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
Have you tried installing
nloptr
too?Can you show the full output of doing
BiocManager::install('GenomeInfoDbData')
andBiocManager::install('nloptr')
. It would also be helpful to include yoursessionInfo()