cannot install various functions in R
0
0
Entering edit mode
Eli • 0
@c58b02f6
Last seen 2.5 years ago
United States

I am new to using bioconductor and am running into a lot of problems just installing the packages. It always seems that there is a component that cannot be installed and has a "non-zero exit status" for no explained reason which is very frustrating. Most recently I am trying to learn how to use Genomic Ranges. Despite just installing Genomic Ranges I get the error "could not find function "GRanges" ". Apparently, installation of both packages ‘GenomeInfoDbData’ and "nloptr" had non-zero exit status. I try to install GenomeInfoDbData separately and receive the same error. Why? Is there something else I need to install first? I had already installed BiocManager. This keeps happening to me. Is it always this hard?

#installation
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GenomicRanges")
library(GenomicRanges)

# also tried
BiocManager::install("GenomeInfoDbData")

#code
gr=GRanges(seqnames=c("chr1"), strand="+","-", "+", ranges=IRanges(start=c(1,3,6), width=3))
print(gr)

#error
Warning messages:
1: In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘nloptr’ had non-zero exit status
GRanges packages installation • 1.4k views
ADD COMMENT
0
Entering edit mode

Have you tried installing nloptr too?

ADD REPLY
0
Entering edit mode

Can you show the full output of doing BiocManager::install('GenomeInfoDbData') and BiocManager::install('nloptr'). It would also be helpful to include your sessionInfo()

ADD REPLY

Login before adding your answer.

Traffic: 769 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6