Adjust page margins, column wrap for pdf outputs

[Robert-Krajcik]

Closes #651

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (d1a4596) 77.17% compared to head (fbb916e) 77.17%.

Additional details and impacted files

@@           Coverage Diff           @@
##              dev     #699   +/-   ##
=======================================
  Coverage   77.17%   77.17%           
=======================================
  Files          33       33           
  Lines        4872     4872           
=======================================
  Hits         3760     3760           
  Misses       1112     1112           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[Robert-Krajcik]

I am convinced that R Markdown and tinytex were never designed to work together.
I managed to get this small .Rmd script to (eventually) run on my Cytel laptop,
TexLive was working and was able to install all the dozen or so missing *.sty files.

Here, the system would just hang, but at least I could see the message in the *.log file

The solution for me was to install the full tinytex. No possibility of any missing *.sty files here.

TinyTeX-2 contains the scheme-full scheme of TeX Live, which means all LaTeX packages that you could possibly install from CTAN. This is the largest bundle, and only available in the daily release.

tinytex::uninstall_tinytex()
tinytex::install_tinytex(bundle = 'TinyTeX-2', repository = "https://ctan.math.illinois.edu/")

Of course, the tinytex distribution is installed in your Appdata/Roaming directory, and is not seen by {renv}

---
title: "IrisData"
output:
  pdf_document:
    latex_engine: xelatex
---

options(tinytex.verbose = TRUE)
knitr::opts_chunk$set(echo = TRUE)

library(knitr)
library(kableExtra)

knitr::kable(iris[1:3, 1:4], format = 'latex',
      caption="Some iris data") 

[Robert-Krajcik]

One way we can "standardize" the installation of tinytex is to have everyone just download
https://yihui.org/tinytex/TinyTeX.zip
(this is the moderately large zip file 225+ Mb that has everything we need)
and then unzip to your AppData\Roaming folder in windows.
(I have found that using tinytex::install_tinytex(bundle = 'TinyTeX') doesn't always work -- missing tlmgr)
The command: tinytex::is_tinytex() should return TRUE after that.

[Jeff-Thompson12]

I think our big problem is deployment though.

[Robert-Krajcik]

Or just use format = 'pipe' (pandoc) and not worry about tinytex distributions.
The issue I have with the tinytex distribution installed in your appdata/roaming folder is that it is not recorded anywhere in {renv}

[Robert-Krajcik]

FYI, when I use format = 'latex' for the maint metrics chunk, I see
Underfull \hbox (badness 10000) in paragraph at lines 179--180
in the log. The first page of the pdf output was written, but it just stops here.

I figured this out. Not an issue anymore.

[Robert-Krajcik]

Maintenance metrics page for {survival} package:

Community usage page for {survival} package:

Both using format = 'latex'

[Robert-Krajcik]

Hi @AARON-CLARK
Everything is working now Ready for your review.

[Jeff-Thompson12]

@Robert-Krajcik I got this working on my machine as well and can see the wrapping. However, in order to accomplish this I had to follow your instructions on "standardizing" the installation of TinyTex (previously kableExtra code would not work for me). I guess my main concern is how do we set up deployment environments. Is this something that we can do on Posit Connect? If not, all this work will have to be discarded when we do #702 which is high priority.

[Jeff-Thompson12]

So another approach to this problem could be to use a package such as {pagedown} to print the HTML outputs. We would need to spend some time making those outputs print friendly, but this has the added benefit of maintaining the look and feel of our application.

[Robert-Krajcik]

Currently in the windows environment, installing the tinytex distributions don't work.
(but they do work on Posit workbench!)
Current workaround is to unzip the TinyTeX.zip (225+ MB) file found on https://github.com/rstudio/tinytex-releases
to your Appdata/Roaming folder

[AARON-CLARK]

Hi @Robert-Krajcik, good to hear that it works in a unix / linux env. Technically, windows is not as important, even though it's our common dev env among contributors. Regarding linux install, which command did you use to gain success? I see you reference three different commands in this PR, so I'm just curious which one I should play with myself?

First

tinytex::uninstall_tinytex()
tinytex::install_tinytex(bundle = 'TinyTeX-2', repository = "https://ctan.math.illinois.edu/")

Second

tinytex::install_tinytex(bundle = 'TinyTeX')

Third

tinytex::install_prebuilt()

One thing I think this PR needs may be a small blurb added to our "Deployments" article describing how users may need this system dependency, if they don't already have it.

Last, I think before merging this PR, we should test it on our Posit Connect instance. It looks like @Jeff-Thompson12 may have cracked the code for system installation, but we can work with Biogen IT to verify.

[Robert-Krajcik]

Hi @AARON-CLARK
This PR will be superceded by Add Package Dependencies to Reports #723
So no need to merge this one

[AARON-CLARK]

Okay, converting to draft. But my comments above apply for any future PRs. I assume #723 will require syncing the tinytex installation?

[Robert-Krajcik]

I would try using tinytex::install_prebuilt()

[Robert-Krajcik]

Redundant with #734, which was merged yesterday