From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id A284IUKfiF/kTwAA0tVLHw (envelope-from ) for ; Thu, 15 Oct 2020 19:13:06 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id uPnRHEKfiF/RIwAA1q6Kng (envelope-from ) for ; Thu, 15 Oct 2020 19:13:06 +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 71CB99404CC for ; Thu, 15 Oct 2020 19:13:05 +0000 (UTC) Received: from localhost ([::1]:48284 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kT8gS-0006II-8J for larch@yhetil.org; Thu, 15 Oct 2020 15:13:04 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:49286) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kT8gJ-0006Hf-2l for help-guix@gnu.org; Thu, 15 Oct 2020 15:12:55 -0400 Received: from mail-40134.protonmail.ch ([185.70.40.134]:20453) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kT8gF-0002XX-HL for help-guix@gnu.org; Thu, 15 Oct 2020 15:12:54 -0400 Date: Thu, 15 Oct 2020 19:12:45 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=protonmail.com; s=protonmail; t=1602789167; bh=gPGOeahCQ3KbBJVHMUc3+DJC+u2s50Yc4BhMM3uU8Z8=; h=Date:To:From:Cc:Reply-To:Subject:In-Reply-To:References:From; b=KkPh4BJkHpuNzS3ZX5FuS0RZb4qCjX3H4ajmhT8lhIOG/gq4mZhxFUTKC2gz+bnUn SI4CEwTGmFL32FbXM9CqzvShXdM5xZItD6Z9Sw3MJ1U8kCbInfNTOsn7yBPK6NKaar KnR8nMBvfLtMchfVOK7Vja8bIXECJsF0ihJ7SfFQ= To: =?utf-8?Q?Todor_Kondi=C4=87?= From: =?utf-8?Q?Todor_Kondi=C4=87?= Cc: "help-guix\\\\@gnu.org" Subject: Re: R, knitr and texlive on Guix (as a package manager) Message-ID: In-Reply-To: References: 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 15:12:48 X-ACL-Warn: Detected OS = Linux 2.2.x-3.x [generic] [fuzzy] X-Spam_score_int: -10 X-Spam_score: -1.1 X-Spam_bar: - X-Spam_report: (-1.1 / 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, TO_EQ_FM_DIRECT_MX=1 autolearn=no 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=KkPh4BJk; 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: RNr83Ylh2V6m wrote: > Hello Guix, > > I am trying to generate a pdf report using R and knitr and PDF LaTeX. Mor= e specifically, I was trying out a sample document that comes with knitr pa= ckage. This is the code to generate the output: > > 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 (wh= ich 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/tin= ytex/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 7= 6. > LaTeX Font Info: No file T1pplx.fd. on input line 76. > > LaTeX Font Warning: Font shape `T1/pplx/m/n' undefined (Font) using`T1/cm= r/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 fo= nt, so I am wondering if any of you would have an idea which (texlive) pack= age 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 ma= rgin) > \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 T= eX > > \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,bookmarkso= penlevel=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= {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{k= frame} > \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 0.160268= 0 > > -------------------------------------------------------------------------= -- > > [8] 0.5858923 0.3600880 -0.0253084 0.1508809 0.1100824 1.3596812 -0.32699= 46 > > -------------------------------------------------------------------------= --- > > [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-Rnw= auto-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-Rnw= auto-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{k= frame} > \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/l= ib/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} 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?