<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><meta charset="utf-8"><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">http://bioconductor.org/biocLite.R"</a>)
</i>BioC_mirror = <a href="http://bioconductor.org/">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'">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></body></html>