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

[Jombart, Thibaut]

Hello, 

I have just tried adegenet on a fresh install of R-2.12.0 (not patched) on windows 7, and it works without any problem. 

But you are the second email reporting the same problem, and I'm eager to see what's wrong. 

Do you get any error/warning when typing:

install.packages("adegenet", dep=TRUE)

?

Best regards

Thibaut



________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of Sébastien Puechmaille [s.puechmaille at gmail.com]
Sent: 08 November 2010 12:34
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Loading problem adegenet_1.2-8,       windows/Mac (R2.12.0 Patched)

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<mailto: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<mailto: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.