Pandoc error 1 when I knit

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1

I am trying to knit an Rmarkdown together for a homework assignment, but I keep getting the following message:

"C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/pandoc" +RTS -K512m -RTS PS2.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output PS2.docx --lua-filter "C:\Users\cms14\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\pagebreak.lua" --highlight-style tango
output file: PS2.knit.md

pandoc.exe: PS2.docx: openBinaryFile: permission denied (Permission denied)
Error: pandoc document conversion failed with error 1
Execution halted

I was able to knit this document earlier before adding Latex equations with the "$$" feature, but once I added them, the knit keeps giving me this error. Does anyone know how to fix this?

Update: In trying to knit to a PDF, I got the following error message.

Sorry, but C:\Users\cms14\AppData\Local\Programs\MiKTeX\miktex\bin\x64\pdflatex.exe did not succeed.

! The log file hopefully contains the information to get MiKTeX going again:

! C:\Users\cms14\AppData\Local\MiKTeX\miktex\log\pdflatex.log

Error: LaTeX failed to compile PS2.tex. See The R package tinytex - Helper Functions to Manage TinyTeX, and Compile LaTeX Documents - Yihui Xie | 谢益辉 for debugging tips. See PS2.log for more info.

Within this file, I see the message "GUI framework cannot be initialized." Does anyone know how to fix this?

2

Welcome to the forum.

I am not an expert in the area but I imagine that we need to see what the file looks like. Can you post a cut dovn version of the document and some sample data here?

These instructions are not really intended for Rmarkdown or Quarto but they may help a bit:

A handy way to supply some sample data is the dput() function. In the case of a large dataset something like dput(head(mydata, 100)) should supply the data we need. Just do dput(mydata) where mydata is your data. Copy the output and paste it here.

3

Thanks for clarifying this. I am working with quarterly GDP data from FRED, and I am primarily working with the data using the arima() function in my markdown file. Here is part of my file

#Question d
Using this AR(3) model, we will determine if it implies the existence of business cycles.
Our model can be written as follows:

gdp_t = 3.19 + .3351gdp_{t-1} + .1514gdp_{t-2} - .1181gdp_{t-3} + \epsilon_t

Using the lag operators, we can develop the characteristic equation of the lag polynomial:

\phi(t) = (1 -.3351L - .1514L^2 + .1181L^3)

As for my data, here is what the dput() function gives me

dput(head(gdp, 10))
structure(c(-1.1, -0.8, 6.4, 6.2, 6.8, 2.3, 0.5, -5.4, -1.4,
4.2), class = c("xts", "zoo"), src = "FRED", updated = structure(1676668369.33708, class = c("POSIXct",
"POSIXt")), index = structure(c(-718070400, -710208000, -702259200,
-694310400, -686448000, -678585600, -670636800, -662688000, -654912000,
-647049600), tzone = "UTC", tclass = "Date"), dim = c(10L, 1L
), dimnames = list(NULL, "A191RL1Q225SBEA"))

I'm not sure if this is helpful, I can also attach the latex file error, too.

