I have encountered difficulty using r kniter to produce a pdf file from R markdown, it has been a while and I really want to fix it. It turns out much complicated than I have expected.

It is related with MikTex installed on a Windows 10 machine

I have issue related to Qt platform plugin, similar to this: “[…] no Qt platform plugin could be initialized”. Not only am I not able to use MikTex properly, it does not even allow me to unstall MikTex!!

I found this link, I followed the instruction and was able to solve this problem.

Following “miktex-qt5-bin-x64” should be repaired made MiKTeX Console to stop #1486

Then, it comes with R markdown related issue

Even Yuhui’s own link does not work

this post offers correct solution by doing

"tinytex:::install_prebuilt()"

then 

"tinytex::tlmgr_update()"

It works!
then I had issues with loading Seurat because it requires SeuratObject with specific version to be loaded also, anyway, it all work out eventually, and I am so happy!!

wanted to give credits to this helping post