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    <p>Just for completeness, there are some ways to prevent you from having this problem. As Dirk said, save your packages in another directory on your computer. </p> <pre><code>install.packages("thepackage",lib="/path/to/directory/with/libraries") </code></pre> <p>You can change the default <code>.Library</code> value using the function <code>.libPaths</code> too</p> <pre><code>.libPaths("/path/to/directory/with/libraries") </code></pre> <p>This will put this path as a first value in the <code>.Library</code> variable, and will make it the default.</p> <p>If you want to automate this further, you can specify this in the Rprofile.site file, which you find in the /etc/ directory of your R build. Then it will load automatically every time R loads, and you don't have to worry about that any more. You can just install and load packages from the specified directory.</p> <p>Finally, I have some small code included in my Rprofile.site allowing me to reinstall all packages when I install a new R version. You just have to list them up <strong>before</strong> you update to the new R version. I do that using an .RData file containing an updated list with all packages.</p> <pre><code>library(utils) ## Check necessary packages load("G:\Setinfo\R\packagelist.RData") # includes a vector "pkgs" installed &lt;- pkgs %in% installed.packages()[, 'Package'] if (length(pkgs[!installed]) &gt;=1){ install.packages(pkgs[!installed]) } </code></pre> <p>I make the packagelist.RData by specifying <code>.Last()</code> in my Rprofile.site. This updates the package list if I installed some :</p> <pre><code>.Last &lt;- function(){ pkgs &lt;- installed.packages()[,1] if (length(pkgs) &gt; length(installed)){ save(pkgs,file="G:\Setinfo\R\packagelist.RData") } } </code></pre> <p>When I install a new R version, I just add the necessary elements to the Rprofile.site file and all packages are reinstalled. I have to adjust the Rprofile.site anyway (using sum contrasts, adding the extra code for Tinn-R, these things), so it's not really extra work. It just takes extra time installing all packages anew.</p> <p>This last bit is equivalent to what is given in the original question as a solution. I just don't need to worry about getting the "installed" list first.</p> <p>Again, this doesn't work flawless if you have packages that are not installed from CRAN. But this code is easily extendible to include those ones too.</p> <p>Edit: There was a missing parenthesis in the code</p>
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    1. USJoris Meys
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    1. CO+1 Very helpful, thanks! I just used this to upgrade to 2.13...
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      1. USPrasad Chalasani
    2. CO@Prasad : Thx. The answer is a bit outdated though, R 2.12 and further automatically save the packages you install yourself somewhere in a standard library outside the main R tree. So all you have to do now is make sure you find that library and link to it, if that didn't happen by itself.
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    3. CO@428790: Where can I find that library that you mention?
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      1. USDaniel Krizian
 

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