Nothing
### al the packages should be installed because it will be easier to process NAMESPACE data
.libPaths("/Volumes/Elements/all_pkg_lib/")
options(repos = BiocManager::repositories(version = "3.15"))
options(timeout = 10000000)
# get available package names
av_df <- available.packages(repos = BiocManager::repositories(version = "3.15"))
av = av_df[, 1]
exc = dir("/Volumes/Elements/all_pkg_lib")
ins <- av[!av %in% exc]
for(i in seq_len(floor(length(ins)/50))) {
ind = 50*(i-1) + 1:50
ind = intersect(ind, 1:length(ins))
try(BiocManager::install(ins[ind],
type = "source", dependency =TRUE,
lib = "/Volumes/Elements/all_pkg_lib"))
}
tb1 = available.packages(repos = BiocManager::repositories(version = "3.15"))
tb2 = installed.packages(lib.loc = "/Volumes/Elements/all_pkg_lib/")
cn = intersect(tb1[, "Package"], tb2[, "Package"])
l = which(tb1[cn, "Version"] != tb2[cn, "Version"])
ins = cn[l]
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