From: Benjamin Buchmuller via ntg-context <ntg-context@ntg.nl>
To: Hans Hagen <j.hagen@xs4all.nl>
Cc: Benjamin Buchmuller <benjamin.buchmuller@gmail.com>,
mailing list for ConTeXt users <ntg-context@ntg.nl>
Subject: Re: lmtx update/t-vim (again)
Date: Mon, 23 Aug 2021 12:32:59 +0200 [thread overview]
Message-ID: <AA7CFE4B-6F4C-4B11-9C50-4EA64518D9FD@gmail.com> (raw)
In-Reply-To: <c60b060b-5f9e-d32d-3dcf-8c696398999b@xs4all.nl>
[-- Attachment #1: Type: text/plain, Size: 1477 bytes --]
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=on,
framecolor=black,
background=,
location=paragraph,
]
\definevimtyping[vimR]
[
syntax=r,
space=off,
lines=split,
numbering=yes,
numberstep=5,
alternative=pscolor,
margin=.5em,
style={\switchtobodyfont[type,small]\setupinterlinespace},
before={\blank[white,small]\startcodebkg}, % a bit of extra space
after={\stopcodebkg},
directory=vimout/, % note: you must create this folder yourself!
]
\starttext
\startvimR
#!/usr/bin/env R
included_aa <- list(
`6d1t` = 2:81,
`6cnq` = 146:225,
`6ccg` = 2:81,
`4lg7` = 76:167,
`3c2i` = 90:181) %>% enframe() %>% unnest(cols = "value") %>%
rename(protein = "name", aa_pos = "value") %>%
mutate(chain = "A") %>% mutate(include_aa = TRUE)
\stopvimR
\stoptext
So, the first "i", "n" etc. come from "include_aa" after I remove the shebang statement.
The lines with "#" and "$" (in other pieces not shown) cause the complaints.
I also realized that I get output for each vim block, but instead of a "vimout", I get a "pdf" (error) and a "log" (some attached) now.
Also, the blocks get recompiled with each run even if their content doesn't change which was the previous behavior.
[-- Attachment #2: xxx-temp-vimR-0-error.log --]
[-- Type: application/octet-stream, Size: 524 bytes --]
return {
["errortype"]=0,
["filename"]="vimout/mbd_scaffold-temp-vimR-0.tmp",
["lastcontext"]="\n<line 3.1> #\n !/usr/bin/env R",
["lastluaerror"]="",
["lasttexerror"]="You can't use 'parameter character #' in vertical mode",
["lasttexhelp"]="Sorry, but I'm not programmed to handle this case;\nI'll just pretend that you didn''t ask for it.\nIf you're in the wrong mode, you might be able to\nreturn to the right one by typing 'I}' or 'I$' or 'I\\par'.",
["linenumber"]=1,
["offset"]=10,
["skiplinenumber"]=0,
}
[-- Attachment #3: xxx-temp-vimR-0.log --]
[-- Type: application/octet-stream, Size: 1599 bytes --]
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
<line 3.1> #
!/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'.
[-- Attachment #4: xxx-temp-vimR-1.log --]
[-- Type: application/octet-stream, Size: 13244 bytes --]
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-1', input 'vimout/mbd_scaffold-temp-vimR-1.tmp', result 'vimout/mbd_scaffold-temp-vimR-1'
fonts > latin modern fonts are not preloaded
languages > language 'en' is active
open source > level 1, order 2, name 'vimout/mbd_scaffold-temp-vimR-1.tmp'
close source > level 1, order 2, name 'vimout/mbd_scaffold-temp-vimR-1.tmp'
system > invalid \starttext ... \stoptext structure
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
fonts > checking > char c (U+00063) in font '' with id 0: missing
fonts > checking > char l (U+0006C) in font '' with id 0: missing
fonts > checking > char u (U+00075) in font '' with id 0: missing
fonts > checking > char d (U+00064) in font '' with id 0: missing
fonts > checking > char e (U+00065) in font '' with id 0: missing
fonts > checking > char _ (U+0005F) in font '' with id 0: missing
fonts > checking > char a (U+00061) in font '' with id 0: missing
fonts > checking > char < (U+0003C) in font '' with id 0: missing
fonts > checking > char - (U+0002D) in font '' with id 0: missing
fonts > checking > char s (U+00073) in font '' with id 0: missing
fonts > checking > char t (U+00074) in font '' with id 0: missing
fonts > checking > char ( (U+00028) in font '' with id 0: missing
fonts > checking > char ` (U+00060) in font '' with id 0: missing
fonts > checking > char 6 (U+00036) in font '' with id 0: missing
fonts > checking > char 1 (U+00031) in font '' with id 0: missing
fonts > checking > char = (U+0003D) in font '' with id 0: missing
fonts > checking > char 2 (U+00032) in font '' with id 0: missing
fonts > checking > char : (U+0003A) in font '' with id 0: missing
fonts > checking > char 8 (U+00038) in font '' with id 0: missing
fonts > checking > char , (U+0002C) in font '' with id 0: missing
fonts > checking > char q (U+00071) in font '' with id 0: missing
fonts > checking > char 4 (U+00034) in font '' with id 0: missing
