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 <p...@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, <pst...@gmail.com > > <mailto:pst...@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@r-project.org <mailto: > R-SIG-Fedora@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]] > > > > > > _______________________________________________ > > > R-SIG-Fedora mailing list > > > R-SIG-Fedora@r-project.org <mailto:R-SIG-Fedora@r-project.org> > > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > <https://stat.ethz.ch/mailman/listinfo/r-sig-fedora> > > > > _______________________________________________ > > R-SIG-Fedora mailing list > > R-SIG-Fedora@r-project.org <mailto:R-SIG-Fedora@r-project.org> > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > <https://stat.ethz.ch/mailman/listinfo/r-sig-fedora> > > > > > > > > -- > > 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 > p...@stat.auckland.ac.nz > www.stat.auckland.ac.nz/~paul/ > > -- Iñaki Úcar [[alternative HTML version deleted]] _______________________________________________ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
