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CummeRbund installation failing

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  • #16
    yeaa i have been trying to upgrade but I am not able to. After all the commands it remains R 2.13.0.

    Comment


    • #17
      Originally posted by dishasharma35 View Post
      yeaa i have been trying to upgrade but I am not able to. After all the commands it remains R 2.13.0.
      Do you have administrator rights on this machine?

      Comment


      • #18
        I had the same problem actually. "Sudo apt-get install r-base" seemed to install an older version (in my case it was 2.14.0 I believe). A friend of mine set it up so that the following text was added to the bottom of /etc/apt/sources.list:

        ## R BACKPORTS
        deb http://cran.uib.no/bin/linux/ubuntu precise/
        You can replace the "cran.uib.no" part with the appropriate CRAN mirror (http://cran.r-project.org/mirrors.html).

        After doing this, running the same command as above installed the latest version of R, and thus also allowing an installation of cummeRbund.

        Perhaps GenoMax can confirm whether this is a correct way to go about it...

        Comment


        • #19
          yes... I did install by using the command for administrator rights. I guess main problem is the up-gradation for R

          Comment


          • #20
            Error in library(cummeRbund) : there is no package called ‘cummeRbund

            I am new to Linux (Ubuntu) and R. I have similar problem when I try to install cummeRbund. I have tried the way that cnyh used. Following are hte detailed message:

            > source("http://bioconductor.org/bioocLite.R")
            Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
            > biocLite("cummeRbund")
            BioC_mirror: http://bioconductor.org
            Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
            Installing package(s) 'cummeRbund'
            also installing the dependencies ‘RCurl’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’, ‘rtracklayer’, ‘Gviz’

            trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-3.tar.gz'
            Content type 'application/x-gzip' length 868491 bytes (848 Kb)
            opened URL
            ==================================================
            downloaded 848 Kb

            trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/biomaRt_2.14.0.tar.gz'
            Content type 'application/x-gzip' length 276758 bytes (270 Kb)
            opened URL
            ==================================================
            downloaded 270 Kb

            trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/GenomicFeatures_1.10.1.tar.gz'
            Content type 'application/x-gzip' length 742663 bytes (725 Kb)
            opened URL
            ==================================================
            downloaded 725 Kb

            trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/biovizBase_1.6.2.tar.gz'
            Content type 'application/x-gzip' length 1026756 bytes (1002 Kb)
            opened URL
            ==================================================
            downloaded 1002 Kb

            trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/rtracklayer_1.18.2.tar.gz'
            Content type 'application/x-gzip' length 1308890 bytes (1.2 Mb)
            opened URL
            ==================================================
            downloaded 1.2 Mb

            trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/Gviz_1.2.1.tar.gz'
            Content type 'application/x-gzip' length 1392463 bytes (1.3 Mb)
            opened URL
            ==================================================
            downloaded 1.3 Mb

            trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/cummeRbund_2.0.0.tar.gz'
            Content type 'application/x-gzip' length 2327551 bytes (2.2 Mb)
            opened URL
            ==================================================
            downloaded 2.2 Mb

            * installing *source* package ‘RCurl’ ...
            ** package ‘RCurl’ successfully unpacked and MD5 sums checked
            checking for curl-config... no
            Cannot find curl-config
            ERROR: configuration failed for package ‘RCurl’
            * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/RCurl’
            ERROR: dependency ‘RCurl’ is not available for package ‘biomaRt’
            * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/biomaRt’
            ERROR: dependency ‘RCurl’ is not available for package ‘rtracklayer’
            * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/rtracklayer’
            ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
            * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/GenomicFeatures’
            ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
            * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/biovizBase’
            ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’
            * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/Gviz’
            ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
            * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/cummeRbund’

            The downloaded source packages are in
            ‘/tmp/RtmpSX1mhe/downloaded_packages’
            Warning messages:
            1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
            installation of package ‘RCurl’ had non-zero exit status
            2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
            installation of package ‘biomaRt’ had non-zero exit status
            3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
            installation of package ‘rtracklayer’ had non-zero exit status
            4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
            installation of package ‘GenomicFeatures’ had non-zero exit status
            5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
            installation of package ‘biovizBase’ had non-zero exit status
            6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
            installation of package ‘Gviz’ had non-zero exit status
            7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
            installation of package ‘cummeRbund’ had non-zero exit status
            8: installed directory not writable, cannot update packages 'boot', 'class',
            'cluster', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet',
            'rpart', 'spatial', 'survival'
            > library(cummeRbund)
            Error in library(cummeRbund) : there is no package called ‘cummeRbund


            BTW, my R version is 2.15.1 (2012-06-22) -

            Is anybody can tell me what libs that I need and how to install them?

