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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Alastair,
<br>
<br>
are you sure this is not FAQ 4:<br>
<span style="color: rgb(0, 153, 0);"># 4: Loading adegenet fails with this error (R >= 2.13.0):
</span><font><font size="2"><br>
<span style="color: rgb(0, 102, 0);">Error in as.environment(pos) : no item called "newtable" on the search list</span></font></font><br>
This is because the package '<span style="font-style: italic;">graph</span>', on which
<span style="font-style: italic;">adegenet</span> depends, has been removed from CRAN. You need to install graph from bioconductor first, and then install adegenet:<br>
<pre>source("http://bioconductor.org/biocLite.R")<br>biocLite("graph")<span style="font-family: monospace;"><br>install.packages("adegenet", dep=TRUE)</span><br></pre>
<span style="color: rgb(0, 0, 0);"><br>
Cheers<br>
<br>
Thibaut<br>
</span>
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<div style="direction: ltr;" id="divRpF718100"><font size="2" color="#000000" face="Tahoma"><b>From:</b> adegenet-forum-bounces@r-forge.wu-wien.ac.at [adegenet-forum-bounces@r-forge.wu-wien.ac.at] on behalf of Alastair Potts [potts.a@gmail.com]<br>
<b>Sent:</b> 01 June 2011 10:34<br>
<b>To:</b> adegenet-forum@r-forge.wu-wien.ac.at<br>
<b>Subject:</b> [adegenet-forum] problems loading adegenet<br>
</font><br>
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<div>Hi All,<br>
I have read the posts and followed the advice surrounding the problems with loading the adegenet package. But I am still getting the familiar error:<br>
Error in as.environment(pos) : <br>
no item called "newtable" on the search list<br>
In addition: Warning message:<br>
In objects(newtable, all.names = TRUE) :<br>
‘newtable’ converted to character string<br>
Error in as.environment(pos) : <br>
no item called "newtable" on the search list<br>
In addition: Warning message:<br>
In objects(newtable, all.names = TRUE) :<br>
‘newtable’ converted to character string<br>
<br>
Now adegenet was working fine on my R 2.12.2. Then I (stupidly?) updated all my packages. All of a sudden - this error pops up. I tracked it down to the MASS package - this now requires a minimum R version of R 2.13 (wowsers, that sure was fast).<br>
I downloaded R 2.13 (over my very slow internet) - and installed MASS_7.3-13.zip and adegenet_1.2-8.zip while running R 2.13 with administrator privileges (#$I*^# Vista) - and I still get the above error.<br>
<br>
So, I think there may be problems for any new users trying to install adegenet. If you are using R 2.12, I suggest you don't update your MASS package anytime soon.<br>
<br>
Any help would be greatly appreciated.<br>
<br>
Cheers,<br>
Alastair<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<div class="moz-signature">-- <br>
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<td align="center">-----------------------------------------------------------------
<br>
Alastair Potts <br>
PhD candidate <br>
Botany Department <br>
University of Cape Town <br>
<a class="moz-txt-link-abbreviated" href="mailto:Alastair.Potts@uct.ac.za" target="_blank">Alastair.Potts@uct.ac.za</a> or
<a class="moz-txt-link-abbreviated" href="mailto:potts.a@gmail.com" target="_blank">
potts.a@gmail.com</a> <br>
University Private Bag, Rondebosch 7700, South Africa <br>
or <br>
PO Box 115, Loxton 6985, South Africa <br>
Cell: 082 491-7275 <br>
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