>  >> R version information follows:
>  >>
>  >>> R.Version()
>  >> $platform
>  >> [1] "i386-apple-darwin8.10.1"
>  >>
>  >> $arch
>  >> [1] "i386"
>  >>
>  >> $os
>  >> [1] "darwin8.10.1"
>  >>
>  >> $system
>  >> [1] "i386, darwin8.10.1"
>  >>
>  >> $status
>  >> [1] ""
>  >>
>  >> $major
>  >> [1] "2"
>  >>
>  >> $minor
>  >> [1] "6.2"
>  >>
>  >> $year
>  >> [1] "2008"
>  >>
>  >> $month
>  >> [1] "02"
>  >>
>  >> $day
>  >> [1] "08"
>  >>
>  >> $`svn rev`
>  >> [1] "44383"
>  >>
>  >> $language
>  >> [1] "R"
>  >>
>  >> $version.string
>  >> [1] "R version 2.6.2 (2008-02-08)"
>  >>
>  >> R.app version information:
>  >> R 2.6.2 GUI 1.23 (4932) (4932)
>  >>
>  >> Mac Information:
>  >> Version 10.5.2, build 9C31
>  >>
>  >> If you have any idea how to work around this bug, I'd be most
>  >> greatful. If you need any more information or I can help in any way,
>  >> please email.
>  >>
>  >> Kind Regards,
>  >>
>  >> Richard Martin
>  >> Research Officer,
>  >> University of Essex,
>  >> Colchester,
>  >> Essex,
>  >> CO4 3SQ
>  >>
>  >>
>  >> --
>  >> Contendere, Explorare, Invenire, et non Cedere
>  >> <2 .pdf>_______________________________________________
>  >> R-SIG-Mac mailing list
>  >> R-SIG-Mac at stat.math.ethz.ch
>  >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>  >
>  > _______________________________________________
>  > R-SIG-Mac mailing list
>  > R-SIG-Mac at stat.math.ethz.ch
>  > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>  _______________________________________________
>  R-SIG-Mac mailing list
>  R-SIG-Mac at stat.math.ethz.ch
>  https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>



-- 
Byron Ellis (byron.ellis at gmail.com)
"Oook" -- The Librarian