Okay, it is required by Bioconductor to provide .Rnw file at submission. It seems that I have to be quite comfortable with Latex.

Working with my first latex example (unfortunately can’t be uploaded to the web). It is located at ~/project2012/makeRpackage/learningLatex/

pdflatex firstLatex.tex

Learning knitR

Install knitr for creating this file.

I have a new windows machine, which may NOT have TeX installed. So, I am installing MikTex on windows 7 64bit machine.

There is too much to learn, we have to stop somewhere!!. Anyway, here comes A good help on RStudio

I encountered an interesting scenario with Rstudio under MacOS. When I launched Rstudio, I found out that my libraries disappeared. It turns out that my Rstudio has different library path:

My system R gives me this:
 
> .libPaths()
[1] "/Users/li11/Library/R/3.6/library"                             
[2] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"
 
Where RStudio gives me this:

> .libPaths()
[1] "/Users/li11/myGit/TCC-GUI/renv/library/R-3.6/x86_64-apple-darwin15.6.0"                
[2] "/private/var/folders/1p/s4h6zl8n06b_n4rdz2prlb880000gs/T/Rtmpi7hSTj/renv-system-library"

My colleague, James Ward, helps me by pointing to this basic set up: