R-3.1.2 is from October 2014, which means that the GO data you are planning to download is from fall 2014 as well. That's pretty old data, especially in the context of gene annotations, so there really isn't much profit in trying to get data from two years ago. Unless of course you are trying to recapitulate some old analyses that you don't want to change.
Anyway, we don't support old versions of Bioconductor, so you should install the current versions of R and Bioc. If you have problems with that, please let us know.
The package size is 54.2 Mb, but only 15.6 is downloaded, so somehow the download has been truncated. The file is actually 54.2Mb; you could troubleshoot the download problem (best in the long run) or try downloading it from the url in the post above (e.g., via your browser) outside of R, and then install.packages("GO.db_3.0.0.zip", repos=NULL, type="binary"). (I'm not 100% sure of the install.packages command).