From mboxrd@z Thu Jan 1 00:00:00 1970 X-Msuck: nntp://news.gmane.io/gmane.comp.tex.context/112560 Path: news.gmane.io!.POSTED.blaine.gmane.org!not-for-mail From: Benjamin Buchmuller via ntg-context Newsgroups: gmane.comp.tex.context Subject: Re: lmtx update/t-vim (again) Date: Mon, 23 Aug 2021 12:32:59 +0200 Message-ID: References: Reply-To: mailing list for ConTeXt users Mime-Version: 1.0 (Mac OS X Mail 14.0 \(3654.120.0.1.13\)) Content-Type: multipart/mixed; boundary="Apple-Mail=_953D55D3-8FEF-4AD1-9C47-C350765B93C0" Injection-Info: ciao.gmane.io; posting-host="blaine.gmane.org:116.202.254.214"; logging-data="32525"; mail-complaints-to="usenet@ciao.gmane.io" Cc: Benjamin Buchmuller , mailing list for ConTeXt users To: Hans Hagen Original-X-From: ntg-context-bounces@ntg.nl Mon Aug 23 12:33:42 2021 Return-path: Envelope-to: gctc-ntg-context-518@m.gmane-mx.org Original-Received: from zapf.boekplan.nl ([5.39.185.232] helo=zapf.ntg.nl) by ciao.gmane.io with esmtps (TLS1.3:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.92) (envelope-from ) id 1mI7Gw-0008F5-Bm for gctc-ntg-context-518@m.gmane-mx.org; Mon, 23 Aug 2021 12:33:42 +0200 Original-Received: from localhost (localhost [127.0.0.1]) by zapf.ntg.nl (Postfix) with ESMTP id 99E7D286BB3; Mon, 23 Aug 2021 12:33:07 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at zapf.boekplan.nl Original-Received: from zapf.ntg.nl ([127.0.0.1]) by localhost (zapf.ntg.nl [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id YeAgN7-AtL5V; Mon, 23 Aug 2021 12:33:06 +0200 (CEST) Original-Received: from zapf.ntg.nl (localhost [127.0.0.1]) by zapf.ntg.nl (Postfix) with ESMTP id 5BC6E286B99; Mon, 23 Aug 2021 12:33:06 +0200 (CEST) Original-Received: from localhost (localhost [127.0.0.1]) by zapf.ntg.nl (Postfix) with ESMTP id 97135286B71 for ; Mon, 23 Aug 2021 12:33:03 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at zapf.boekplan.nl Original-Received: from zapf.ntg.nl ([127.0.0.1]) by localhost (zapf.ntg.nl [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id ZS-y6hxpMRZb for ; Mon, 23 Aug 2021 12:33:01 +0200 (CEST) Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=209.85.128.44; helo=mail-wm1-f44.google.com; envelope-from=benjamin.buchmuller@gmail.com; receiver= Original-Received: from mail-wm1-f44.google.com (mail-wm1-f44.google.com [209.85.128.44]) (using TLSv1.3 with cipher TLS_AES_128_GCM_SHA256 (128/128 bits)) (No client certificate requested) by zapf.ntg.nl (Postfix) with ESMTPS id C97472864C5 for ; Mon, 23 Aug 2021 12:33:01 +0200 (CEST) Original-Received: by mail-wm1-f44.google.com with SMTP id f10so10204907wml.2 for ; Mon, 23 Aug 2021 03:33:01 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:message-id:mime-version:subject:date:in-reply-to:cc:to :references; bh=UDqaCaauHnM2d3b9sp0uDZEiMeEeUQsG73dqNXLT90g=; b=WhmcQBzwDwR8dmJ3dyHNSwxJ9MRpppgUXWl7d3mZwr7fcbWmhrDwRFiIjwanopIbQ3 842YsYvDWsPPRv0uRl8JwXOtFB5hLT0i0/x1GQkbiA6swnzpW2cDbt1mBltukP9tDE4t vXQwjIcTq4xs+DdwDbgrjurxfSVULVbaVIEMHxPqgUyyAA5FF8jKAD5emH5hUtTsL+8o