cannot install various functions in R
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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
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Have you tried installing nloptr too?

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

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