[adegenet-forum] Loading problem adegenet_1.2-8, windows/Mac (R2.12.0 Patched)

[Sébastien Puechmaille]

Hello,

I just updated R on Windows (tried 2.12.0 and then the patched version) and
whenever I load the adegenet package ( adegenet 1.2-8), I got error messages
and none of the function of the package are working (loading the library
'MASS' prior to loading 'adegenet' does not change the problem):

###############################################################
> R.version.string
[1] "R version 2.12.0 Patched (2010-11-04 r53530)"
> library(adegenet)
Loading required package: MASS
   ==========================
    adegenet 1.2-8 is loaded
   ==========================

 - to start, type '?adegenet'
 - to browse adegenet website, type 'adegenetWeb()'
 - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org


Error in as.environment(pos) :
  no item called "newtable" on the search list
In addition: Warning message:
In objects(newtable, all.names = TRUE) :
  ‘newtable’ converted to character string
Error in as.environment(pos) :
  no item called "newtable" on the search list
In addition: Warning message:
In objects(newtable, all.names = TRUE) :
  ‘newtable’ converted to character string
> packageDescription("adegenet", fields = "Version")
[1] "1.2-8"
> #for example
> t463=df2genind(input, ncode=6, missing=NA, pop=datat$sitabb,ploidy=2)
Error: could not find function "df2genind"
###############################################################

I repeated the same on a Mac version of R and got the same problem:

###############################################################
  ==========================
   adegenet 1.2-8 is loaded
  ==========================

 - to start, type '?adegenet'
 - to browse adegenet website, type 'adegenetWeb()'
 - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org


Error in as.environment(pos) :
 no item called "newtable" on the search list
In addition: Warning message:
In objects(newtable, all.names = TRUE) :
 ‘newtable’ converted to character string
Error in as.environment(pos) :
 no item called "newtable" on the search list
In addition: Warning message:
In objects(newtable, all.names = TRUE) :
 ‘newtable’ converted to character string
###############################################################

Using the patches as follows does not change anything to the problem.

###############################################################
> source("makefreq.R")
> source("export.R")
> #for example
> t463=df2genind(input, ncode=6, missing=NA, pop=datat$sitabb,ploidy=2)
Error: could not find function "df2genind"
###############################################################

Finally, I tired to install the devel version (as adviced on the website)
and got this:

###############################################################
> install.packages("adegenet",repos="http://r-forge.r-project.org")
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘adegenet’ is not available
###############################################################

Older versions of R (2.9.2 Patched) and adegenet (1.2-3) are working well on
the same computer.

Any idea what could be causing the problem and how to fix it?

Thanks,

 Sébastien.
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