<tk.c...@protonmail.com> wrote: > Hello Guix, > > I am trying to generate a pdf report using R and knitr and PDF LaTeX. More > specifically, I was trying out a sample document that comes with knitr > package. This is the code to generate the output: > > require(knitr) > s = system.file("misc", "stitch-test.R", package = "knitr") > stitch(s) > > > Now, tangling this into a pdf revealed several missing LaTeX packages (which > I installed), but then it finally died with this error, > > output file: stitch-test.tex > > ! Math formula deleted: Insufficient symbol fonts. > <inserted text> \setbox \z@ \vbox {\hbox {$($ > > }\\kern \\z@ }\\global > \\big@size 1.2\\ht \\z@ > > > l.87 T > he results below are generated from an R script. > > Error: LaTeX failed to compile stitch-test.tex. See > https://yihui.org/tinytex/r/#debugging for debugging tips. See > stitch-test.log for more info. > > The full tangled tex file is all the way at the bottom; > > Looking through the log file, I noticed > > LaTeX Font Info: Try loading font information for T1+pplx on input line 76. > LaTeX Font Info: No file T1pplx.fd. on input line 76. > > LaTeX Font Warning: Font shape `T1/pplx/m/n' undefined (Font) > using`T1/cmr/m/n' instead on input line 76. > > and also, a couple of additional font warnings just before the error, > > LaTeX Font Info: Try loading font information for OT1+pplx on input line 87. > LaTeX Font Info: No file OT1pplx.fd. on input line 87. > > LaTeX Font Warning: Font shape `OT1/pplx/m/n' undefined (Font) > using`OT1/cmr/m/n' instead on input line 87. > > LaTeX Font Info: Try loading font information for OML+zplm on input line 87. > LaTeX Font Info: No file OMLzplm.fd. on input line 87. > > LaTeX Font Warning: Font shape `OML/zplm/m/it' undefined (Font) > using`OML/cmm/m/it' instead on input line 87. > > LaTeX Font Info: Try loading font information for OMS+zplm on input line 87. > LaTeX Font Info: No file OMSzplm.fd. on input line 87. > > LaTeX Font Warning: Font shape `OMS/zplm/m/n' undefined (Font) > using`OMS/cmsy/m/n' instead on input line 87. > > LaTeX Font Info: Try loading font information for OMX+zplm on input line 87. > LaTeX Font Info: No file OMXzplm.fd. on input line 87. > > LaTeX Font Warning: Font shape `OMX/zplm/m/n' undefined (Font) > using`OMX/cmex/m/n' instead on input line 87. > > LaTeX Font Info: External font `cmex10' loaded for size > (Font) <12> on input line 87. > LaTeX Font Info: External font `cmex10' loaded for size > (Font) <9> on input line 87. > LaTeX Font Info: External font `cmex10' loaded for size > (Font) <7> on input line 87. > LaTeX Font Info: Try loading font information for OT1+zplm on input line 87. > LaTeX Font Info: No file OT1zplm.fd. on input line 87. > > LaTeX Font Warning: Font shape `OT1/zplm/m/n' undefined (Font) > using`OT1/cmr/m/n' instead on input line 87. > > The tangled tex file itself uses T1 fonts, > > \\usepackage[T1]{fontenc} > > > I guess this is a question of installing the right texlive package, or font, > so I am wondering if any of you would have an idea which (texlive) package to > install. I found mention of those "*.fd" files in the psnfss package, but > installing it (texlive-latex-psnfss) did not change a thing. > > The entire tex file follows (try pdflatex stitch-test.tex): > **************** stitch-test.tex ******************* > \documentclass{article}\usepackage[]{graphicx}\usepackage[]{color} > % maxwidth is the original width if it is less than linewidth > % otherwise use linewidth (to make sure the graphics do not exceed the margin) > \makeatletter > \def\maxwidth{ % > \ifdim\Gin@nat@width>\linewidth > > \\linewidth > > > \else > \Gin@nat@width > \fi > } > \makeatother > > \definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345} > \newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}% > \newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}% > \newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}% > \newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}% > \newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}% > \newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}% > \newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}% > \newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}% > \newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}% > \let\hlipl\hlkwb > > \usepackage{framed} > \makeatletter > \newenvironment{kframe}{% > \def\at@end@of@kframe{}% > \ifinner\ifhmode% > \def\at@end@of@kframe{\end{minipage}}% > \begin{minipage}{\columnwidth}% > \fi\fi% > \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep > \colorbox{shadecolor}{##1}\hskip-\fboxsep > % There is no \\@totalrightmargin, so: > \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}% > \MakeFramed {\advance\hsize-\width > \@totalleftmargin\z@ \linewidth\hsize > \@setminipage}}% > {\par\unskip\endMakeFramed% > \at@end@of@kframe} > \makeatother > > \definecolor{shadecolor}{rgb}{.97, .97, .97} > \definecolor{messagecolor}{rgb}{0, 0, 0} > \definecolor{warningcolor}{rgb}{1, 0, 1} > \definecolor{errorcolor}{rgb}{1, 0, 0} > \newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX > > \usepackage{alltt} > \usepackage[sc]{mathpazo} > \renewcommand{\sfdefault}{lmss} > \renewcommand{\ttdefault}{lmtt} > \usepackage[T1]{fontenc} > \usepackage{geometry} > \geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm} > \setcounter{secnumdepth}{2} > \setcounter{tocdepth}{2} > \usepackage[unicode=true,pdfusetitle, > bookmarks=true,bookmarksnumbered=true,bookmarksopen=true,bookmarksopenlevel=2, > breaklinks=false,pdfborder={0 0 1},backref=false,colorlinks=false] > {hyperref} > \hypersetup{ > pdfstartview={XYZ null null 1}} > > \makeatletter > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands. > \renewcommand{\textfraction}{0.05} > \renewcommand{\topfraction}{0.8} > \renewcommand{\bottomfraction}{0.8} > \renewcommand{\floatpagefraction}{0.75} > > \makeatother > \IfFileExists{upquote.sty}{\usepackage{upquote}}{} > \begin{document} > > \title{ A test script for the function stitch()} > > \author{ Yihui Xie% > \thanks{This report is automatically generated with the R package > \textbf{knitr} > (version 1.29).}} > > \maketitle > The results below are generated from an R script. > > \begin{knitrout} > \definecolor{shadecolor}{rgb}{0.969, 0.969, > 0.969}\color{fgcolor}\begin{kframe} > \begin{alltt} > \hlkwd{set.seed}\hlstd{(}\hlnum{1121}\hlstd{)} > \hlstd{(x} \hlkwb{=} \hlkwd{rnorm}\hlstd{(}\hlnum{20}\hlstd{))} > \end{alltt} > \begin{verbatim} > > [1] 0.1449583 0.4383221 0.1531912 1.0849426 1.9995449 -0.8118832 0.1602680 > > --------------------------------------------------------------------------- > > [8] 0.5858923 0.3600880 -0.0253084 0.1508809 0.1100824 1.3596812 -0.3269946 > > ---------------------------------------------------------------------------- > > [15] -0.7163819 1.8097690 0.5084011 -0.5274603 0.1327188 -0.1559430 > > -------------------------------------------------------------------- > > \end{verbatim} > \begin{alltt} > \hlkwd{mean}\hlstd{(x);}\hlkwd{var}\hlstd{(x)} > \end{alltt} > \begin{verbatim} > > [1] 0.3217385 > > -------------- > > [1] 0.5714534 > > -------------- > > \end{verbatim} > \begin{alltt} > \hlkwd{boxplot}\hlstd{(x)} > \end{alltt} > \end{kframe} > > {\centering > \includegraphics[width=.6\linewidth]{figure/stitch-test-Rnwauto-report-1} > > } > > \begin{kframe}\begin{alltt} > \hlkwd{hist}\hlstd{(x,} \hlkwc{main} \hlstd{=} \hlstr{''}\hlstd{)} > \end{alltt} > \end{kframe} > > {\centering > \includegraphics[width=.6\linewidth]{figure/stitch-test-Rnwauto-report-2} > > } > > \end{knitrout} > > The R session information (including the OS info, R version and all > packages used): > > \begin{knitrout} > \definecolor{shadecolor}{rgb}{0.969, 0.969, > 0.969}\color{fgcolor}\begin{kframe} > \begin{alltt} > \hlkwd{sessionInfo}\hlstd{()} > \end{alltt} > \begin{verbatim} > > R version 4.0.2 (2020-06-22) > > ----------------------------- > > Platform: x86_64-unknown-linux-gnu (64-bit) > > -------------------------------------------- > > Running under: Pop!