[adegenet-forum] installation problems, fixed

[Jombart, Thibaut]

Dear Brice,

thanks for the post. I can only hope this was a temporary issue on Bioconductor...

Cheers

Thibaut
________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Brice Sarver [bsarver1337 at gmail.com]
Sent: 01 June 2011 21:22
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] installation problems, fixed


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).

No clue what was causing the problem last night, but for those of you who are still having some, this may be a fix.


Thanks!

Brice


---------------


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:

> source("http://bioconductor.org/biocLite.R"<http://bioconductor.org/biocLite.R%22>)
BioC_mirror = http://bioconductor.org<http://bioconductor.org/>
Change using chooseBioCmirror().


Fine so far...

> biocLite("graph")
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:

> install.packages("adegenet", dep=TRUE)
Installing package(s) into ‘/Users/XXX/Library/R/2.13/library’
(as ‘lib’ is unspecified)
Warning: dependencies ‘hierfstat’, ‘graph’ are not available
trying URL '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'>
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!

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