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Question: VariantAnnotation installation error in R package
0
gravatar for MAPK
4.6 years ago by
MAPK • 1.7k
MAPK • 1.7k wrote:

I have been trying to install VariantAnnotation in R, but keep getting the following installation errors: Can someone please suggest me how to fix these issues.

>  biocLite("VariantAnnotation")  Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :  
 installation of package ‘VariantAnnotation’ had non-zero exit status
>  library("VariantAnnotation") #load the package Error in library("VariantAnnotation") :    ‘VariantAnnotation’ is not a valid
 installed package
R • 2.7k views
ADD COMMENT • link •
modified 4.6 years ago by Steven Lakin • 1.5k • written 4.6 years ago by MAPK • 1.7k
2
gravatar for Steven Lakin
4.6 years ago by
Steven Lakin • 1.5k
Fort Collins, CO, USA
Steven Lakin • 1.5k wrote:

This set of commands worked for me, from the Bioconductor installation page for VariantAnnotation:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("VariantAnnotation")
library("VariantAnnotation")

So if you're getting errors with the install process, it's likely to be something underlying your version of biocLite or your system. If there's a way to get more verbose error output, that would help in debugging the problem.
ADD COMMENT • link written 4.6 years ago by Steven Lakin • 1.5k

kinit user@server was the issue. The directory was not accessible. Thanks anyway!

ADD REPLY • link written 4.6 years ago by MAPK • 1.7k
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