F0ASurqOm1yZGFIlIpxEfwoGzlAwwr0oX/M12d/quMx+dGKj+VIJbxowpouR7i46rMFu K4gp8R2cnF3hFq2XulAQOBu4ZBNdw9oI6UG+BtFUTnPQBXOIcGbZ4F+5dZaX/aYs/KRx Io/g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:message-id:mime-version:subject:date :in-reply-to:cc:to:references; bh=UDqaCaauHnM2d3b9sp0uDZEiMeEeUQsG73dqNXLT90g=; b=gxkHgUPLh5ZJrOCGhspvMM234DmunL2raFEZ4QaHbsld5jWgs5ppl86cPCwylQKcJp 8N/1jg29OzfWWWPq3xMlfrjE0FTUoit/J1NsmgLJDOzhmF/ckf/s9zpeXyMhEYLkFGzW 7wzqs+3+gSY8a4bIkkc08aW+SrjsYMWyUWKCOrezmtXGJbvpnbyrar96AcjizvUVvaIh ImshEcFuMd+yE0e45Jrkqje5IL80OqZ8so1/Y5OQ01wl8S0XOvV8D+jVjiYtDETsbMzM 3QUC5BpuV6U7MO78XE7+7MuO7ljHPR5R7p4bjBixIp5lNAyIsHPQYxayuInwRtkO07IA h8Yw== X-Gm-Message-State: AOAM533ywDYL/pCmzUX8arMx/Qwt/TKKj5XiplrNW3ViqvAjjfaoXZRd NymlY1h9jBShhRdhxfS3c2w= X-Google-Smtp-Source: ABdhPJzZVeM+VZcyPtkUwp53DnttKg01P0+kN83AFUl/uDKoXqAKY7Gwj4xEctTrbPibcEHtLCDsHg== X-Received: by 2002:a7b:ce8b:: with SMTP id q11mr15912366wmj.30.1629714781445; Mon, 23 Aug 2021 03:33:01 -0700 (PDT) Original-Received: from smtpclient.apple (dynamic-093-133-148-115.93.133.pool.telefonica.de. [93.133.148.115]) by smtp.gmail.com with ESMTPSA id k12sm15321261wrd.75.2021.08.23.03.33.00 (version=TLS1_2 cipher=ECDHE-ECDSA-AES128-GCM-SHA256 bits=128/128); Mon, 23 Aug 2021 03:33:00 -0700 (PDT) X-Google-Original-From: Benjamin Buchmuller In-Reply-To: X-Mailer: Apple Mail (2.3654.120.0.1.13) X-BeenThere: ntg-context@ntg.nl X-Mailman-Version: 2.1.26 Precedence: list List-Id: mailing list for ConTeXt users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: ntg-context-bounces@ntg.nl Original-Sender: "ntg-context" Xref: news.gmane.io gmane.comp.tex.context:112560 Archived-At: --Apple-Mail=_953D55D3-8FEF-4AD1-9C47-C350765B93C0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii This is the setup I have been using, but I'm unsure if the problem could = be related to the other problem I had. (Not scaled to a MWE, but short = enough.) I figured the issue by removing some of the lines. \usemodule[vim] \definetextbackground[codebkg] [ frame=3Don,=20 framecolor=3Dblack, background=3D, location=3Dparagraph, ] \definevimtyping[vimR] [ syntax=3Dr, space=3Doff, lines=3Dsplit, numbering=3Dyes, numberstep=3D5, alternative=3Dpscolor, margin=3D.5em, style=3D{\switchtobodyfont[type,small]\setupinterlinespace}, before=3D{\blank[white,small]\startcodebkg}, % a bit of extra = space=20 after=3D{\stopcodebkg}, directory=3Dvimout/, % note: you must create this folder = yourself! ] \starttext \startvimR #!/usr/bin/env R included_aa <- list( `6d1t` =3D 2:81, `6cnq` =3D 146:225, `6ccg` =3D 2:81, `4lg7` =3D 76:167, `3c2i` =3D 90:181) %>% enframe() %>% unnest(cols =3D "value") %>%=20 rename(protein =3D "name", aa_pos =3D "value") %>% mutate(chain =3D "A") %>% mutate(include_aa =3D TRUE) \stopvimR \stoptext So, the first "i", "n" etc. come from "include_aa" after I remove the = shebang statement.