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:
```r
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,
```tex
\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}
**********************************************************
