Stat 585 - Error Fixing Process

Prompt:

The goal of this week’s blog is to document what you are doing when things do not go according to plan.

Similar to previous exercises, we have a specific use case in mind: we want to build a book from a github repository.

What happens in practice usually, is that we run into some problems. So your real task turns into that of a bug-hunter and fixer. Luckily, you have a community (the class discussion board) who might be able to help you.

What we want: build a book

Build the html version of the 2nd edition for Hadley Wickham’s book Advanced R Programming from a github repository.

Steps:

Clone the repository https://github.com/hadley/adv-r.
Open the R project in the repository in RStudio.
Activate the Build tab (by default in the top right panel). Click on the Build Book button.
The book will be available in html format as index.html

Deliverable (1): what is the last word in chapter 15? - You don’t have to answer this question, if things don’t work.

What to do when things don’t work?

Errors happen, they are frustrating, but if we learn something from them, we can turn them into valuable experiences.

check the Questions and Answers forum in Canvas whether there is a solution available for your problem.
if the above document does (not yet) include your question, document the error you encounter (be as concise and specific as you can at the same time)
if the Question and Answers forum does (not yet) include a solution, describe one approach on how you tried to solve the problem (and how this did not work).
submit the description of your problem in Canvas at Discussions > Questions and Answers. Write the paragraph in the mindset that you want to get help from somebody, and you try to describe the problem you are encountering.
Extra points (1 pt for the first suggested working solution): post a solution to one of the problems in the Questions and Answers forum (your own does not count!).

Deliverable (2): Write a paragraph on the biggest problem you encountered when you were building the book, (and how you managed to solve it.)

You can write your experience directly into the README.Rmd file. Just make sure that you change the yaml at the top: change the author at the top, and give your post a new title (don’t change the category :))

Commit and push to your repo and you are done!

ANSWER SECTION

LAST WORD

The last word in Chapter 15 is class in the sentence, Define a length method for the Person class.

PROCESS:

Unfortunately, I was unable to compile the pdf book, but I was able to get the bs4 version! Here was the process I followed to working through the errors.

I was able to copy the repository into a local folder on my PC and open up all the files without an issue. I ran into a problem initially because I didn’t have the library(bookdown) package. As I was trying to download the package, I came across the error

WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

Which I tried to overcome with a clean install of R once again. This unfortunately did not fix the error that I had and so I ran install.packages("Rtools") to be greeted with another error.

Warning in install.packages :
  package ‘Rtools’ is not available for this version of R

At which point I did a run around forums on “community.rstudio” to find that I had to download Rtools from the Cran project. I am still unsure of why I need Rtools given that the documentation for Rtools43 indicates that “Moreover, online build services are available to check and build R packages for Windows, for which again one does not need to install Rtools43 locally.”

Installing Rtools43 did not make a noticeable difference, though I think this was because I actually needed the Rtools40 instead. However, I was now able to download the bookdown package and could see it in my packages list in Rstudio to start compiling.

Once I ran the compile, I saw that I had the same issue as everyone else regarding the ‘wrap’ argument in the registerS3method() argument which I then changed and re-compiled. I ran into an error about a package called lobstr which I did not have so I installed that package as well and the compiler continued.

I came across an error regarding a package called emo that I did not have and followed the suggestion on the discussions forum to use devtools to install it. At this point in the console, I was asked to install Rtools40 which I realized might have been the correct version to install since my Rtools43 installation did not help here. I installed Rtools40 and followed Landon’s suggestion in the Canvas Discussions to add it to my PATH.

I was able to successfully install emo and recompiled. I then ran into another error about not having the package sloop and ran an install on that. I followed the same procedure for package zeallot, bench, and ggbeeswarm. After this, the compiler ran without error for longer than 5 minutes to tweak the files that were generated from the first processing of the knit. The following error then came about.

Error: LaTeX failed to compile _main.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See _main.log for more info.
Execution halted
Error: bookdown::render_book() failed to render the output format 'bookdown::pdf_book'.
Execution halted

Knowing it was the _main.tex file, I tried to check where the error might be and I found within my error log the following code.

2023-02-11 13:58:26,032-0600 INFO  xelatex - starting with command line: C:\Users\harun\AppData\Local\Programs\MIKTEX~1.9\miktex\bin\x64\xelatex.exe -halt-on-error -interaction=batchmode _main.tex
2023-02-11 13:58:26,046-0600 INFO  xelatex - allowing known shell commands
2023-02-11 13:58:26,046-0600 INFO  xelatex - enabling input (output) from (to) processes
2023-02-11 13:58:26,062-0600 INFO  xelatex - going to create file: xelatex.fmt
2023-02-11 13:58:30,355-0600 FATAL xelatex - GUI framework cannot be initialized.
2023-02-11 13:58:30,355-0600 FATAL xelatex - Info: 
2023-02-11 13:58:30,355-0600 FATAL xelatex - Source: Libraries\MiKTeX\UI\Qt\mikuiqt.cpp
2023-02-11 13:58:30,355-0600 FATAL xelatex - Line: 77
2023-02-11 13:58:30,356-0600 INFO  xelatex - finishing with exit code 1

Line 77 of _main.tex has the code:

library(calc)

I’m not LateX savvy enough to understand what’s going on here but the former error in Rstudio indicates that the problem is with the pdf_book format of the build and this seems to be confirmed reading through the discussions on Canvas. I could not find the problem within the specified tex file to overcome the compiling issue.

As a workaround suggested by a classmate, I decided to run the bookdown::bs4_book build to see if I could at least get that working. It compiled without error and I was able to submit the deliverable through that format instead.