Problem with packages on R-project

[RumilSH]

Hello all,

I'm new here and following memilanuk's suggestion I have opened this threat to tell you my problem (I've written the same question in a 1 year old thread but it could be better write one new,isn't it?). First I have to tell I'm Spanish and not very good at English so maybe I'll write something meaningless. If you don't understand something, tell me and I'll try to explain it better.

After that I'll expose my doubt. I've installed R on my Ubuntu (11.10). It works but the trouble is I have to use some packages like BiodiversityR and I've to install it every time I want to use them. I've already started R as root but nothing changes.

Do you have any suggestion? Thanks a lot.

[gunksta]

Interesting.

1 - What version of Ubuntu are you using? (10.10, 11.04, 11.10, etc.)
2 - What folders can be found in '~/R'
ls ~
3 - What folders can be found in '/root/R'?
sudo ls /root/R
4 - Do you know which packages you have tried to install via the Ubuntu repos as opposed to install.packages()?

[RumilSH]

Hi, thanks for reply.

I use Ubuntu 11.10 (Oneiric Ocelot I guess, isn't it?).

With "ls ~/R" y found just one folder: x86_64-pc-linux-gnu-library.

I've entered into the folder and there are another folder called 2.14 (I guess it's the R version) and finally into this folder:


ACCLMA ade4 BiodiversityR permute tclust xtermStyle
accuracy ade4TkGUI mclust sn texmex
acepack bayesm mnormt tcltk2 vegan


About the third question, I haven't found any folder

ls: can not access / root / R: No such file or directory

I've installed all packages with "install.packages()". I edited the sourcers.list and added this one

http://cran.r-project.org/bin/linux/ubuntu oneiric/

[PGScooter]

what happens when you open R and you run
library(BiodiversityR)
?

[gunksta]

I agree with PGScooter. It looks like you have successfully (and correctly) installed the necessary packages into your local user's profile. If you want to see what packages are recognized by R, you can use the command, 'library()'.

[RumilSH]

When y run "library(BiodiversityR)" this message appears:

> library(BiodiversityR)
Loading required package: vegan
Loading required package: permute
This is vegan 2.0-2

I've already installed these packages several times and it keep asking for they.
If I use the command "library()" I can see the next packages:

ACCLMA ACC & LMA Graph Plotting
accuracy Tools for testing and improving accuracy of
statistical results.
acepack ace() and avas() for selecting regression
transformations
ade4 Analysis of Ecological Data : Exploratory and
Euclidean methods in Environmental sciences
ade4TkGUI ade4 Tcl/Tk Graphical User Interface
bayesm Bayesian Inference for
Marketing/Micro-econometrics
BiodiversityR GUI for biodiversity and community ecology
analysis
mclust Model-Based Clustering / Normal Mixture
Modeling
mnormt The multivariate normal and t distributions
permute Functions for generating restricted
permutations of data
sn The skew-normal and skew-t distributions
tcltk2 Tcl/Tk Additions
tclust Robust Trimmed Clustering
texmex Threshold exceedences and multivariate extremes


I thought I've to install all of them so, Why I can't install only these packages?

Thanks a lot.

[gunksta]

What are you expecting to happen? It looks like the BiodiversityR package is loading. I don't see any errors. I have never used this package, but most packages load their dependencies and then sit there waiting for instructions.

[RumilSH]

BiodiversityR keep loading but it never starts, and when I run Rmcdr I have to reinstall several packages that I've already installed before. For that reason if I don't have internet I can't run this packages.

[gunksta]

Hmmmm. Like I said before, I've never used this and I don't use RCMDR either, but I did some quick searching and found this (http://nbx4.nugo.org/bioinformatics/docs/BiodiversityR.html).

What happens if you:


library(BiodiversityR)
BiodiversityRGUI()


This appears to be what you have to do to start RCMDR with the BiodiversityR menu items.

[RumilSH]

Happy New Year!

I've done what you said gunksta and this message appears
http://img59.imageshack.us/img59/6273/msg1l.png

but I just have to click on yes and, in the next window, select the folder where the packages are installed.

http://img576.imageshack.us/img576/6532/instalarpaquetes.png

Finally it Works!! Thanks a lot. I don't know why R don't search first the packages, anyway, I'm glad to have worked it out.

[rewyllys]

Hmmmm. Like I said before, I've never used this and I don't use RCMDR either, but I did some quick searching and found this (http://nbx4.nugo.org/bioinformatics/docs/BiodiversityR.html).

What happens if you:


library(BiodiversityR)
BiodiversityRGUI()


This appears to be what you have to do to start RCMDR with the BiodiversityR menu items.
@Gunsta, Thanks for finding this URL and reporting it here. These statistics interest me also.