From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp10.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id WLimG2TZQmK/UgAAgWs5BA (envelope-from ) for ; Tue, 29 Mar 2022 12:03:16 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp10.migadu.com with LMTPS id MAbTFGTZQmINawAAG6o9tA (envelope-from ) for ; Tue, 29 Mar 2022 12:03:16 +0200 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 A2B6E2D5AB for ; Tue, 29 Mar 2022 12:03:15 +0200 (CEST) Received: from localhost ([::1]:55342 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZ8h0-0000oD-0j for larch@yhetil.org; Tue, 29 Mar 2022 06:03:14 -0400 Received: from eggs.gnu.org ([209.51.188.92]:38134) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZ8gY-0000mW-BE for help-guix@gnu.org; Tue, 29 Mar 2022 06:02:47 -0400 Received: from mail-40134.protonmail.ch ([185.70.40.134]:14141) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZ8gT-0003t3-Jr for help-guix@gnu.org; Tue, 29 Mar 2022 06:02:45 -0400 Date: Tue, 29 Mar 2022 10:02:29 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=protonmail.com; s=protonmail; t=1648548150; bh=zcj0CnEdzrQi4xlcDOd8bwsUkHFy4geX16vdtbl0m8c=; h=Date:To:From:Cc:Reply-To:Subject:Message-ID:In-Reply-To: References:From:To:Cc:Date:Subject:Reply-To:Feedback-ID: Message-ID; b=DMHm7+6bwwm0vE20wYAY55BfK8KZBj9f9trOOGhBw/9Fqm/xd+FmM7K7FSViI1F7Z T3FHC7XaKMn2rTDI/nKEs1zQfW971BU8Tpv8uSvHNxS4J1LJ+VRzbb+gQp8TqtfXvx ikk0wHgwRnKRF0j/eW/pfYXb1WnRj+jpIwbQFF7xgMK+GLvNILiBKnzbGnjGeIGRNH wZ+FLeRBJDRZPFhrhoxVi9jKEB+MxAagwEBaUM/Jo53/QiZY3m7lCW+woxE4EJP6c0 YEfn22245fpVdhoA4aaHyB04Oz/GYfschDaMYflEKyIKQJTzrnZEbmuzjCskuIKSAQ qswdZ00UgtKqQ== To: TK From: TK Cc: Ricardo Wurmus , help-guix@gnu.org Subject: Re: Missing LaTeX font (R related) Message-ID: In-Reply-To: References: <8735j9doy3.fsf@elephly.net> 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=tkprom@protonmail.com; helo=mail-40134.protonmail.ch 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_H5=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, TO_EQ_FM_DIRECT_MX=0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: help-guix@gnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-To: TK Errors-To: help-guix-bounces+larch=yhetil.org@gnu.org Sender: "Help-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1648548195; h=from:from:sender:sender:reply-to:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding: in-reply-to:in-reply-to:references:references:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=zcj0CnEdzrQi4xlcDOd8bwsUkHFy4geX16vdtbl0m8c=; b=BQWxLc0CIWUD/Hn6q1vOIulut+bXL114dBl5+WEbv1yLtzm5YQiier0+TySg8dgP2KRekR m0CLHQkdWER/ZuwCJ8D6wZHrRoYXH/o8ubcLwu00OD20dDcwofkcDb1/eDqHtAfgsL+J43 8xrOuwNe6R3tzMs/PoTnDys3UK1JaFKxW7LYc+WlqejJFmHygeQ6aWb8W7u5MPI5b3YgWL oRbmp5CUoQ+LjqSeAXNP5FuBdP62pDp70M0LQUJjvJAcgNJaHuhEuK48m5WUXiiB0/Enml DidsJIdDExR187wyvibHrq6fjZZHXpv2fIJymHHl7UGjXSOxvgP4f+QbkHejgQ== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1648548195; a=rsa-sha256; cv=none; b=P1OxeDOXHuWLuR2rmfrtyW/Q+gZYJ3gV5g6A6wH4pzjVfG5t7Yqp/V0+Lf5eSXoHUwpdhh gjlzr0whyyB+WGMw4eFARkhi46CHMxhZGe8cDxm9DMDdkxNBaFmbL4fqJK0Vj43StkMtjj sD5Yh2Grbn4fNYmfkGnRg9E9qBFJFdcE2y4WGB1uuPoSac1kqZBSvGyPZamiJP3I2Aad96 w+uW6ecEjAZWaHn9MG9IA5MvR/qLazOUSu8paO9ftKoMVkEZRZWcrROqs9PPF0QaV5IZQC UEcEFMP7w4etnYX8pjQh3XG2SacJCWuov3zeCQpt9BAJDwPJaphtQ8G+kbdNtw== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=pass header.d=protonmail.com header.s=protonmail header.b=DMHm7+6b; dmarc=pass (policy=quarantine) header.from=protonmail.com; spf=pass (aspmx1.migadu.com: domain of "help-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="help-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: -4.07 Authentication-Results: aspmx1.migadu.com; dkim=pass header.d=protonmail.com header.s=protonmail header.b=DMHm7+6b; dmarc=pass (policy=quarantine) header.from=protonmail.com; spf=pass (aspmx1.migadu.com: domain of "help-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="help-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: A2B6E2D5AB X-Spam-Score: -4.07 X-Migadu-Scanner: scn0.migadu.com X-TUID: qfGaUE4wB3Vw On Wednesday, March 23rd, 2022 at 11:02 AM, TK wrot= e: > On Wednesday, March 23rd, 2022 at 9:58 AM, Ricardo Wurmus rekado@elephly.