_OS 20.04 LTS > > --------------------------------- > > -- > > Matrix products: default > > ------------------------- > > BLAS/LAPACK: > /gnu/store/bs9pl1f805ins80xaf4s3n35a0x2lyq3-openblas-0.3.9/lib/libopenblasp-r0.3.9.so > > --------------------------------------------------------------------------------------------------- > > -- > > locale: > > -------- > > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > > -------------------------------------- > > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > > ----------------------------------------------- > > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > > ---------------------------------------------------- > > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=en_GB.UTF-8 > > --------------------------------------------- > > [9] LC_ADDRESS=en_GB.UTF-8 LC_TELEPHONE=en_GB.UTF-8 > > ---------------------------------------------------- > > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=en_GB.UTF-8 > > -------------------------------------------------------------- > > -- > > attached base packages: > > ------------------------ > > [1] stats graphics grDevices utils datasets methods base > > --------------------------------------------------------- > > -- > > other attached packages: > > ------------------------- > > [1] knitr_1.29 Rcpp_1.0.5 > > -------------------------- > > -- > > loaded via a namespace (and not attached): > > ------------------------------------------- > > [1] xfun_0.17 listenv_0.8.0 rJava_0.9-13 > > ----------------------------------------- > > [4] lattice_0.20-41 colorspace_1.4-1 vctrs_0.3.4 > > ------------------------------------------------- > > [7] stats4_4.0.2 fingerprint_3.5.7 yaml_2.2.1 > > ---------------------------------------------- > > [10] vsn_3.56.0 XML_3.99-0.5 rlang_0.4.7 > > ----------------------------------------- > > [13] pillar_1.4.6 glue_1.4.2 MSnbase_2.14.2 > > -------------------------------------------- > > [16] mzR_2.22.0 BiocParallel_1.22.0 affy_1.66.0 > > ------------------------------------------------ > > [19] BiocGenerics_0.34.0 affyio_1.58.0 foreach_1.5.0 > > ----------------------------------------------------- > > [22] lifecycle_0.2.0 plyr_1.8.6 stringr_1.4.0 > > ---------------------------------------------- > > [25] mzID_1.26.0 ProtGenerics_1.20.0 zlibbioc_1.34.0 > > ----------------------------------------------------- > > [28] munsell_0.5.0 pcaMethods_1.80.0 gtable_0.3.0 > > -------------------------------------------------- > > [31] rcdklibs_2.0 future_1.18.0 evaluate_0.14 > > ---------------------------------------------- > > [34] codetools_0.2-16 Biobase_2.48.0 IRanges_2.22.2 > > ---------------------------------------------------- > > [37] doParallel_1.0.15 parallel_4.0.2 highr_0.8 > > ------------------------------------------------ > > [40] itertools_0.1-3 preprocessCore_1.50.0 scales_1.1.1 > > -------------------------------------------------------- > > [43] BiocManager_1.30.10 limma_3.44.3 rcdk_3.4.3 > > ------------------------------------------------- > > [46] S4Vectors_0.26.1 impute_1.62.0 rjson_0.2.20 > > ------------------------------------------------- > > [49] ggplot2_3.3.2 png_0.1-7 digest_0.6.25 > > ------------------------------------------- > > [52] stringi_1.5.3 ncdf4_1.17 grid_4.0.2 > > ----------------------------------------- > > [55] RMassBank_2.99.2 tools_4.0.2 magrittr_1.5 > > ----------------------------------------------- > > [58] RCurl_1.95-0.1.2 tibble_3.0.3 crayon_1.3.4 > > ------------------------------------------------ > > [61] pkgconfig_2.0.3 enviPat_2.4 MASS_7.3-53 > > --------------------------------------------- > > [64] ellipsis_0.3.1 iterators_1.0.12 R6_2.4.1 > > ---------------------------------------------- > > [67] globals_0.12.5 MALDIquant_1.19.3 compiler_4.0.2 > > ----------------------------------------------------- > > \end{verbatim} > \begin{alltt} > \hlkwd{Sys.time}\hlstd{()} > \end{alltt} > \begin{verbatim} > > [1] "2020-10-15 15:45:57 CEST" > > ------------------------------- > > \end{verbatim} > \end{kframe} > \end{knitrout} > > \end{document}
Okay, after wasting few hours of my life installing various texlive package (did not help), I went for the full, ueber-bloated texlive distribution ("texlive" package). Of course, this "solved" the knittr problem. Interestingly, looking into $GUIX_PROFILE/share/texmf-dist/tex/latex/psnfss directory, I found bunch of *.fd files present that were not there when I tried to install texlive-latex-psnfss package individually. Perhaps a bug?