=20 The lines with "#" and "$" (in other pieces not shown) cause the = complaints. I also realized that I get output for each vim block, but instead of a = "vimout", I get a "pdf" (error) and a "log" (some attached) now. Also, the blocks get recompiled with each run even if their content = doesn't change which was the previous behavior. --Apple-Mail=_953D55D3-8FEF-4AD1-9C47-C350765B93C0 Content-Disposition: attachment; filename=xxx-temp-vimR-0-error.log Content-Type: application/octet-stream; x-unix-mode=0644; name="xxx-temp-vimR-0-error.log" Content-Transfer-Encoding: 7bit return { ["errortype"]=0, ["filename"]="vimout/mbd_scaffold-temp-vimR-0.tmp", ["lastcontext"]="\n #\n !/usr/bin/env R", ["lastluaerror"]="", ["lasttexerror"]="You can't use 'parameter character #' in vertical mode", ["lasttexhelp"]="Sorry, but I'm not programmed to handle this case;\nI'll just pretend that you didn''t ask for it.\nIf you're in the wrong mode, you might be able to\nreturn to the right one by typing 'I}' or 'I$' or 'I\\par'.", ["linenumber"]=1, ["offset"]=10, ["skiplinenumber"]=0, } --Apple-Mail=_953D55D3-8FEF-4AD1-9C47-C350765B93C0 Content-Disposition: attachment; filename=xxx-temp-vimR-0.log Content-Type: application/octet-stream; x-unix-mode=0644; name="xxx-temp-vimR-0.log" Content-Transfer-Encoding: 7bit system > system > ConTeXt ver: 2021.08.22 11:54 LMTX fmt: 2021.8.22 int: english/english system > system > 'cont-new.mkxl' loaded open source > level 1, order 1, name '/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkxl/cont-new.mkxl' system > beware: some patches loaded from cont-new.mkiv close source > level 1, order 1, name '/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkxl/cont-new.mkxl' system > files > jobname 'vimout/mbd_scaffold-temp-vimR-0', input 'vimout/mbd_scaffold-temp-vimR-0.tmp', result 'vimout/mbd_scaffold-temp-vimR-0' fonts > latin modern fonts are not preloaded languages > language 'en' is active open source > level 1, order 2, name 'vimout/mbd_scaffold-temp-vimR-0.tmp' tex error > tex error on line 1 in file vimout/mbd_scaffold-temp-vimR-0.tmp: You can't use 'parameter character #' in vertical mode # !/usr/bin/env R 1 >> #!/usr/bin/env R 2 library(tidyverse) 3 4 read_csa <- function(file) { 5 6 readr::read_tsv(file) %>% 7 tidyr::pivot_longer(-1) %>% 8 magrittr::set_colnames(c("target", "buried_by", "value")) %>% 9 dplyr::mutate( 10 tar = stringr::str_extract(target, "^.+(?=/.+/)"), 11 tar_chain = stringr::str_extract(target, "(?<=/)[A-Z]+(?=/)"), Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn''t ask for it. If you're in the wrong mode, you might be able to return to the right one by typing 'I}' or 'I$' or 'I\par'. --Apple-Mail=_953D55D3-8FEF-4AD1-9C47-C350765B93C0 Content-Disposition: attachment; filename=xxx-temp-vimR-1.log Content-Type: application/octet-stream; x-unix-mode=0644; name="xxx-temp-vimR-1.log" Content-Transfer-Encoding: quoted-printable system=20=20=20=20=20=20=20=20=20=20>=20=0Asystem=20=20=20=20=20=20=20=20= =20=20>=20ConTeXt=20=20ver:=202021.08.22=2011:54=20LMTX=20=20fmt:=20= 