= net wrote: > > > TK tkprom@protonmail.com writes: > > > > > `!pdfTeX error: pdflatex (file t1-zi4r-0): Font t1-zi4r-0 at 540 not = found` > > > > > > A web search reveals that t1-zi4r-0 is an inconsolata font, but insta= lling "texlive-inconsolata" package does not sort this issue out. > > > > The texlive-inconsolata package does indeed include that font: > > > > /gnu/store/=E2=80=A6-texlive-inconsolata-59745/share/texmf-dist/fonts/t= fm/public/inconsolata/t1-zi4r-0.tfm > > > > > Is granular texlive install even possible on Guix? :) > > > > Yes, it is. > > > > -- > > > > Ricardo > > Hi Ricardo, > > Thanks for the reply. > > Since texlive-inconsolata is part of my manifest specification, there mig= ht be an issue in how I create the environment. > > For my work in R, I use the following bash script: > > `#!/bin/sh theme_dir=3D$HOME/.local/share/guix-themes guix shell --pure -= c4 -m "$theme_dir/foundation.scm" \\ -m "$theme_dir/eci.scm" -m "$theme_dir= /texpack.scm"` > > I am creating an environment from several manifests. They are shown below= , together with the channels file, for the sake of reproducibility and the = mailing list. Also, for anyone's convenience, should they actually want to = reproduce the problem, > > those files have been attached. > > Issuing `R CMD check somepackage` within the shell of the environment wil= l die with the message outlined above. > > The package in the command line is just a skeleton created by `Rcpp.packa= ge.skeleton`. > > Thanks, > > T > > # Appendix > > ## channels.scm > > `(use-modules (guix packages) (guix inferior) (guix channels) (guix profi= les) (gnu packages) (srfi srfi-1)) (define channels ;; This is custom Envir= onmental Cheminformatics LCSB channel. (list (channel (name 'eci-addons) (u= rl "https://git.sr.ht/~condor/eci-guix") (branch "master") (introduction (m= ake-channel-introduction "e7ccb0c185133e23a9a75867e0deef5881ab2d49" (openpg= p-fingerprint "EDC3 9790 A06D 5F72 41D9 70F9 BBEF E71B 7A28 3C6F")))) (chan= nel (name 'nonguix) (url "https://gitlab.com/nonguix/nonguix") (introductio= n (make-channel-introduction "897c1a470da759236cc11798f4e0a5f7d4d59fbc" (op= enpgp-fingerprint "2A39 3FFF 68F4 EF7A 3D29 12AF 6F51 20A0 22FB B2D5")))) (= channel (name 'guix) (url "https://git.savannah.gnu.org/git/guix.git") ;; (= commit "c852d897551f514de95c224fa79e748f48808068") )))` > > ## foundation.scm > > ``` > > (use-modules (guix packages) > > (gnu packages autotools) > > (gnu packages gcc) > > (gnu packages perl) > > (gnu packages mpi) > > (gnu packages ssh) > > (gnu packages gawk) > > (gnu packages base)) > > (define specs '("bash" > > "make" > > "sbc" > > "openssh" > > "git:send-email" > > "git" > > "grep" > > "sed" > > "gawk" > > "procps" > > "coreutils-minimal" > > "glibc-locales" > > "make" > > "emacs" > > "lesspipe" > > "glibc-locales" > > "guile" > > "pkg-config" > > "nss-certs" > > "wget" > > "xz" > > "tar" > > "gzip" > > "bzip2")) > > (define misc-specs '("ispell" > > "sshpass" > > "the-silver-searcher" > > "xdg-utils" > > "xdg-user-dirs" > > "pango" > > "gnupg" > > "openssl" > > "gtk+" > > "man-db" > > "texinfo")) > > (define font-specs '("unicode-emoji" > > "fontconfig" > > "font-dejavu" > > "font-gnu-freefont" > > ;"font-ubuntu" > > "font-terminus" > > "font-liberation" > > "font-inconsolata" > > "font-gnu-unifont" > > "font-public-sans" > > "font-misc-misc" > > "font-awesome" > > "font-hack" > > "font-iosevka" > > "font-iosevka-term" > > "font-iosevka-term-slab" > > ;"font-iosevka-sparkle" > > "font-iosevka-slab" > > "font-iosevka-etoile" > > "font-iosevka-aile" > > "font-google-noto")) > > (define emacs-specs `("emacs-guix" "emacs-circe" "emacs-geiser" "emacs-pa= redit" "emacs-bbdb" "emacs-circe" "emacs-use-package" "emacs-ag" "emacs-mag= it" "emacs-org" "emacs-paredit" ;; "emacs-ess" "emacs-company" "emacs-ivy" = "emacs-counsel" "emacs-zenburn-theme" "emacs-solarized-theme" "emacs-cyberp= unk-theme" "emacs-atom-one-dark-theme" "emacs-polymode" "emacs-polymode-org= " "emacs-polymode-ansible" "emacs-csv" "emacs-smartparens" ;"emacs-elpy" "e= macs-wgrep" "emacs-emojify" "emacs-rust-mode" "emacs-flycheck-rust" "emacs-= spacemacs-theme" "emacs-punpun-theme" "emacs-org-beautify-theme" "emacs-dre= am-theme" "emacs-base16-theme" "emacs-ample-theme" "emacs-doom-themes" "ema= cs-alect-themes" "emacs-almost-mono-themes" ;; "emacs-bluetooth" "emacs-csv= " "emacs-csv-mode" "emacs-org-reveal")) (specifications->manifest` (,@specs > > ,@emacs-specs > > ,@misc-specs > > ,@font-specs)) > > `## eci.scm` > > (use-modules (eci packages bioinformatics) > > (eci packages cran) > > (guix packages) > > (gnu packages chemistry) > > (gnu packages bioinformatics) > > (gnu packages bioconductor) > > (gnu packages statistics) > > (gnu packages web) > > (gnu packages image) > > (gnu packages cran) > > (gnu packages) > > (srfi srfi-1)) > > (define misc-spec '("openbabel" > > "inchi" > > "gcc-toolchain")) > > (define r-spec `("r" "r-scales" "r-devtools" "r-openssl" "r-foreach" "r-m= arkdown" "r-rmarkdown" "r-dofuture" "r-ff" "r-ffbase" "r-yaml" "r-batchtool= s" "r-future" "r-mzr" "r-bit64" "r-data-table" "r-msnbase" "r-assertthat" "= r-withr" "r-ggplot2" "r-cowplot" "r-rcolorbrewer" "r-curl" "r-shiny" "r-han= dsontable" "r-dt" "r-tcltk2" "r-protgenerics" "r-massbank" "r-chemmass" "r-= r-utils")) (specifications->manifest` (,@misc-spec > > ,@r-spec)) > > `## texpack.scm` > > (use-modules (guix packages) > > (gnu packages tex)) > > (define specs '("texlive-latex-base" > > "texlive-tiny" > > "texlive-latex-tools" > > "texlive-latex-graphics" > > "texlive-kpfonts" > > "texlive-url" > > "texlive-inconsolata" > > "texlive-latex-xkeyval" > > "texlive-fonts-latex" > > "texlive-fonts-ec" > > "texlive-fontspec" > > "texlive-fontname" > > "texlive-fontinst" > > "texlive-hyph-utf8" > > "texlive-hyphen-serbian" > > "texlive-cm" > > "texlive-txfonts" > > "texlive-metafont" > > "texlive-amsfonts" > > "texlive-latex-type1cm" > > "texlive-times" > > "texlive-helvetic" > > "texlive-psnfss" > > "texlive-psnfss-fixed")) > > (specifications->manifest `(,@specs)) > > ``` After some more investigation, I think I narrowed down the issue. Package t= exlive-inconsolata indeed installs the `t1-zi4r-0' font. However, the `map'= for that font exists only under dvips, not in the pdftex subdir. On my system, under the dvips map directory of the profile associated with = the corresponding Guix environment, `/gnu/store/m2g80qz67lxxa7744wkclaifvbwa1bdi-profile/share/texmf-dist/fonts= /map/dvips/inconsolata', there exists a `zi4.map` file which lists the prob= lematic font. In contrast, the flat `pdftex' map file, `/gnu/store/m2g80qz6= 7lxxa7744wkclaifvbwa1bdi-profile/share/texmf-dist/fonts/map/pdftex/updmap/p= dftex.map' does not contain any Inconsolata (zi4) entry. I am not a TeX magus, but it is indicative that the file on the official Te= XLive repo https://tug.org/svn/texlive/trunk/Master/texmf-dist/fonts/map/pd= ftex/updmap/pdftex.map does contain `zi4' entries. Shouldn't the installation of texlive-inconsolata put the corresponding ent= ries into `pdftex.map'? Any hints on where to go from here? Thanks! Cheers, T