У меня была такая же проблема при установке пакета графа из архива. Пакет необходим для другого пакета (bnclasify).
chooseBioCmirror() #select a different mirror than CRAN. This mirror may be #because is the one that has bnclasify in it (check this statement)
setRepositories() #In here you can select as many as you want to search for the #package you need
ap <- available.packages() #list of all available packages
"graph" %in% rownames(ap) #search the package you need by name (return TRUE or #FALSE).
install.packages("graph", dependencies=TRUE) #if the last statement TRUE then #install the package like normally