From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id uHhsJtldiF8MbgAA0tVLHw (envelope-from ) for ; Thu, 15 Oct 2020 14:34:01 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id INtVItldiF99HgAAbx9fmQ (envelope-from ) for ; Thu, 15 Oct 2020 14:34:01 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id E002B9402A4 for ; Thu, 15 Oct 2020 14:34:00 +0000 (UTC) Received: from localhost ([::1]:49174 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kT4B4-0003eU-TU for larch@yhetil.org; Thu, 15 Oct 2020 10:24:22 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:35308) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kT4Au-0003cY-Sn for help-guix@gnu.org; Thu, 15 Oct 2020 10:24:12 -0400 Received: from mail-40134.protonmail.ch ([185.70.40.134]:49899) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kT4Ar-0006Ge-7w for help-guix@gnu.org; Thu, 15 Oct 2020 10:24:12 -0400 Date: Thu, 15 Oct 2020 14:23:40 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=protonmail.com; s=protonmail; t=1602771824; bh=47wGQlCy1hl1vOU3pnLMG69XaxgclrKHtCxIt0iEnJY=; h=Date:To:From:Reply-To:Subject:From; b=u2xmDgy70aisAlu7ellC6IKNaLlleYO+KcZv1GsFCHhkbk7q7yuPCWJQqUaOEqAtm P946aKIHap6I7T1OOhkGWbJ/AVz+epaolgEiVPjtTbXLW4OCJ/7JmW4uj2JvdDiRGu 8j50CKs+GoLv2qYPK9mHjc4GGFKUWvvgvUkfnCE0= To: "help-guix\\@gnu.org" From: =?utf-8?Q?Todor_Kondi=C4=87?= Subject: R, knitr and texlive on Guix (as a package manager) Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=185.70.40.134; envelope-from=tk.code@protonmail.com; helo=mail-40134.protonmail.ch X-detected-operating-system: by eggs.gnu.org: First seen = 2020/10/15 10:23:44 X-ACL-Warn: Detected OS = Linux 2.2.x-3.x [generic] [fuzzy] X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_MSPIKE_H2=-0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: help-guix@gnu.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-To: =?utf-8?Q?Todor_Kondi=C4=87?= Errors-To: help-guix-bounces+larch=yhetil.org@gnu.org Sender: "Help-Guix" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=pass header.d=protonmail.com header.s=protonmail header.b=u2xmDgy7; dmarc=pass (policy=quarantine) header.from=protonmail.com; spf=pass (aspmx1.migadu.com: domain of help-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=help-guix-bounces@gnu.org X-Spam-Score: -1.71 X-TUID: VX6NB4Ip1sMA 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 pack= age. This is the code to generate the output: ```r require(knitr) s =3D system.file("misc", "stitch-test.R", package =3D "knitr") stitch(s) ``` Now, tangling this into a pdf revealed several missing LaTeX packages (whic= h I installed), but then it finally died with this error, ********************* output file: stitch-test.tex ! Math formula deleted: Insufficient symbol fonts. \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/tinyt= ex/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) packag= e 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 marg= in) \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=3D2.5cm,bmargin=3D2.5cm,lmargin=3D2.5cm,rmargin= =3D2.5cm} \setcounter{secnumdepth}{2} \setcounter{tocdepth}{2} \usepackage[unicode=3Dtrue,pdfusetitle, bookmarks=3Dtrue,bookmarksnumbered=3Dtrue,bookmarksopen=3Dtrue,bookmarksop= enlevel=3D2, breaklinks=3Dfalse,pdfborder=3D{0 0 1},backref=3Dfalse,colorlinks=3Dfalse] {hyperref} \hypersetup{ pdfstartview=3D{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{k= nitr} (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{kfr= ame} \begin{alltt} \hlkwd{set.seed}\hlstd{(}\hlnum{1121}\hlstd{)} \hlstd{(x} \hlkwb{=3D} \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=3D.6\linewidth]{figure/stitch-test-Rnwau= to-report-1} } \begin{kframe}\begin{alltt} \hlkwd{hist}\hlstd{(x,} \hlkwc{main} \hlstd{=3D} \hlstr{''}\hlstd{)} \end{alltt} \end{kframe} {\centering \includegraphics[width=3D.6\linewidth]{figure/stitch-test-Rnwau= to-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{kfr= ame} \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=3Den_GB.UTF-8 LC_NUMERIC=3DC ## [3] LC_TIME=3Den_GB.UTF-8 LC_COLLATE=3Den_GB.UTF-8 ## [5] LC_MONETARY=3Den_GB.UTF-8 LC_MESSAGES=3Den_GB.UTF-8 ## [7] LC_PAPER=3Den_GB.UTF-8 LC_NAME=3Den_GB.UTF-8 ## [9] LC_ADDRESS=3Den_GB.UTF-8 LC_TELEPHONE=3Den_GB.UTF-8 ## [11] LC_MEASUREMENT=3Den_GB.UTF-8 LC_IDENTIFICATION=3Den_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} **********************************************************