rmarkdown matrices not functioning as expected or seen in rstudio - r

Question

I am trying create a blogdown post using Rmarkdown but the matrix I am trying to create is not giving the correct output. In Rstudio it looks like the image below, however when I run the rmarkdown I get a different result.
Gives output in blogdown:
Rmarkdown code:
$$
\left(\begin{array}{cccc}
\text{var } & ... & -1 \\
\text{cov } & ... & ...\\
\text{mat } & ... & -1 \\
... & ... & -1\\
1 & ... & 0
\end{array}\right)
\left(\begin{array}{c}
w_{1} \\
... \\
... \\
... \\
w_{k} \\
\lambda
\end{array}\right)
=
\left(\begin{array}{c}
0 \\
... \\
... \\
... \\
0 \\
1
\end{array}\right)
$$
Any ideas on where I am going wrong and how I can make a matrix equation be on the same line as in the RStudio output?

Answer 1

The empty lines are breaking things. From https://tex.stackexchange.com/q/230338
An empty line in TeX should never be used just to arrange the source. It is an instruction exactly the same as the command \par which ends a paragraph and starts TeX's line breaking algorithm to split a paragraph into lines.
So it is not allowed in display math and it should never be used on the line before display math either, in that position it does not generate an error but forces TeX to take recovery action that produces a spurious white paragraph on the line above the display.
David Carlisle, Feb 26 '15 at 21:29
While it might not seem obvious that a LaTeX limitation would impose itself on an HTML target, the rendering uses MathJax (javascript library) that renders LaTeX math mode.
If you remove them, it seems to render correctly.
---
title: Quux
output: html_document
---
$$
\left(\begin{array}{cccc}
\text{var } & ... & -1 \\
\text{cov } & ... & ...\\
\text{mat } & ... & -1 \\
... & ... & -1\\
1 & ... & 0
\end{array}\right)
\left(\begin{array}{c}
w_{1} \\
... \\
... \\
... \\
w_{k} \\
\lambda
\end{array}\right)
=
\left(\begin{array}{c}
0 \\
... \\
... \\
... \\
0 \\
1
\end{array}\right)
$$
It also works with output: pdf_document:
R.version
# _
# platform x86_64-w64-mingw32
# arch x86_64
# os mingw32
# system x86_64, mingw32
# status
# major 3
# minor 5.3
# year 2019
# month 03
# day 11
# svn rev 76217
# language R
# version.string R version 3.5.3 (2019-03-11)
# nickname Great Truth
packageVersion("knitr")
# [1] '1.23'
packageVersion("rmarkdown")
# [1] '1.13'