I would like to call a pandoc filter (this one) from rmarkdown/RStudio. However, pandoc seems not to recognize the filter. I've handed over the filter in the YAML header. Consider this rmd file:
---
title: "test"
output: pdf_document
header-includes:
- \usepackage{xspace}
pandoc_args:
- --filter
- pandoc-filter/typography.py
---
test
s.S.
The knitting output shows no sign that the filter was handed over to pandoc:
/usr/local/bin/pandoc +RTS -K512m -RTS test_typography-py.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test_typography-py.pdf --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmarkdown/rmd/latex/default-1.17.0.2.tex --highlight-style tango --pdf-engine pdflatex --variable graphics=yes --variable 'geometry:margin=1in'
The rendered pdf file does not show the effects of the filter, see image
(The effect of the filter is to render a thin space between phrases such as "z.B." or "e.g.".)
What can I do to get this filter run by pandoc via rmarkdown (preferably using the YAML header)?
I just realized (thanks to #NMarkgraf) that I had an intendation error. The correct intendation in YAML is this:
---
title: "test"
header-includes:
- \usepackage{xspace}
output:
pdf_document:
pandoc_args:
- --filter
- typography.py
---
Then it works - the filter is recognized.
Related
I have been trying to convert a plain text file (containing ASCII sentences / lines) into an JPEG image - not caring about any formats or styles - just a first try - keen on quick results:
After half a day trials and errors in all variations - all failing with the below (or similar) errors - and nearly going mad I have solved the following error message :
...
convert-im6.q16: not authorized `#a.txt' # error/property.c/InterpretImageProperties/3516.
I have gotten the wanted result when I have deactivitated
/etc/ImageMagick-6/policy.xml
into
/etc/ImageMagick-6/_policy.xml
Can somebody explain - please - what the magic behind is with this (deactivated) file ???
And please - being sure this file should become re-activated as it is by default - what do I need to change instead (in the file ???)
Thanks in advance with BR
If you are not on a shared server, you can edit your ImageMagick policy.xml file to give read|write permissions for the use of "#".
I suspect the defaults are still "none" for the use of "#" even if you disable the policy.xml file.
Then you can read a text file (in this case ipsum_lorem.txt) :
convert -size 1000x -font arial -pointsize 28 caption:"#ipsum_lorem.txt" x.jpg
or
cat ipsum_lorem.txt | convert -size 1000x -font arial -pointsize 28 caption:"#-" x.jpg
and the result should be:
I'm using TexMaker (on Windows 10), using the pdflatex (F6) and yet I can't open the PNG file in the folder of my .tex
\usepackage{graphicx}
\begin{document}
\begin{figure}[h!]
\includegraphics[width=\linewidth]{File.png}
\end{figure}
\end{document}
so I tried to create an bb file from the PNG. I opened cmd at the folder and typed:
ebb File.png
ebb: file not writable for security reasons: File.bb
ebb: fatal: Unable to open output file File.bb
When clicking in the properties and security of File.png I see that my user both: is the owner of the folder and has all permissions set in (even tho I cannot uncheck any of the permissions I have, weirdly).
The folder which I'm working on has that black square marked on the "read only" attribute (in properties). Which I can't quite keep unchecked even tho I'm the owner of it. What is wrong?
EDIT: Here's what happens when I click on show permissions (>properties >security >advanced >show permissions) my user is the owner.
I can't click on anything even tho I'm the owner.
Edit, the logfile:
LOG FILE :
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (MiKTeX 20.10) (preloaded format=pdflatex 2020.10.24) 25 OCT 2020 10:47
entering extended mode
**./test.tex
(test.tex
LaTeX2e <2020-10-01> patch level 1
L3 programming layer <2020-10-05> xparse <2020-03-03>
("C:\Program Files\MiKTeX\tex/latex/base\article.cls"
Document Class: article 2020/04/10 v1.4m Standard LaTeX document class
("C:\Program Files\MiKTeX\tex/latex/base\size12.clo"
File: size12.clo 2020/04/10 v1.4m Standard LaTeX file (size option)
)
\c#part=\count175
\c#section=\count176
\c#subsection=\count177
\c#subsubsection=\count178
\c#paragraph=\count179
\c#subparagraph=\count180
\c#figure=\count181
\c#table=\count182
\abovecaptionskip=\skip47
\belowcaptionskip=\skip48
\bibindent=\dimen138
)
("C:\Program Files\MiKTeX\tex/latex/graphics\graphicx.sty"
Package: graphicx 2020/09/09 v1.2b Enhanced LaTeX Graphics (DPC,SPQR)
("C:\Program Files\MiKTeX\tex/latex/graphics\keyval.sty"
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
\KV#toks#=\toks15
)
("C:\Program Files\MiKTeX\tex/latex/graphics\graphics.sty"
Package: graphics 2020/08/30 v1.4c Standard LaTeX Graphics (DPC,SPQR)
("C:\Program Files\MiKTeX\tex/latex/graphics\trig.sty"
Package: trig 2016/01/03 v1.10 sin cos tan (DPC)
)
("C:\Program Files\MiKTeX\tex/latex/graphics-cfg\graphics.cfg"
File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration
)
Package graphics Info: Driver file: pdftex.def on input line 105.