4

The MikTek error file contains this

2023-02-17 18:30:51,700-0500 INFO pdflatex - this process (24312) started by Rterm in directory C:\Users\cms14\OneDrive\Desktop\School\Time Series with command line: C:\Users\cms14\AppData\Local\Programs\MiKTeX\miktex\bin\x64\pdflatex.exe -halt-on-error -interaction=batchmode PS2.tex
2023-02-17 18:30:51,700-0500 INFO pdflatex - running on Windows 10.0.22621
2023-02-17 18:30:51,720-0500 INFO pdflatex - this is MiKTeX-PDFTEX 4.11.0 (1.40.24) (MiKTeX 22.10)
2023-02-17 18:30:51,765-0500 INFO pdflatex - allowing known shell commands
2023-02-17 18:30:51,912-0500 INFO pdflatex - going to create file: pdflatex.fmt
2023-02-17 18:30:51,912-0500 INFO pdflatex.core - start process: miktex formats build pdflatex --engine pdftex
2023-02-17 18:31:04,178-0500 FATAL pdflatex.core - GUI framework cannot be initialized.
2023-02-17 18:31:04,178-0500 FATAL pdflatex.core - Data:
2023-02-17 18:31:04,180-0500 FATAL pdflatex.core - Source: Libraries\MiKTeX\UI\Qt\mikuiqt.cpp:126
2023-02-17 18:31:04,180-0500 FATAL pdflatex - GUI framework cannot be initialized.
2023-02-17 18:31:04,180-0500 FATAL pdflatex - Info:
2023-02-17 18:31:04,180-0500 FATAL pdflatex - Source: Libraries\MiKTeX\UI\Qt\mikuiqt.cpp
2023-02-17 18:31:04,180-0500 FATAL pdflatex - Line: 126
2023-02-17 18:31:04,185-0500 INFO pdflatex - this process (24312) finishes with exit code 1
2023-02-17 18:31:04,200-0500 WARN pdflatex.core - still open: PS2.tex
2023-02-17 18:31:04,200-0500 WARN pdflatex.core - still open: PS2.log
2023-02-17 19:00:02,345-0500 INFO pdflatex - this process (8608) started by Rterm in directory C:\Users\cms14\OneDrive\Desktop\School\Time Series with command line: C:\Users\cms14\AppData\Local\Programs\MiKTeX\miktex\bin\x64\pdflatex.exe -halt-on-error -interaction=batchmode PS2.tex
2023-02-17 19:00:02,347-0500 INFO pdflatex - running on Windows 10.0.22621
2023-02-17 19:00:02,351-0500 INFO pdflatex - this is MiKTeX-PDFTEX 4.11.0 (1.40.24) (MiKTeX 22.10)
2023-02-17 19:00:02,357-0500 INFO pdflatex - allowing known shell commands
2023-02-17 19:00:02,811-0500 FATAL pdflatex.core - GUI framework cannot be initialized.
2023-02-17 19:00:02,811-0500 FATAL pdflatex.core - Data:
2023-02-17 19:00:02,811-0500 FATAL pdflatex.core - Source: Libraries\MiKTeX\UI\Qt\mikuiqt.cpp:126
2023-02-17 19:00:02,811-0500 FATAL pdflatex - GUI framework cannot be initialized.
2023-02-17 19:00:02,811-0500 FATAL pdflatex - Info:
2023-02-17 19:00:02,811-0500 FATAL pdflatex - Source: Libraries\MiKTeX\UI\Qt\mikuiqt.cpp
2023-02-17 19:00:02,811-0500 FATAL pdflatex - Line: 126
2023-02-17 19:00:02,811-0500 INFO pdflatex - this process (8608) finishes with exit code 1
2023-02-17 19:00:02,811-0500 WARN pdflatex.core - still open: PS2.tex
2023-02-17 19:00:02,811-0500 WARN pdflatex.core - still open: PS2.log

5

Thanks for the data.

As a cut-down example I was thinking of something that included code and YAMAL . See example below, but note it is a Quaro not Rmarkdown file.

A bit of googling suggests that this may be a MikTeX problem and suggests a missing LaTeX package. See R cmd check Latex error: FATAL pdflatex - GUI framework cannot be initialized

It is an old post but with a recent update, and it looks similar. If you are using TinyTex my understanding is that it should install missing packages on the fly but I don't use TinyTex so I may be wrong. When I started using Rmarkdown I already had a full TexLive installation.

My brute force suggestion if you are using TinyTex and you have enough space is to wipe TinyTex and do a complete MikTeX installation.

More sensible people may have less drastic solutions

---
title: "Exercise 2"
author: "Anon."
date: 2022-12-25
date-format: iso
number-sections: true
format: pdf
header-includes:
  - \usepackage{lipsum}
editor: visual

---

{r}
#| label: setup
#| include: false
library(tidyverse); library(kableExtra); library(lubridate); library(janitor);
library(readODS)

dat1  <- data.frame(xx = 1:5, yy = 5:1)


Introduction

Roses are \textcolor{red}{red}, violets are \textcolor{blue}{blue}.

\lipsum[1]

{r}
#| echo: false
#| label: fig-silly.plot
#| fig-cap: Amazingly Useless Plot.
ggplot(dat1, aes(xx, yy)) + geom_line(aes(colour = "red"), show.legend = FALSE)


\lipsum[4]

\newpage

\lipsum[5]
6

This error can happen if the document is already opened - Rendering docx with rmarkdown* requires to have a document close so that it can be overwrite.

Did you check that ?

This is indeed a MikTeX issue as described by @jrkrideau

Yes this is right - auto installation does not work with MikTeX but does with a TexLive installation, including TinyTeX

7

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