Kind of a basic question, but I am trying to install the following TF footprinting package and running into a problem:

https://sourceforge.net/projects/bagfootr/?source=typ_redirect

R does not allow installation of bagfoot_0.9.6.tar.gz because it has two dependencies that I do not wish to install:

install.packages("~/Downloads/bagfoot_0.9.6.tar.gz", repos = NULL, type = "source")
ERROR: dependencies ‘BSgenome.Hsapiens.UCSC.hg19’, ‘BSgenome.Mmusculus.UCSC.mm9’ are not available for package ‘bagfoot’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/bagfoot’

Instead I installed ‘BSgenome.Mmusculus.UCSC.mm10’

Otherwise I installed all of the dependencies requires and indicated in the README file. 

How can I go about changing the dependency related to the assembly I want to work with? Thanks.

You would need to:

1. Download the source package.
2. Modify the DESCRIPTION file (at least)
3. Install from source.

Doing so is very likely to lead to a broken package, so I do not recommend doing so. In your case, it appears that you want to use mm10 instead of mm9. I would suggest installing the package as normal and then install the mm10 package in addition.

Note that bigfootr is not a bioconductor package, so you will likely need to ask elsewhere about whether or not using mm10 should be expected to work with the package.