I wanted to install DECIPHER in R environment and I used the following command lines to install.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DECIPHER")
It looks like installed, but I got an update message like the following.
Update all/some/none? [a/s/n]:
I am new to R and I don't know what to do for this. I couldn't proceed with other commands, I get same update message when I give any other commands.
I greatly appreciate any advice to resolve this issue.
Bioconductor packages are strongly interconnected. A message like Update all/some/none? [a/s/n]: Is saying that you potentially have older versions of packages installed and asking if you would like to update any package that has a newer version number. Generally we would recommend a for all but if you are on limited internet capabilities or really eager to get working maybe do n for none and update at a time that is more convenient. Package work best when all are in their current state.
Without trying to be too confusing, there is also the BiocManager::valid() function that will tell you a more detailed message if packages are out-of-date.
Hope this clarifies.
Cheers and welcome to the R community.
