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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hello,
<br>
<br>
please see my post on the forum from yesterday; this is now FAQ #4 on the website:<br>
<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 'graph', on which adegenet 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);">It should be fixed in the next release.<br>
<br>
Cheers<br>
<br>
Thibaut<br>
</span><br style="color: rgb(0, 0, 0);">
<div><br>
<div class="BodyFragment"><font size="2">
<div class="PlainText">-- <br>
######################################<br>
Dr Thibaut JOMBART<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - Faculty of Medicine<br>
St Mary’s Campus<br>
Norfolk Place<br>
London W2 1PG<br>
United Kingdom<br>
Tel. : 0044 (0)20 7594 3658<br>
t.jombart@imperial.ac.uk<br>
http://sites.google.com/site/thibautjombart/<br>
http://adegenet.r-forge.r-project.org/<br>
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<div style="direction: ltr;" id="divRpF379991"><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 Cheng-Hua Huang [arhua@ufl.edu]<br>
<b>Sent:</b> 16 May 2011 19:23<br>
<b>To:</b> adegenet-forum@r-forge.wu-wien.ac.at<br>
<b>Cc:</b> arhuahuang@gmail.com<br>
<b>Subject:</b> [adegenet-forum] Importing data<br>
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<p class="MsoNormal">Dear adegenet users,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I am a beginner of Adegenet and have been playing around how to import my Struture and Genepop files. However, I am stuck here because I cannot import my files for DAPC. I appreciate if anyone could helps this out. Thank you in advance.
My questions are listed as follow:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">1. After loading MASS, Ade4, I loaded the Adegenet package (either 1.3.0 or 1.2.8). R. 2.13.0 shows the following message. How do I need to do to fix this problem?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> ==========================</p>
<p class="MsoNormal"> adegenet 1.3-0 is loaded</p>
<p class="MsoNormal"> ==========================</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">- to start, type '?adegenet'</p>
<p class="MsoNormal">- to browse adegenet website, type 'adegenetWeb()'</p>
<p class="MsoNormal">- to post questions/comments: adegenet-forum@lists.r-forge.r-project.org</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Error in as.environment(pos) : </p>
<p class="MsoNormal"> no item called "newtable" on the search list</p>
<p class="MsoNormal">In addition: Warning message:</p>
<p class="MsoNormal">In objects(newtable, all.names = TRUE) :</p>
<p class="MsoNormal"> ‘newtable’ converted to character string</p>
<p class="MsoNormal">Error in as.environment(pos) : </p>
<p class="MsoNormal"> no item called "newtable" on the search list</p>
<p class="MsoNormal">In addition: Warning message:</p>
<p class="MsoNormal">In objects(newtable, all.names = TRUE) :</p>
<p class="MsoNormal"> ‘newtable’ converted to character string</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">2. I used “Change dir” to direct R to read files in a folder and then used following commands to import files.</p>
<p class="MsoNormal">obj <- import2genind ("structure.str") or </p>
<p class="MsoNormal">obj <- read.structure ("structure.str", package="adegenet", onerowperind=TRUE,n.ind=85, n.loci=10, col.lab=1, col.pop=3,ask=true)
</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">But R shows “Error: could not find function "import2genind"” and Error: could not find function "read.structure""</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Thank you for your time and help. </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Regards,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Arhua</p>
<p class="MsoNormal"> </p>
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