Question: Problem running (loading) systemPipeR package after downloading
gravatar for rj.innet
15 months ago by
rj.innet0 wrote:

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. 

rnaseq systempiper • 283 views
ADD COMMENTlink written 15 months ago by rj.innet0

Please make sure you are installing Bioc packages, including systemPipeR, as outlined here: Also make sure you have a recent R version installed >=3.5.0.

ADD REPLYlink written 15 months ago by Thomas Girke1.7k

Thanks! I was missing most Biconductor packages so the problem was coming which has been dealt now.

ADD REPLYlink written 15 months ago by rj.innet0
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