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Thread: Problem with packages on R-project

  1. #1
    Join Date
    Dec 2011
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    6

    Problem with packages on R-project

    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.
    Last edited by RumilSH; December 22nd, 2011 at 06:04 PM.

  2. #2
    Join Date
    Oct 2005
    Location
    Albany, NY
    Beans
    842
    Distro
    Ubuntu

    Re: Problem with packages on R-project

    Interesting.

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

  3. #3
    Join Date
    Dec 2011
    Beans
    6

    Re: Problem with packages on R-project

    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:

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

  4. #4
    Join Date
    Mar 2007
    Beans
    763

    Re: Problem with packages on R-project

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

  5. #5
    Join Date
    Oct 2005
    Location
    Albany, NY
    Beans
    842
    Distro
    Ubuntu

    Re: Problem with packages on R-project

    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()'.
    Please Insert Funny Statement Here.

  6. #6
    Join Date
    Dec 2011
    Beans
    6

    Re: Problem with packages on R-project

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

  7. #7
    Join Date
    Oct 2005
    Location
    Albany, NY
    Beans
    842
    Distro
    Ubuntu

    Re: Problem with packages on R-project

    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.
    Please Insert Funny Statement Here.

  8. #8
    Join Date
    Dec 2011
    Beans
    6

    Re: Problem with packages on R-project

    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.

  9. #9
    Join Date
    Oct 2005
    Location
    Albany, NY
    Beans
    842
    Distro
    Ubuntu

    Re: Problem with packages on R-project

    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.

    What happens if you:
    Code:
    library(BiodiversityR)
    BiodiversityRGUI()
    This appears to be what you have to do to start RCMDR with the BiodiversityR menu items.
    Please Insert Funny Statement Here.

  10. #10
    Join Date
    Dec 2011
    Beans
    6

    Re: Problem with packages on R-project

    Happy New Year!

    I've done what you said gunksta and this message appears


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



    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.

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