fonts > checking > char 5 (U+00035) in font '' with id 0: missing
fonts > checking > char g (U+00067) in font '' with id 0: missing
fonts > checking > char 7 (U+00037) in font '' with id 0: missing
fonts > checking > char 3 (U+00033) in font '' with id 0: missing
fonts > checking > char 9 (U+00039) in font '' with id 0: missing
fonts > checking > char 0 (U+00030) in font '' with id 0: missing
fonts > checking > char ) (U+00029) in font '' with id 0: missing
fonts > checking > char r (U+00072) in font '' with id 0: missing
fonts > checking > char m (U+0006D) in font '' with id 0: missing
fonts > checking > char p (U+00070) in font '' with id 0: missing
fonts > checking > char o (U+0006F) in font '' with id 0: missing
fonts > checking > char " (U+00022) in font '' with id 0: missing
fonts > checking > char v (U+00076) in font '' with id 0: missing
fonts > checking > char h (U+00068) in font '' with id 0: missing
fonts > checking > char A (U+00041) in font '' with id 0: missing
backend > xmp > using file '/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkiv/lpdf-pdx.xml'
pages > flushing realpage 1, userpage 1, subpage 1
system > start used files
system > text: mbd_scaffold-temp-vimR-1
system > stop used files
system > start used files
system > 1: filename=publ-imp-default.lua filetype=lua foundname=/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkiv/publ-imp-default.lua fullname=/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkiv/publ-imp-default.lua usedmethod=database
system > 2: filename=cont-new.mkxl filetype=tex foundname=/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkxl/cont-new.mkxl fullname=/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkxl/cont-new.mkxl usedmethod=database
system > 3: filename=lang-exc.lua filetype=lua foundname=/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkiv/lang-exc.lua fullname=/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkiv/lang-exc.lua usedmethod=database
system > 4: filename=lang-us.lua filetype=lua foundname=/Applications/ConTeXt/tex/texmf-context/tex/context/patterns/mkiv/lang-us.lua fullname=/Applications/ConTeXt/tex/texmf-context/tex/context/patterns/mkiv/lang-us.lua usedmethod=database
system > 5: filename=vimout/mbd_scaffold-temp-vimR-1.tmp format=tex foundname=vimout/mbd_scaffold-temp-vimR-1.tmp fullname=/Users/benjamin/Documents/university/1712-2103-PhD/thesis-PhD/_sync/02_thesis/publication-thesis_P-v2/maintexts/vimout/mbd_scaffold-temp-vimR-1.tmp usedmethod=direct
system > 6: filename=lmmono10-regular filetype=otf format=otf foundname=/Applications/ConTeXt/tex/texmf/fonts/opentype/public/lm/lmmono10-regular.otf fullname=/Applications/ConTeXt/tex/texmf/fonts/opentype/public/lm/lmmono10-regular.otf usedmethod=database
system > 7: filename=lpdf-pdx.xml filetype=tex foundname=/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkiv/lpdf-pdx.xml fullname=/Applications/ConTeXt/tex/texmf-context/tex/context/base/mkiv/lpdf-pdx.xml usedmethod=database
system > stop used files
system > start commandline options
system > currentrun="1"
system > fulljobname="vimout/mbd_scaffold-temp-vimR-1.tmp"
system > input="vimout/mbd_scaffold-temp-vimR-1.tmp"
system > kindofrun="1"
system > maxnofruns="9"
system > texmfbinpath="/Applications/ConTeXt/tex/texmf-osx-64/bin"
system > stop commandline options
system > start commandline files
system > 1: vimout/mbd_scaffold-temp-vimR-1.tmp
system > stop commandline files
modules > start used modules
modules > stop used modules
system >
system > status after finishing run
system >
system > -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
system > string pool hash lookup node token buffer input file nest parameter save font language mark insert
system > -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
system > max 2097152 100000000 2097152 2097152 50000000 10000000 100000000 100000 2000 10000 100000 500000 100000 10000 10000 500
system > min 150000 10000000 150000 150000 1000000 1000000 1000000 10000 500 1000 20000 100000 250 250 50 10
system > set 500000 10000000 250000 250000 50000000 10000000 10000000 100000 2000 10000 100000 500000 100000 250 250 250
system > stp 100000 1000000 100000 100000 500000 250000 1000000 10000 250 1000 10000 10000 250 250 50 25
system >
system > mem 150000 840622 150000 1000000 1000000 1000000 10000 500 1000 20000 10000 46440 96 1200 240
system > all 3600000 840622 2400000 9000000 8000000 1000000 320000 16000 48000 80000 160000 46440 96 28800 5760
system >
system > ini 2141682 840331 0 44513 0 489954 0
system > ptr 44554 8606 44537 489941 0 0 0 0 0 0 1 0 0 7
