<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style id="owaParaStyle" type="text/css">P {margin-top:0;margin-bottom:0;}</style>
</head>
<body ocsi="0" fpstyle="1" style="word-wrap: break-word;">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Brice,
<br>
<br>
thanks for the post. I can only hope this was a temporary issue on Bioconductor...<br>
<br>
Cheers<br>
<br>
Thibaut<br>
<div style="font-family: Times New Roman; color: rgb(0, 0, 0); font-size: 16px;">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF156303"><font color="#000000" face="Tahoma" size="2"><b>From:</b> adegenet-forum-bounces@r-forge.wu-wien.ac.at [adegenet-forum-bounces@r-forge.wu-wien.ac.at] on behalf of Brice Sarver [bsarver1337@gmail.com]<br>
<b>Sent:</b> 01 June 2011 21:22<br>
<b>To:</b> adegenet-forum@r-forge.wu-wien.ac.at<br>
<b>Subject:</b> [adegenet-forum] installation problems, fixed<br>
</font><br>
</div>
<div></div>
<div><span class="Apple-style-span" style="font-family: Times;">
<pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;">I posted the problem below late last night. Upon trying it today with a fresh install of R 2.13.0 32-bit on a different system, everything seems to be going smoothly (so far).</span></font></pre>
<pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;">No clue what was causing the problem last night, but for those of you who are still having some, this may be a fix.</span></font></pre>
<pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;"><br></span></font></pre>
<pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;">Thanks!</span></font></pre>
<pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;">Brice</span></font></pre>
<pre><br></pre>
<pre>---------------</pre>
<pre><br></pre>
<pre>Hi all,
The fix described for adegenet in R 2.13.0 doesn't work, pointing to an incompatibility with this version of R and Bioconductor. Specifically:
><i> source("<a href="http://bioconductor.org/biocLite.R%22" target="_blank">http://bioconductor.org/biocLite.R"</a>)
</i>BioC_mirror = <a href="http://bioconductor.org/" target="_blank">http://bioconductor.org</a>
Change using chooseBioCmirror().
Fine so far...
><i> biocLite("graph")
</i>Using R version 2.13.0, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "graph"
Please wait...
Error in list(...)[["type"]] : subscript out of bounds
This happens for every package installed this way (including running biocLite() alone). Now we're back to the same old problem:
><i> install.packages("adegenet", dep=TRUE)
</i>Installing package(s) into ‘/Users/XXX/Library/R/2.13/library’
(as ‘lib’ is unspecified)
Warning: dependencies ‘hierfstat’, ‘graph’ are not available
trying URL '<a href="http://cran.cnr.berkeley.edu/bin/macosx/leopard/contrib/2.13/adegenet_1.2-8.tgz'" target="_blank">http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.13/adegenet_1.2-8.tgz'</a>
Content type 'application/x-gzip' length 3046842 bytes (2.9 Mb)
opened URL
==================================================
downloaded 2.9 Mb
Any thoughts on getting the dependencies installed, minus waiting a couple weeks for the new release(s)?
Thanks in advance!</pre>
</span>
<div><br>
</div>
</div>
</div>
</div>
</body>
</html>