[R-sig-Fedora] evince not showing "greek" and "math" in *.pdf plots
Iñaki Ucar
|uc@r @end|ng |rom |edor@project@org
Thu Mar 14 01:48:35 CET 2024
Paul, what I still cannot understand is why Standard Symbols PS doesn't
show all the symbols, if it is supposed to be a replacement of the legacy
Standard Symbols L, see
https://github.com/ArtifexSoftware/urw-base35-fonts/blob/3c0ba3b5687632dfc66526544a4e811fe0ec0cd9/appstream/de.urwpp.StandardSymbolsPS.metainfo.xml#L14-L30
and
https://github.com/ArtifexSoftware/urw-base35-fonts/blob/3c0ba3b5687632dfc66526544a4e811fe0ec0cd9/fontconfig/urw-fallback-specifics.conf#L28
.
Iñaki
On Wed, 13 Mar 2024 at 16:53, Iñaki Ucar <iucar using fedoraproject.org> wrote:
> I see. Peter, you are right about the font that causes the issue. Paul,
> thanks for your insights. I'll bring this to the Fedora font experts to see
> if we can arrive at a more permanent fix. I'll report back with any
> conclusion.
>
> @Martin: Meanwhile, at least you have options. One is to embed the fonts,
> either as Peter suggested or using cairo_pdf instead. Alternatively, Peter
> also has shown how to instruct fontconfig to select other fonts as
> replacements.
>
> Hope it helps,
> Iñaki
>
> On Tue, 12 Mar 2024 at 22:10, Paul Murrell <paul using stat.auckland.ac.nz>
> wrote:
>
>> 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>
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>> > <https://stat.ethz.ch/mailman/listinfo/r-sig-fedora>
>> > > >>
>> > >
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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/
>>
>>
>
> --
> Iñaki Úcar
>
--
Iñaki Úcar
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