            Thanks,
            Last edited by myRNA_Seq; 02-25-2013, 12:52 PM.

            Comment


            • #21
              Error in library(cummeRbund) : there is no package called ‘cummeRbund

              duplicated posting
              Last edited by myRNA_Seq; 02-25-2013, 01:08 PM. Reason: duplicated

              Comment


              • #22
                > library(cummeRbund) Error in library(cummeRbund) : there is no package called ‘cumm

                I also tried the following as GenoMax suggested to cnyh:

                [email protected]:/$ sudo apt-get install libxml2 libcurl
                [sudo] password for liuzi:
                Reading package lists... Done
                Building dependency tree
                Reading state information... Done
                E: Unable to locate package libcurl

                Comment


                • #23
                  I also tried the following
                  sudo apt-get install libxml2-dev;
                  and still get the same error message...

                  Comment


                  • #24
                    Originally posted by myRNA_Seq View Post
                    I also tried the following
                    sudo apt-get install libxml2-dev;
                    and still get the same error message...
                    I think you will need one of the dev packages for curl. Try this one

                    Code:
                    sudo apt-get install libcurl4-openssl-dev

                    Comment


                    • #25
                      Thank you,GenoMax for your quick reply.

                      I installed "sudo apt-get install libcurl4-openssl-dev" as you suggested.
                      I still get the same error below.

                      > library(cummeRbund)
                      Error in library(cummeRbund) : there is no package called ‘cummeRbund’

                      Comment


                      • #26
                        Originally posted by myRNA_Seq View Post
                        Thank you,GenoMax for your quick reply.

                        I installed "sudo apt-get install libcurl4-openssl-dev" as you suggested.
                        I still get the same error below.

                        > library(cummeRbund)
                        Error in library(cummeRbund) : there is no package called ‘cummeRbund’
                        Did you try to re-install cummeRbund in R after installing the curl library?

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

                        Comment


                        • #27
                          Thank you so much GenoMax!
                          Following your instruction, I re-installed cummeRbund in R, now it works very well.

                          Comment


                          • #28
                            I have another problem now.

                            I downloaded latest version of cufflinks binary and also added them to my path as following:
                            export PATH=$PATH:~/cufflinks-2.0.2.Linux_x86_64/cufflinks
                            export PATH=$PATH:~/cufflinks-2.0.2.Linux_x86_64/cuffdiff
                            export PATH=$PATH:~/cufflinks-2.0.2.Linux_x86_64/cuffcompare

                            When I tried to run cuffcompare, it gave me a warning:

                            Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.0.2 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).

                            and without *.tmap file generated.

                            So far I have checked, there isn't a copy of cufflinks in other PATHs, such as .: /usr/bin /usr/local/bin etc...

                            Is there any problem in terms of the path setting?

                            Thanks a lot
                            Last edited by myRNA_Seq; 02-27-2013, 06:41 AM.

                            Comment


                            • #29
                              Originally posted by myRNA_Seq View Post
                              I have another problem now.


                              So far I have checked, there isn't a copy of cufflinks in other PATHs, such as .: /usr/bin /usr/local/bin etc...

                              Is there any problem in terms of the path setting?

                              Thanks a lot
                              Can you check the following and verify that you are indeed pointing to the right cufflinks executable?

                              Code:
                              $which cufflinks

                              Comment


                              • #30
                                It says: /usr/bin/cufflinks.
                                When I use echo $PATH, it didn't show there, why?

                                ************
                                I have tried full path. It works without warning anymore, and got all the output files except *.refmap *.tmap file. Do you know why?

                                I followed the instruction from the paper "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks" (http://www.nature.com/nprot/journal/....2012.016.html) and use exact files in the examples.

                                $ find . -name transcripts.gtf > gtf_out_list.txt
                                $ ~/cufflinks-2.0.2.Linux_x86_64/cuffcompare - i gtf_out_list.txt -r gene.gtf

                                Comment

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