[adegenet-forum] Installation problems, continued

[Brice Sarver]

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")
BioC_mirror = 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'
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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