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  • DBI and RSQLite Errors plus other Warnings when Installing CummeRbund

    Hello RNA Seq community,

    Could someone please help me? I am using the command "source('http://www.bioconductor.org/biocLite.R')
    biocLite('cummeRbund')" in the R environment, and my output is:

    ERROR: dependency ‘DBI’ is not available for package ‘RSQLite’
    * removing ‘/home/jmwhitha/R/x86_64-pc-linux-gnu-library/2.14/RSQLite’
    ERROR: dependency ‘RSQLite’ is not available for package ‘cummeRbund’
    * removing ‘/home/jmwhitha/R/x86_64-pc-linux-gnu-library/2.14/cummeRbund’

    The downloaded packages are in
    ‘/tmp/Rtmp8pQWJT/downloaded_packages’
    Warning messages:
    1: In install.packages(pkgs = pkgs, repos = repos, ...) :
    installation of package ‘RSQLite’ had non-zero exit status
    2: In install.packages(pkgs = pkgs, repos = repos, ...) :
    installation of package ‘cummeRbund’ had non-zero exit status
    3: 'cluster' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'foreign' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'KernSmooth' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'mgcv' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'nnet' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'rpart' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'survival' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable

  • #2
    Hello RNA Seq community,

    Sorry, I think I posted this at a time when no would answer it.

    Could someone please help me? I am using the command "source('http://www.bioconductor.org/biocLite.R')
    biocLite('cummeRbund')" in the R environment, and my output is:

    ERROR: dependency ‘DBI’ is not available for package ‘RSQLite’
    * removing ‘/home/jmwhitha/R/x86_64-pc-linux-gnu-library/2.14/RSQLite’
    ERROR: dependency ‘RSQLite’ is not available for package ‘cummeRbund’
    * removing ‘/home/jmwhitha/R/x86_64-pc-linux-gnu-library/2.14/cummeRbund’

    The downloaded packages are in
    ‘/tmp/Rtmp8pQWJT/downloaded_packages’
    Warning messages:
    1: In install.packages(pkgs = pkgs, repos = repos, ...) :
    installation of package ‘RSQLite’ had non-zero exit status
    2: In install.packages(pkgs = pkgs, repos = repos, ...) :
    installation of package ‘cummeRbund’ had non-zero exit status
    3: 'cluster' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'foreign' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'KernSmooth' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'mgcv' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'nnet' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'rpart' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable
    'survival' cannot be updated, installed directory '/usr/lib/R/library' not
    writeable

    Comment


    • #3
      You need to install the following packages at a minimum:




      Check the dependancy section for cummerbund package for anything else you may need: http://www.bioconductor.org/packages...ummeRbund.html

      There also appears to be an issue where /usr/lib/R/library is not writable from the account you are trying to install the packages from.

      I remember you being the "sys admin" for this system from past posts. Try doing the cummerbund install as a user with write privileges to that directory path.
      Last edited by GenoMax; 05-20-2013, 05:36 AM.

      Comment


      • #4
        Good morning GenoMax,

        Thank you for the quick reply!

        Before posting this topic, I used the following commands to get DBI and RSQLite.
        wget http://cran.fhcrc.org/src/contrib/DBI_0.2-7.tar.gz -O DBI_0.2-7.tar.gz
        tar zxvf DBI_0.2-7.tar.gz
        wget http://cran.r-project.org/src/contri..._0.11.3.tar.gz -O RSQLite_0.11.3.tar.gz
        tar zxvf RSQLite_0.11.3.tar.gz

        I guess that's not enough code to get the job done though. I also just noticed that DBI requires R version >= 2.15.0

        The following command only gets me version 2.14.1 though.
        sudo apt-get install r-base-core

        What commands can I use to get >= 2.15.0?


        Concerning the following, would I use the command?
        sudo chmod 777 /usr/lib/R/library

        Could you break the second sentence down for me a little more. I'm not really sure what installing as a user with write privileges to that directory path entails.

        Originally posted by GenoMax View Post
        You need to install the following packages at a minimum:

        There also appears to be an issue where /usr/lib/R/library is not writable from the account you are trying to install the packages from.

        I remember you being the "sys admin" for this system from past posts. Try doing the cummerbund install as a user with write privileges to that directory path.
        Thank you so much!
        Jason

        Comment


        • #5
          Jason,

          Just downloading the packages in not enough to install them. Here is a reference for installing packages in R. It is possible to install R libraries under your own user directory (so you do not need to write in /usr area, which is system reserved).

          Since you are the only user on your system it may be worth trying the install cummerBund by starting R as root. This should give you write permissions to the /usr/lib/R/library directory.

          Code:
          sudo R
          Then in R do the "cummerBund" install.
          Code:
          source("http://bioconductor.org/biocLite.R")
          biocLite("cummeRbund")
          If that works then remember to close R and then start R back as a regular user.

          Comment


          • #6
            Thanks for the document.

            Most of the installation seems to work, except DBI still needs a newer version of R.

            I tried to use the document to get 2.15.0 using the following code:

            wget http://cran.stat.ucla.edu/src/base/R-2/R-2.15.0.tar.gz -O R-2.15.0.tar.gz
            tar xf R-2.15.0.tar.gz
            #Before executing ./configure you need to get X11 headers
            #http://forum.linuxcareer.com/threads...-not-available
            sudo apt-get install xorg-dev
            ./configure
            make

            Again, this seemed to work great, except when I execute "R", it's still using 2.14.1. How do I get it to launch the 2.15.0 version?

            Thank you again!

            Comment


            • #7
              Oh, I figured that out.

              I just went into ~/bin/R-2.15.0/bin and executed ./R

              Installation of cummeRbund worked in this version!
              source("http://bioconductor.org/biocLite.R")
              biocLite("cummeRbund")

              Unfortunately, executing just "R" gives me the old version.

