[R-sig-Fedora] evince not showing "greek" and "math" in *.pdf plots
Paul Murrell
p@u| @end|ng |rom @t@t@@uck|@nd@@c@nz
Tue Mar 12 22:10:15 CET 2024
Hi
I don't think this is an R issue (it is separate from the Cairo Symbol
font problem).
For PDF output, R actually relies on the Symbol font having the Adobe
Symbol Encoding (Appendix D of the PDF Reference
https://opensource.adobe.com/dc-acrobat-sdk-docs/pdfstandards/pdfreference1.7old.pdf)
and just outputs the font as "Symbol", which relies on it being one of
the Standard 14 Fonts ...
"These fonts have built-in encodings that are unique to each
font."
... and ...
"These fonts, or their font metrics and suitable substitution fonts,
must be available to the consumer application."
In other words, R passes the buck to the viewer to either have access to
the Adobe Symbol font or use a substitute that has all of the necessary
glyphs (and in that case, presumably to also take care of satisfying the
Adobe Symbol Encoding).
It is possible for the R user to specify a different font name for the
symbol font for PDF output, but that font has to have all of the
necessary glyphs and it has to follow the Adobe Symbol Encoding or all
bets are off.
Paul
On 12/03/24 06:59, Iñaki Ucar wrote:
> Martin, I wouldn't rule out an R issue yet. Fonts are... tricky. So I'm
> cc'ing Paul Murrell here.
>
> I tried several viewers here and I see the following: Chrome, Firefox
> and Libreoffice Draw show the symbols; however, evince, okular and
> xournal++ agree on **not** showing the symbols. **If** there is a bug,
> the bug would be in fontconfig, because these ones AFAIK properly
> delegate on fontconfig, which is the system-wide component that decides
> what font substitution should be made for any given font. However, I see:
>
> $ fc-match Helvetica
> NimbusSans-Regular.otf: "Nimbus Sans" "Regular"
>
> which is the right choice. And okular confirms this by showing in a
> properties dialog that it is substituting Helvetica with URW's Nimbus
> Sans Regular. So why aren't the symbols displayed? My best guess is that
> this has something to do with how R encodes such symbols. Paul
> introduced some changes to fix similar issues for Cairo devices when
> Fedora dropped support for Type 1 fonts, see [1]. Now, I'm no font
> expert, but it seems to me that the pdf device may require similar
> fixes. (And why do xpdf or Firefox show the glyphs... I have no idea. I
> guess they do their thing without asking fontconfig).
>
> [1]
> https://blog.r-project.org/2020/04/17/changes-to-symbol-fonts-for-cairo-graphics-devices/ <https://blog.r-project.org/2020/04/17/changes-to-symbol-fonts-for-cairo-graphics-devices/>
>
> Peter, as an aside, note that cairo_pdf embeds the fonts by default.
>
> Best,
> Iñaki
>
> On Mon, 11 Mar 2024 at 15:31, <pstils using gmail.com
> <mailto:pstils using gmail.com>> wrote:
>
> Hi Martin and Tim,
>
> I also have this bug. Though I think not necessarily with all the same
> fonts as Martin.
>
> Using Martin's code:
>
> https://imgur.com/a/ILUoe3H
> <https://imgur.com/a/ILUoe3H>
>
> Fedora 39, Evince 45.0
>
> It's a bug with Evince. I think. I think it's substituting in a font
> set that doesn't have all the required symbols. I think it should be
> possible to install the required fonts, but I haven't found a solution
> that way, yet.
>
> Nevertheless, the following should work, and may be a better solution
> anyway, given that embedding the fonts is probably more cross-
> platform/viewer friendly:
>
>
> You can embed the fonts if you have Ghostscript installed (I think it
> comes with Fedora already(?) if not then:
>
> sudo dnf install ghostscript
>
> )
>
>
> You can then use the embedFonts() function in R:
>
> (pdfil <- paste0("plotmath-example_R",
> with(R.version, paste0(major, sub("[.]", "", minor))),
> ".pdf"))
>
> pdf(pdfil)
> example(plotmath); mtext(R.version.string)
> dev.off()
>
> # Use embedFonts to embed the fonts in the PDF
> embedFonts(file = pdfil, outfile = paste0("embedded-example", pdfil),
> options = "-dPDFSETTINGS=/prepress")
>
>
> if(interactive()) {
> system(paste("evince", paste0("embedded-example", pdfil), "&"))
> }
>
>
>
> Or you can do it in the terminal:
>
>
> gs -dNOPAUSE -dBATCH -dPDFSETTINGS=/prepress -sDEVICE=pdfwrite -
> dEmbedAllFonts=true -sOutputFile=plotmath-example-output_embedded.pdf -
> f plotmath-example_R432.pdf
>
>
> Compare:
>
>
> Embedded:
>
> ❯ pdffonts plotmath-example-output_embedded.pdf
> name type encoding emb sub uni object ID
> ---------------------- -------- -------- --- --- --- ------ ---
> KHEPSB+Helvetica Type 1C Custom yes yes no 10 0
> WNPVSJ+Symbol Type 1C Custom yes yes no 12 0
> MQBKOK+Helvetica-Bold Type 1C WinAnsi yes yes no 20 0
>
>
> Original:
>
> ❯ pdffonts plotmath-example_R432.pdf
> name type encoding emb sub uni object ID
> ---------------------- -------- -------- --- --- --- ------ ---
> Helvetica Type 1 Custom no no no 16 0
> Helvetica-Bold Type 1 Custom no no no 17 0
> Symbol Type 1 Symbol no no no 18 0
>
>
> I hope this works for you. Like I said, I *think* it's a problem with
> Evince so it's probably better to file a bug report with them, but I
> also think embedding fonts isn't such a bad idea anyway - you'll know
> the output will display as intended regardless of the viewer on the
> user's system. It does lead to a larger file-size, but I think these
> days we can live with that.
