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/ 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> 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 > > 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 > > >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > >> > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-SIG-Fedora mailing list > > R-SIG-Fedora@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > _______________________________________________ > R-SIG-Fedora mailing list > R-SIG-Fedora@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > -- 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
