I was unable to install Biostrings using my R GUI (RKWard for Ubuntu), so
this may help if anyone runs into the same problem as me ...
I was getting the error "Error in `row.names<-.data.frame`(`*tmp*`, value =
aa) : duplicate 'row.names' are not allowed".
This appeared to be a GUI specific error, so I ran R as root in the
terminal ('sudo R') and then could install Biostrings with no problems:
source("http://bioconductor.org/biocLite.R";)
biocLite("Biostrings")
Then you can exit R and open up the GUI and use the package manager or
script to install/upgrade phangorn and phytools as per normal.
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