point to caret GitHub repo

[znmeb]

The "github-repo" tag in index.Rmd needs to point to the caret repo, not bookdown-demo

[coveralls]

Coverage remained the same at 16.514% when pulling b6b7ede on znmeb:master into 4b5f580 on topepo:master.

[coveralls]

Coverage remained the same at 16.514% when pulling 84f0f0b on znmeb:master into 4b5f580 on topepo:master.

[coveralls]

Coverage remained the same at 16.514% when pulling bca4cf0 on znmeb:master into 4b5f580 on topepo:master.

[znmeb]

More fixes:

1. type = "both" doesn't work on Linux. See https://github.com/znmeb/caret/issues/1. I've added guards to call installers without type = "both" on Linux.
2. The loop to install missing packages at the end doesn't find a number of the packages because they're in BioConductor, not CRAN. So I use biocLite in the loop instead.

Note also that the fresh switch is used before it's defined. I didn't change that; I set fresh to TRUE before running the script.