I'm following the systemPipeR package to carry out rnaseq workflow in my own standalone Ubuntu 18.04 machine. But while downloading the required package and necessary dependency packages I encounter the similar ERROR messages (a number of errors show meanwhile) and a particular ERROR at the end, as given below
ERROR: dependencies ‘Rsamtools’, ‘ShortRead’, ‘GenomicRanges’, ‘GenomicFeatures’, ‘SummarizedExperiment’, ‘VariantAnnotation’, ‘DESeq2’, ‘GOstats’, ‘annotate’ are not available for package ‘systemPipeR’ * removing ‘/home/rupjdas/Desktop/Rupjyoti/Packages/systemPipeR’
I've tried installing each dependencies individually though out of vein and could not load each one and systemPipeR successfully at last.
I also tried editing the .Renviron and .Rprofile files in my R still the problem persists. I am not sure where I'm doing wrong!!
Any suggestions and answers will be of immense help.