2021.8.22=20=20int:=20english/english=0Asystem=20=20=20=20=20=20=20=20=20= =20>=20=0Asystem=20=20=20=20=20=20=20=20=20=20>=20'cont-new.mkxl'=20= loaded=0Aopen=20source=20=20=20=20=20>=20level=201,=20order=201,=20name=20= '/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkxl/cont-new.mk= xl'=0Asystem=20=20=20=20=20=20=20=20=20=20>=20beware:=20some=20patches=20= loaded=20from=20cont-new.mkiv=0Aclose=20source=20=20=20=20>=20level=201,=20= order=201,=20name=20= 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lua=20stats=20=20>=20tex=20properties:=20740037=20hash=20slots=20used=20= of=202097152,=2044537=20control=20sequences,=20approximate=20memory=20= usage:=2025=20MB=0Amkiv=20lua=20stats=20=20>=20lua=20properties:=20= engine:=20lua=205.4,=20used=20memory:=2036=20MB,=20ctx:=2034=20MB,=20= max:=2034=20MB,=20symbol=20mask:=20utf=20(=CF=84=CE=B5=CF=87)=0Amkiv=20= lua=20stats=20=20>=20runtime:=200.340=20seconds,=201=20processed=20= pages,=201=20shipped=20pages,=202.939=20pages/second=0A= --Apple-Mail=_953D55D3-8FEF-4AD1-9C47-C350765B93C0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 > On Aug 23, 2021, at 08:19, Hans Hagen wrote: >=20 > On 8/23/2021 12:10 AM, Benjamin Buchmuller via ntg-context wrote: >> Hi, >> Thanks for having had a look into the t-vim. >> At least the document compiles fine (I get a PDF), although multiple = complaints from the lua end when I use "$" or "#" in my source, for = example >> #!/usr/bin/bash >> etc. culminating in >> Sorry, but I'm not programmed to handle this case; >> I'll just pretend that you didn''t ask for it. >> If you're in the wrong mode, you might be able to >> return to the right one by typing 'I}' or 'I$' or 'I\par'. >> Seems as if LMTX tried to interpret something literally here =E2=80=A6 >> Further, I get a lot of >> fonts > beware: no fonts are loaded yet, using 'lm mono' in = box >> fonts > checking > char i (U+00069) in font '' with id 0: = missing >> fonts > checking > char n (U+0006E) in font '' with id 0: = missing >> warnings. Maybe some things need to be adjusted? > THis normally means that you have someting before the \starttext that = gets typeset (here the word "in") >=20 > Hans >=20 > ----------------------------------------------------------------- > Hans Hagen | PRAGMA ADE > Ridderstraat 27 | 8061 GH Hasselt | The Netherlands > tel: 038 477 53 69 | www.pragma-ade.nl | www.pragma-pod.nl > ----------------------------------------------------------------- --Apple-Mail=_953D55D3-8FEF-4AD1-9C47-C350765B93C0 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: base64 Content-Disposition: inline X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX18KSWYgeW91ciBxdWVzdGlvbiBpcyBvZiBpbnRlcmVz dCB0byBvdGhlcnMgYXMgd2VsbCwgcGxlYXNlIGFkZCBhbiBlbnRyeSB0byB0aGUgV2lraSEKCm1h aWxsaXN0IDogbnRnLWNvbnRleHRAbnRnLm5sIC8gaHR0cDovL3d3dy5udGcubmwvbWFpbG1hbi9s aXN0aW5mby9udGctY29udGV4dAp3ZWJwYWdlICA6IGh0dHA6Ly93d3cucHJhZ21hLWFkZS5ubCAv IGh0dHA6Ly9jb250ZXh0LmFhbmhldC5uZXQKYXJjaGl2ZSAgOiBodHRwczovL2JpdGJ1Y2tldC5v cmcvcGhnL2NvbnRleHQtbWlycm9yL2NvbW1pdHMvCndpa2kgICAgIDogaHR0cDovL2NvbnRleHRn YXJkZW4ubmV0Cl9fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fCg== --Apple-Mail=_953D55D3-8FEF-4AD1-9C47-C350765B93C0--