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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi there,<br>
<br>
this is 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>
<br style="font-family: monospace;">
<br>
Cheers<br>
<br>
Thibaut<br>
<div style="font-family: Times New Roman; color: rgb(0, 0, 0); font-size: 16px;">
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<div style="direction: ltr;" id="divRpF374960"><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 Martin van der Meer [martinhvandermeer@gmail.com]<br>
<b>Sent:</b> 26 May 2011 05:17<br>
<b>To:</b> adegenet-forum@r-forge.wu-wien.ac.at<br>
<b>Subject:</b> [adegenet-forum] Loading problem adegenet_1.2-8, Mac (R64)<br>
</font><br>
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<div></div>
<div>Hi<br>
<br>
I can seem to load up adegenet v1.2-8 on R64. It comes up with the following errors:<br>
<br>
[History restored from /Users/jc216923/.Rapp.history]<br>
<br>
Warning: dependencies ‘hierfstat’, ‘graph’ are not available<br>
trying URL '<a href="http://cran.ms.unimelb.edu.au/bin/macosx/leopard/contrib/2.13/adegenet_1.2-8.tgz" target="_blank">http://cran.ms.unimelb.edu.au/bin/macosx/leopard/contrib/2.13/adegenet_1.2-8.tgz</a>'<br>
Content type 'application/x-tar' length 3046842 bytes (2.9 Mb)<br>
opened URL<br>
==================================================<br>
downloaded 2.9 Mb<br>
<br>
<br>
The downloaded packages are in<br>
/var/folders/RU/RUdQ1Y1lEcamHshypf82kLM8L+s/-Tmp-//RtmpYi0SS0/downloaded_packages<br>
Loading required package: MASS<br>
==========================<br>
adegenet 1.2-8 is loaded<br>
==========================<br>
<br>
- to start, type '?adegenet'<br>
- to browse adegenet website, type 'adegenetWeb()'<br>
- to post questions/comments: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">
adegenet-forum@lists.r-forge.r-project.org</a><br>
<br>
<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>
starting httpd help server ... done<br>
<br>
<br>
I then tried:<br>
<br>
> install.packages("adegenet", dep=TRUE)<br>
Installing package(s) into ‘/Users/jc216923/Library/R/2.13/library’<br>
(as ‘lib’ is unspecified)<br>
Warning: dependencies ‘hierfstat’, ‘graph’ are not available<br>
trying URL '<a href="http://cran.ms.unimelb.edu.au/bin/macosx/leopard/contrib/2.13/adegenet_1.2-8.tgz" target="_blank">http://cran.ms.unimelb.edu.au/bin/macosx/leopard/contrib/2.13/adegenet_1.2-8.tgz</a>'<br>
Content type 'application/x-tar' length 3046842 bytes (2.9 Mb)<br>
opened URL<br>
==================================================<br>
downloaded 2.9 Mb<br>
<br>
<br>
The downloaded packages are in<br>
/var/folders/RU/RUdQ1Y1lEcamHshypf82kLM8L+s/-Tmp-//RtmpYi0SS0/downloaded_packages<br>
<br>
<br>
But its still not being able to load.<br>
<br>
Please can someone suggest a solution for a Mac OS system.<br>
<br>
cheers<br>
Martin<br clear="all">
<br>
-- <br>
<div>Martin van der Meer<br>
PhD candidate<br>
Molecular Ecology and Evolutionary Laboratory<br>
Australian Tropical Sciences and Innovation Precinct</div>
<div>School of Marine and Tropical Biology<br>
James Cook University<br>
Townsville<br>
Australia</div>
<br>
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