Problem running (loading) systemPipeR package after downloading
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rj.innet • 0
@rjinnet-17036
Last seen 5.5 years ago

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. 

systemPipeR rnaseq • 1.2k views
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Please make sure you are installing Bioc packages, including systemPipeR, as outlined here: https://bioconductor.org/install/. Also make sure you have a recent R version installed >=3.5.0.

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

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