Dependency on GitHub only package bigmemoryExt

[nathansam]

MethylPipeR currently depends on bigmemoryExt which also requires a forked version of the bigmemory package not on CRAN. As all dependencies for a CRAN package have to be on either CRAN or Bioconductor, MethylPipeR cannot be submitted to CRAN in this state.

If the dependencies are absolutely necessary, it may be possible to simply add the necessary code from these packages to MethylPipeR whilst respecting the restrictions of the open source license these packages are both under (you would need to add attribution).

[MoMaz123]

I have the same issues, see below

Installing package into ‘C:/Users/XXXX/AppData/Local/R/win-library/4.2’ (as ‘lib’ is unspecified) ERROR: dependency 'bigmemoryExt' is not available for package 'MethylPipeR'

• removing 'C:/Users/XXXX/AppData/Local/R/win-library/4.2/MethylPipeR' Warning messages: 1: package ‘bigmemoryExt’ is not available for this version of R

[KyleRowe1230]

I have the same problem, any solution?

[nathansam]

As a workaround for now, you'll have to install a fork of {bigmemory} maintained by the developer of the bigmemoryExt package and then install {bigmemoryExt} from GitHub. You can then install {MethylPipeR}.

# Install fork of bigmemory
devtools::install_github('cdeterman/bigmemory')
# install bigmemoryExt (GitHub only)
devtools::install_github('cdeterman/bigmemoryExt')
# install MethylPipeR
devtools::install_github("marioni-group/MethylPipeR")

[KyleRowe1230]

thanks！