              Can I do something to make it so that when I execute "R" without setting a path, it gives me the new version?

              Thank you!

              Comment


              • #8
                Originally posted by jmwhitha View Post
                Oh, I figured that out.

                I just went into ~/bin/R-2.15.0/bin and executed ./R

                Installation of cummeRbund worked in this version!
                source("http://bioconductor.org/biocLite.R")
                biocLite("cummeRbund")

                Unfortunately, executing just "R" gives me the old version.

                Can I do something to make it so that when I execute "R" without setting a path, it gives me the new version?

                Thank you!
                Open a new terminal window. Check to see where is the default "R" that you are getting is located.

                Code:
                which R
                Then do a

                Code:
                ls -l full_path_to_location_from_above_command
                Depending on what the answer is we can decide on an appropriate method.

                Comment


                • #9
                  Thanks GenoMax,

                  Just was emailing with another friend and he helped me get these two commands...

                  sudo rm -f ./R #after cd'ing to the directory containing the old version /usr/bin
                  sudo ln -s /path/to/new/R R #where R is an executable, not a directory

                  ...and they worked great!!

                  PROBLEM SOLVED

                  God bless,
                  Jason

                  Comment


                  • #10
                    still errors

                    Hey, guys

                    I was following your discussion, but still have error messages, could you share some thoughts on this, thanks a lot!
                    :

                    wget http://cran.stat.ucla.edu/src/base/R-2/R-2.15.0.tar.gz -O R-2.15.0.tar.gz

                    tar xf R-2.15.0.tar.gz

                    sudo apt-get install xorg-dev

                    ./configure

                    make

                    ~/bin/R-2.15.0/bin

                    ./R

                    source("http://bioconductor.org/biocLite.R")
                    biocLite("cummeRbund")

                    However, still have the following errors:
                    The downloaded source packages are in
                    ‘/tmp/Rtmpk15EqK/downloaded_packages’
                    Updating HTML index of packages in '.Library'
                    Making packages.html ... done
                    Warning messages:
                    1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                    installation of package ‘XML’ had non-zero exit status
                    2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                    installation of package ‘RCurl’ had non-zero exit status
                    3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                    installation of package ‘biomaRt’ had non-zero exit status
                    4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                    installation of package ‘rtracklayer’ had non-zero exit status
                    5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                    installation of package ‘GenomicFeatures’ had non-zero exit status
                    6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                    installation of package ‘biovizBase’ had non-zero exit status
                    7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                    installation of package ‘Gviz’ had non-zero exit status
                    8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                    installation of package ‘cummeRbund’ had non-zero exit status

                    Comment


                    • #11
                      It appears that you are missing some libraries:

                      If this is ubuntu then

                      Code:
                      sudo apt-get install libxml2-dev libxml2 curl curl-devel
                      You may also need to install some R-packages. Check the "depends" section from the cummerBund package page: http://www.bioconductor.org/packages...ummeRbund.html

                      Comment


                      • #12
                        ok, problem solved now.

                        I used one of the code you gave to other threads

                        sudo apt-get install libcurl4-openssl-dev

                        after installation, then reinstall it, now the biocLite("cummeRbund")
                        is loaded.

                        Thanks!

                        Comment


                        • #13
                          compiled info to install cummeRbund in ubuntu

                          wget http://cran.stat.ucla.edu/src/base/R-2/R-2.15.0.tar.gz -O R-2.15.0.tar.gz

                          tar xf R-2.15.0.tar.gz

                          sudo apt-get install xorg-dev

                          ./configure

                          make

                          ~/bin/R-2.15.0/bin

                          ./R
                          source("http://bioconductor.org/biocLite.R")
                          biocLite("cummeRbund")
                          # if the installation is not success, quit R and go back to ubuntu console
                          q()

                          sudo apt-get install libcurl4-openssl-dev

                          R

                          #Reinstall it
                          source("http://bioconductor.org/biocLite.R")
                          biocLite("cummeRbund")

                          #then load the library, to see if all of the dependent packages are there
                          library(cummeRbund)

                          #change the directory of R
                          sudo rm -f ./R #after cd'ing to the directory containing the old version /usr/bin
                          sudo ln -s /path/to/new/R R #where R is an executable, not a directory

                          Comment


                          • #14
                            Sorry I didn't get to this sooner. I just got back from Thailand.

                            Comment


                            • #15
                              Thats cool.

                              But I do have the following up question though. After load the library(CummeRbund). All of the dependents were loaded simultaneously. I would assume that the package is install properly. However, when i was trying to run the analysis.

                              > cuff_data = readCufflinks('diff_out')
                              > cuff_data
                              CuffSet instance with:
                              2 samples
                              5902 genes
                              0 isoforms
                              0 TSS
                              0 CDS
                              0 promoters
                              0 splicing
                              0 relCDS
                              > csScatter(genes(cuff_data), '024', '025')
                              Error in .local(object, x, y, logMode, pseudocount, labels, smooth, ...) :
                              One or more values of 'x' or 'y' are not valid sample names!
                              Both instances are strange to me, because when I open the expression files. Those files are not empty(not necessarily mean not possible to have no isoforms or something else, how can i visually check the isoforms in the data sheet or TSS, etc, is there any thing specific labels with those?

                              Further more, when i was looking at the different expressed gene.
                              > gene_diff_data = diffData(genes(cuff_data))
                              > sig_gene_data = subset(gene_diff_data, (significant =='yes'))
                              > nrow(sig_gene_data)
                              [1] 0
                              This is certainly not the case, clearly in the result datasheet, dozens of genes have been listed as significant difference.

                              Best,
                              Last edited by Baoqing; 06-10-2013, 06:36 AM.

                              Comment

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