optigrab

[nsheff]

Rscript -e 'install.packages("PEPPROr", repos=NULL, type="source")'
Installing package into ‘/usr/local/lib/R/host-site-library’
(as ‘lib’ is unspecified)
ERROR: dependency ‘optigrab’ is not available for package ‘PEPPROr’
* removing ‘/usr/local/lib/R/host-site-library/PEPPROr’
Warning message:
In install.packages("PEPPROr", repos = NULL, type = "source") :
  installation of package ‘PEPPROr’ had non-zero exit status

Can we make it install dependencies automatically? It worked after I did:

Rscript -e 'install.packages("optigrab")'

first. But it would be better if it did this automatically.

[jpsmith5]

I had tried setting that up with a dependencies=TRUE clause but it wasn’t working for me. Not sure if I was missing something in proper usage. Ideally, yes I would prefer it to install all dependencies but not sure how R handles that with some packages being cran, bioconductor, or github based.

[nsheff]

https://stackoverflow.com/questions/25017195/install-a-local-r-package-with-dependencies-from-cran-mirror

[jpsmith5]

Unfortunately those suggestions still won't help. First, it would require a user to manually install both devtools and BiocInstaller. Then, I'm still not sure how you would specify a github repo for the install command. Any other thoughts?

[jpsmith5]

Just found this: https://cran.r-project.org/web/packages/miniCRAN/index.html

Maybe an option.

[jpsmith5]

Using devtools::install can roughly achieve this as we've discussed before, but it still requires a separate install of both devtools, 'pepr', and GenomicRanges which is required by GenomicDistributions which this package requires. I don't know yet if that can be a recursive, if this needs that, also install that type scenario.

So this works, but only if the requirements of the requirements already exist:

Rscript -e 'devtools::install(file.path("/path/to/peppro/PEPPROr/"), dependencies=TRUE, repos="https://cloud.r-project.org/")'

Still need to keep playing around with options here.