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copied!<p>It's not as easy as it seems.</p> <ul> <li><p><code>apt-get update</code> is good if and when</p> <ul> <li><p>packages exist -- but there are only around 150 or so <code>r-cran-*</code> packages out of a pool of 2100+ packages on CRAN, so rather sparse coverage</p></li> <li><p>packages are maintained, bug free and current</p></li> <li><p>you are happy enough with the bi-annual releases by Ubuntu</p></li> </ul></li> <li><p><code>install.packages()</code> and later <code>update.packages()</code> is good if and when </p> <ul> <li><p>you know what it takes to have built-time dependencies (besides <code>r-base-dev</code>) installed</p></li> <li><p>you don't mind running <code>update.packages()</code> by hand as well as the <code>apt-get</code> updates.</p></li> </ul></li> </ul> <p>On my Ubuntu machine at work, I go with the second solution. But because the first one is better <em>if you have enough coverage</em>, we have built <a href="http://debian.cran.r-project.org/" rel="noreferrer"><strong>cran2deb</strong></a> which provides 2050+ binary deb packages for amd64 and i386 --- but only for Debian testing. That is what I use at home.</p> <p>As for last question of whether you 'should you expect trouble': No, because <code>R_LIBS_SITE</code> is set in <code>/etc/R/Renvironment</code> to be </p> <pre><code># edd Apr 2003 Allow local install in /usr/local, also add a directory for # Debian packaged CRAN packages, and finally the default dir # edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:\ /usr/lib/R/site-library:/usr/lib/R/library'} </code></pre> <p>which means that <em>your</em> packages go into <code>/usr/local/lib/R/site-library</code> whereas those managed by <code>apt</code> go into <code>/usr/lib/R/site-library</code> and (in the case of base packages) <code>/usr/lib/R/library</code>.</p> <p>Hope that clarifies matters. The r-sig-debian mailing list is a more informed place for questions like this.</p>

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