@Rohit-Satyam I am still reviewing your work; however, I tried to R CMD build the package as it would on the build system, but it's only finding the .Rnw:

R CMD build ggbio
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* preparing ‘ggbio’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ggbio.Rnw’ using Sweave
--- finished re-building ‘ggbio.Rnw’

cp realvignettes/*.Rnw .
cp: cannot stat 'realvignettes/*.Rnw': No such file or directory
make: *** [Makefile:14: ggbio.pdf] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted

I know I can rmarkdown::render() the html, so that isn't the issue and it's likely because of the path.

Since the .Rmd is replacing the need for the other files--fakevignettes, realvignettes, Makefile, knit.sh, and ggbio.Rnw--they can be removed and what you put in realvignettes should be moved to the /vignettes directory. I think you should still the original figures and their names in your .Rmd file.

@Rohit-Satyam I am still reviewing your work; however, I tried to R CMD build the package as it would on the build system, but it's only finding the .Rnw:

R CMD build ggbio
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* preparing ‘ggbio’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ggbio.Rnw’ using Sweave
--- finished re-building ‘ggbio.Rnw’

cp realvignettes/*.Rnw .
cp: cannot stat 'realvignettes/*.Rnw': No such file or directory
make: *** [Makefile:14: ggbio.pdf] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted

I know I can rmarkdown::render() the html, so that isn't the issue and it's likely because of the path.

Since the .Rmd is replacing the need for the other files--fakevignettes, realvignettes, Makefile, knit.sh, and ggbio.Rnw--they can be removed and what you put in realvignettes should be moved to the /vignettes directory. I think you should still the original figures and their names in your .Rmd file.

I have removed the aforementioned files and folders. The vignette HTML file is also attached:

ggbio.zip