>
> Thanks,
> Peter
>
>
>
>
> On Mon, 2024-03-11 at 14:15 +0100, Martin Maechler wrote:
> > > > > > > Tim Taylor
> > > > > > > on Mon, 11 Mar 2024 11:42:35 +0000 writes:
> >
> > > Hi Martin
> > > Probably not the answer you're looking for but on the latest
> > Fedora 39 (workstation edition) both locally, and on a freshly
> > installed VM (with just R-core installed), all fonts render correctly
> > for me in evince.
> >
> > > $ evince --version
> > > GNOME Document Viewer 45.0
> >
> > > $ R --version
> > > R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
> > > Copyright (C) 2024 The R Foundation for Statistical Computing
> > > Platform: x86_64-redhat-linux-gnu (64-bit)
> >
> > > It may be worth sharing more details about your installation
> > (e.g. Fedora version) to see if anyone has any ideas.
> >
> > > Tim
> >
> > Thank you, Tim.
> >
> >
> > Fedora is 38 :
> >
> > $ lsb_release -a
> > LSB Version: :core-5.0-amd64:core-5.0-noarch:cxx-5.0-amd64:cxx-
> > 5.0-noarch:desktop-5.0-amd64:desktop-5.0-noarch:languages-5.0-
> > amd64:languages-5.0-noarch:printing-5.0-amd64:printing-5.0-noarch
> > Distributor ID: Fedora
> > Description: Fedora release 38 (Thirty Eight)
> > Release: 38
> > Codename: ThirtyEight
> >
> > $ evince --version
> > GNOME Document Viewer 44.3
> >
> > R version does not matter at all.
> > Same phenomenon in several versions of R I have installed
> > simultaneously (from source).
> > As I mentioned, I'm slightly misusing the list for non-R problem
> > that I encounter a lot with R {because I like to use
> > "plotmath"}, so I apologize in advance.
> >
> > Maybe it's rather a matter of fonts installed in
> > /usr/share/fonts/ ??
> >
> > Martin
> >
> > > On Mon, 11 Mar 2024, at 10:51 AM, Martin Maechler wrote:
> > >> This problem has bugged me for several years now,
> > >> and our own IT staff has tried a few things, but then never
> > >> cared enough to persist fixing it.
> > >>
> > >> It *is* a bug in evince, the standard pdf viewer on Fedora and
> > >> IIUC also quite few other Linux distributions, and
> > >> *not* a bug in R; hence I am asking for help/hints here.
> > >>
> > >> A very simple example:
> > >>
> > >> --------------------------------------------------------------
> > -----------------
> > >>
> > >> (pdfil <- paste0("plotmath-example_R",
> > >> with(R.version, paste0(major, sub("[.]", "", minor))),
> > ".pdf"))
> > >> ## "plomath-example_R433.pdf"
> > >>
> > >> pdf(pdfil)
> > >> example(plotmath); mtext(R.version.string)
> > >> dev.off()
> > >>
> > >> if(interactive())
> > >> system(paste("evince", pdfil, "&"))
> > >>
> > >> --------------------------------------------------------------
> > -----------------
> > >>
> > >> The pdf contains 4 pages, and in all of them *some* of the
> > math
> > >> symbols are replaced by open rectangles -- because evince does
> > >> not find the fonts it should.
> > >>
> > >> E.g.
> > >> - page 1: \pi is properly shown, \phi not
> > >> - page 2: all greek letters, \theta, \xi, \eta are *not*
> > shown
> > >> ...
> > >>
> > >> Simply typing
> > >>
> > >> example(plotmath)
> > >>
> > >> in the R console will show you everything as it should be but
> > is
> > >> not for us, using evince.
> > >>
> > >> However, *everything* is rendered correctly, if I use very old
> > >> 'xpdf' {which you may have to install
> > >>
> > >> ## OTOH: This always work fine with the very old 'xpdf' :
> > >> system(paste("xpdf", pdfil, "&"))
> > >>
> > >> So the fonts *are* somewhere on my machine, but evince does
> > not
> > >> find them;
> > >>
> > >> How should our IT people fix this?
> > >>
> > >> IIRC they did install the Zapf Dingbats fonts -- which then
> > are
> > >> found by xpdf but not by evince ?
> > >>
> > >>
> > >> Thank you in advance,
> > >> Martin
> > >>
> > >> _______________________________________________
> > >> R-SIG-Fedora mailing list
> > >> R-SIG-Fedora using r-project.org <mailto:R-SIG-Fedora using r-project.org>
> > >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
> <https://stat.ethz.ch/mailman/listinfo/r-sig-fedora>
> > >>
> >
> > > [[alternative HTML version deleted]]
> >
> > _______________________________________________
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>
> --
> Iñaki Úcar
--
Dr Paul Murrell (he/him)
Te Kura Tatauranga | Department of Statistics
Waipapa Taumata Rau | The University of Auckland
Private Bag 92019, Auckland 1142, New Zealand
64 9 3737599 x85392
paul using stat.auckland.ac.nz
www.stat.auckland.ac.nz/~paul/
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