Question: Changing R package dependencies
gravatar for rbronste
23 months ago by
rbronste60 wrote:

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

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.

ADD COMMENTlink modified 23 months ago by Sean Davis21k • written 23 months ago by rbronste60
Answer: Changing R package dependencies
gravatar for Sean Davis
23 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

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.

ADD COMMENTlink written 23 months ago by Sean Davis21k
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