system > top 44555 740037 131074 4574 490748 141 37 4 12 36 406 250 250 50 10
system > -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
system >
system > current input type : initial
system >
system > approximate memory : 27242854 (25 MB)
system >
system > expansion depth : min: 10000, max: 1000000, set: 10000, top: 7
system >
system > luabytecode registers : 997
system > luabytecode bytes : 15968 (0 MB)
system > luastate bytes now : 36129040 (34 MB)
system > luastate bytes max : 36590329 (34 MB)
system >
system > file callbacks : 63
system > saved callbacks : 422
system > direct callbacks : 2
system > function callbacks : 187
system > value callbacks : 1
system > message callbacks : 0
system > bytecode callbacks : 597
system >
system > mp instances : 0
system > mp estimated memory : 0 (0 MB)
system > mp file callbacks : 0
system > mp text callbacks : 0
system > mp script callbacks : 0
system > mp log callbacks : 0
system >
system > total callbacks : 1272
system > mp total callbacks : 0
system > backend callbacks : 0
system >
mkiv lua stats > used config file: selfautoparent:/texmf/web2c/texmfcnf.lua
mkiv lua stats > used cache path: /Applications/ConTeXt/tex/texmf-cache/luametatex-cache/context/5fe67e0bfe781ce0dde776fb1556f32e
mkiv lua stats > resource resolver: loadtime 0.006 seconds, 0 scans with scantime 0.000 seconds, 0 shared scans, 7 found files, scanned paths: <none>
mkiv lua stats > stored bytecode data: 497 modules (0.255 sec), 100 tables (0.012 sec), 597 chunks (0.267 sec)
mkiv lua stats > traced context: maxstack: 1591, freed: 0, unreachable: 1591
mkiv lua stats > cleaned up reserved nodes: 69 nodes, 9 lists of 434
mkiv lua stats > node memory usage: 6 attribute, 3 attribute_list, 1 glue, 58 glue_spec, 3 kern, 2 penalty, 2 temp
mkiv lua stats > node list callback tasks: 9 unique task lists, 8 instances (re)created, 46 calls
mkiv lua stats > used backend: pdf (backend for directly generating pdf output)
mkiv lua stats > jobdata time: 0.001 seconds saving, 0.000 seconds loading
mkiv lua stats > callbacks: file: 63, saved: 422, direct: 2, function: 187, value: 1, message: 0, bytecode: 597, late 0, total: 1272 (1272 per page)
mkiv lua stats > randomizer: resumed with value 0.82560840936925
mkiv lua stats > loaded patterns: en::1, load time: 0.000
mkiv lua stats > loaded fonts: 1 files: lmmono10-regular.otf
mkiv lua stats > font engine: otf 3.119, afm 1.513, tfm 1.000, 1 instances, load time 0.010 seconds
mkiv lua stats > font embedding time: 0.001 seconds, 1 fonts
mkiv lua stats > result saved in file: vimout/mbd_scaffold-temp-vimR-1.pdf, compresslevel 1, objectcompresslevel 3
mkiv lua stats > positions: 4 collected, 0 deltas, 0 shared partials, 0 partial entries
mkiv lua stats > used platform: osx-64, type: unix, binary subtree: texmf-osx-64
mkiv lua stats > used engine: luametatex version: 2.0918, functionality level: 20210804, format id: 589, compiler: clang
mkiv lua stats > tex properties: 740037 hash slots used of 2097152, 44537 control sequences, approximate memory usage: 25 MB
mkiv lua stats > lua properties: engine: lua 5.4, used memory: 36 MB, ctx: 34 MB, max: 34 MB, symbol mask: utf (τεχ)
mkiv lua stats > runtime: 0.340 seconds, 1 processed pages, 1 shipped pages, 2.939 pages/second
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> On Aug 23, 2021, at 08:19, Hans Hagen <j.hagen@xs4all.nl> wrote:
>
> 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 …
>> 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")
>
> Hans
>
> -----------------------------------------------------------------
> Hans Hagen | PRAGMA ADE
> Ridderstraat 27 | 8061 GH Hasselt | The Netherlands
> tel: 038 477 53 69 | www.pragma-ade.nl | www.pragma-pod.nl
> -----------------------------------------------------------------
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next prev parent reply other threads:[~2021-08-23 10:32 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
[not found] <mailman.0.1629453601.23792.ntg-context@ntg.nl>
2021-08-22 22:10 ` Benjamin Buchmuller via ntg-context
2021-08-22 22:21 ` Wolfgang Schuster via ntg-context
2021-08-23 6:19 ` Hans Hagen via ntg-context
2021-08-23 10:32 ` Benjamin Buchmuller via ntg-context [this message]
2021-08-23 17:42 ` Aditya Mahajan via ntg-context
2021-08-23 17:45 ` Hans Hagen via ntg-context
2021-08-25 2:45 ` Aditya Mahajan via ntg-context
2021-08-22 22:55 ` lmtx update Benjamin Buchmuller via ntg-context
2021-08-23 6:21 ` Hans Hagen via ntg-context
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