("C:\Program Files\MiKTeX\tex/latex/graphics-def\pdftex.def"
File: pdftex.def 2020/10/05 v1.2a Graphics/color driver for pdftex
))
\Gin#req#height=\dimen139
\Gin#req#width=\dimen140
)
("C:\Program Files\MiKTeX\tex/latex/l3backend\l3backend-pdftex.def"
File: l3backend-pdftex.def 2020-09-24 L3 backend support: PDF output (pdfTeX)
\l__kernel_color_stack_int=\count183
\l__pdf_internal_box=\box47
) (test.aux)
\openout1 = `test.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 3.
LaTeX Font Info: ... okay on input line 3.
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 3.
LaTeX Font Info: ... okay on input line 3.
LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 3.
LaTeX Font Info: ... okay on input line 3.
LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 3.
LaTeX Font Info: ... okay on input line 3.
LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 3.
LaTeX Font Info: ... okay on input line 3.
LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 3.
LaTeX Font Info: ... okay on input line 3.
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 3.
LaTeX Font Info: ... okay on input line 3.
("C:\Program Files\MiKTeX\tex/context/base/mkii\supp-pdf.mkii"
[Loading MPS to PDF converter (version 2006.09.02).]
\scratchcounter=\count184
\scratchdimen=\dimen141
\scratchbox=\box48
\nofMPsegments=\count185
\nofMParguments=\count186
\everyMPshowfont=\toks16
\MPscratchCnt=\count187
\MPscratchDim=\dimen142
\MPnumerator=\count188
\makeMPintoPDFobject=\count189
\everyMPtoPDFconversion=\toks17
) ("C:\Program Files\MiKTeX\tex/latex/epstopdf-pkg\epstopdf-base.sty"
Package: epstopdf-base 2020-01-24 v2.11 Base part for package epstopdf
Package epstopdf-base Info: Redefining graphics rule for `.eps' on input line 4
85.
)
<semirreta.png, id=1, 368.1253pt x 99.37125pt>
[1{C:/Users/JoaoV/AppData/Local/MiKTeX/pdftex/config/pdftex.map}] (test.aux) )
Here is how much of TeX's memory you used:
1167 strings out of 480236
17436 string characters out of 2890433
280939 words of memory out of 3000000
17769 multiletter control sequences out of 15000+200000
535555 words of font info for 31 fonts, out of 3000000 for 9000
1141 hyphenation exceptions out of 8191
60i,4n,66p,199b,236s stack positions out of 5000i,500n,10000p,200000b,50000s
<C:/Program Files/MiKTeX/fonts/type1/public/amsfonts/cm/cmr12.pfb><C:/Program F
iles/MiKTeX/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on test.pdf (1 page, 13448 bytes).
PDF statistics:
15 PDF objects out of 1000 (max. 8388607)
0 named destinations out of 1000 (max. 500000)
6 words of extra memory for PDF output out of 10000 (max. 10000000)
I made a little test:
the real image is suposed to be these two lines: https://ibb.co/yYQCfnd
Remove the draft option, this prevents images from showing up
While trying to knit .rmd file to pdf, if code chunks has stargazer function, the file is not knitting to pdf format. I have several tables (both long and short) with combination of regression output via stargazer in latex format but none of them are converting to pdf. I am using MikTeX as LaTeX distribution. I have used following code (as an example)
stargazer(pre.ols.sp01SIOI,pre.ols.sp02SIOI,pre.ols.sp03SIOI,pre.ols.sp04SIOI,
post.ols.sp01SIOI,post.ols.sp02SIOI,post.ols.sp03SIOI,post.ols.sp04SIOI,
style = "qje", type = "latex", header=FALSE, title = "Regression Analysis").
I am getting the following error.
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (MiKTeX 2.9.7440 64-bit) entering extended mode
I was unable to find any missing LaTeX packages from the error log Paper1.v7_11Jun2020.log.
Error: LaTeX failed to compile Paper1.v7_11Jun2020.tex. See
https://yihui.org/tinytex/r/#debugging for debugging tips.
In addition: Warning messages:
1: In readLines(log) : line 888 appears to contain an embedded nul
2: In readLines(log) :
incomplete final line found on 'Paper1.v7_11Jun2020.log'
3: In readLines(log) : line 888 appears to contain an embedded nul
4: In readLines(log) :
incomplete final line found on 'Paper1.v7_11Jun2020.log'
5: In readLines(log) : line 888 appears to contain an embedded nul
6: In readLines(log) :
incomplete final line found on 'Paper1.v7_11Jun2020.log'
Execution halted
I have followed the debugging tips mentioned on the yihui.org. But still no luck.
I have also tried to assign the stargazer output and then use kable() and still
it's not working. Moreover, I have tried to using landscape style.
I appreciate any assistance with the issue.
