Installation

Rawcopy dependencies:

R:

Rawcopy is an R-package, download and install the development version of R (r-base-dev) from:
https://cran.r-project.org/

The installation now require the package devtools from cran. On Ubuntu 20.04 and R 4.3.0 it needed the following dependencies:

sudo apt install libcurl4-openssl-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev

R-code from Bioconductor:

install.packages("BiocManager")
BiocManager::install()
BiocManager::install(c("DNAcopy", "affxparser",'aroma.light'))

R-code from cran:

install.packages(c('foreach','doMC','PSCBS','squash','digest','ape', 'devtools'))
install.packages('https://cran.r-project.org/src/contrib/Archive/SDMTools/SDMTools_1.1-221.2.tar.gz', type='source', repos=NULL)

Rawcopy installation:

library(devtools)
install_bitbucket('n0s3n/rawcopy/rawcopyPackage')

When running on windows you may get these warnings messages:

1. package ‘foreach’ was built under R version 3.1.2
2. package ‘PSCBS’ was built under R version 3.1.2
3. executing %dopar% sequentially: no parallel backend registered

Source code:

The source code is available on bitbucket:
https://bitbucket.org/n0s3n/rawcopy