Thanks
Edit: The YAML header
title: XXX
documentclass: article
date: "r format(Sys.Date(),'%d %B, %Y')"
output:
pdf_document:
df_print: paged
fig_caption: yes
highlight: tango
number_sections: yes
citation_package: natbib
keep_tex: yes
bibliography: library.bib
header-includes:
-\usepackage{amsmath}
-\usepackage[utf8]{inputenc}
-\usepackage{autobreak}
-\usepackage{setspace}
-\usepackage{hyperref}
-\usepackage[authoryear]{natbib}
-\usepackage{caption}
-\usepackage{babel
-\usepackage{multirow}
-\usepackage{pdflscape}
-\usepackage{dcolumn}
-\usepackage{rotating}
I have a Rmarkdown document that uses googleVis library.
It works fine on RStudio. I just press "Knit HTML" button and "voilá": I get a beautiful HTML.
However, when I try to generate on the command line, I get an error in Pandoc.
I just run:
Rscript --verbose -e 'script.R'
Where script.R is:
rmarkdown::render("inputFile.Rmd", output_dir=file.path("/path/to/my/dir"), output_file="outfile.html", encoding="UTF-8");
The error I get is this:
(.....)
output file: 5c86eb19-d29f-4ac6-ac35-87e72fb42bbd2787560825121738853.knit.md
/opt/local/bin/pandoc +RTS -K512m -RTS 5c86eb19-d29f-4ac6-ac35-87e72fb42bbd2787560825121738853.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output /Users/rodrigo/Documents/Nitryx/Technical/Projects/NitroERP/repository/5c86eb19-d29f-4ac6-ac35-87e72fb42bbd.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 2 --variable toc_float=1 --variable toc_selectors=h1,h2 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --template /opt/local/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rmarkdown/rmd/h/default.html --number-sections --variable 'theme:bootstrap' --include-in-header /var/folders/dd/y3fs2t5j1n3fg8nfq1syrzym0000gn/T//RtmpTjWUT6/rmarkdown-str301943f9d761.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --no-highlight --variable highlightjs=/opt/local/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rmarkdown/rmd/h/highlight --variable navigationjs=/opt/local/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rmarkdown/rmd/h/navigation-1.0
Fetching https://www.google.com/jsapi?callback=displayChartGaugeID30195c82acb7...
pandoc: Failed to retrieve https://www.google.com/jsapi?callback=displayChartGaugeID30195c82acb7
user error (https not supported)
Error: pandoc document conversion failed with error 61
Execution halted
Note the:
pandoc: Failed to retrieve https://www.google.com/jsapi?callback=displayChartGaugeID30195c82acb7
user error (https not supported)
But it works on RStudio...
Can you help?
RStudio probably uses a different pandoc version than the one you get on the command line... (see e.g. this issue.)
Try installing the newest pandoc and make sure you're using that with pandoc -v
My problem is explained in the title. I've tried compiling a sample .Rmd I found here: http://www.ssc.wisc.edu/~hemken/Stataworkshops/Stata%20and%20R%20Markdown/
in addition to looking up various resources online to no avail. While my resource, Doug, was able to compile an RMarkdown, I am getting an error for the MWE below.
The MWE is:
---
title: "Stata and R Markdown (Windows)"
author: "Doug Hemken"
date: "July 2015"
output:
html_document:
toc: yes
---
```{r, echo=FALSE, message=FALSE}
require(knitr)
statapath <- "/Applications/Stata/Stata.app"
opts_chunk$set(engine="stata", engine.path=statapath, comment="")
```
### Descriptive Statistics
A simple example.
```{r}
sysuse auto
summarize
```
The output/error from the RStudio console is:
processing file: stata.Rmd
|................ | 25%
ordinary text without R code
|................................ | 50%
label: unnamed-chunk-1 (with options)
List of 2
$ echo : logi FALSE
$ message: logi FALSE
Loading required package: knitr
|................................................. | 75%
ordinary text without R code
|.................................................................| 100%
label: unnamed-chunk-2
running: /Applications/Stata/Stata.app -q -b stata47b9d14e1c.do
Quitting from lines 20-22 (stata.Rmd)
Error in engine(options) :
sh: /Applications/Stata/Stata.app: is a directory
Calls: <Anonymous> ... process_group.block -> call_block -> block_exec -> in_dir -> engine
In addition: Warning message:
running command ''/Applications/Stata/Stata.app' -q -b stata47b9d14e1c.do 2>&1' had status 126
Execution halted
The page you link to points to this page. There, it is written: "For example, if Stata is installed in /Applications/Stata/, then the path to the Stata executable is /Applications/Stata/Stata.app/Contents/MacOS/", and they give appropriate links for all different flavours of Stata. Also, you need to refer to the executable, not the folder where it is located. If I change your MWE as below, everything works for me (note that I use Stata-SE; you might need to change this for your system).
---
title: "Stata and R Markdown (Windows)"
author: "Doug Hemken"
date: "July 2015"
output:
html_document:
toc: yes
---
```{r, echo=FALSE, message=FALSE}
require(knitr)
statapath <- "/Applications/Stata/StataSE.app/Contents/MacOS/stata-se"
opts_chunk$set(engine="stata", engine.path=statapath, comment="")
```
### Descriptive Statistics
A simple example.
```{r}
sysuse auto
summarize
```