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  • Shortread Package INSTALL

    Hi All,

    Sorry to ask a very basic question:

    I downloaded ShortRead package from: http://www.bioconductor.org/packages...ShortRead.html

    But can someone tell me how to load the ShortRead package, I could not install this package in R. Error always like this:

    >library("ShortRead")
    Error in library("ShortRead") : there is no package called 'ShortRead'

    Did I choose the wrong directory?

    Thanks in advance!

  • #2
    Well you downloaded it, but you clearly haven't installed it.

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

    using biocLite to install packages is much better than downloading the packages from the download page.

    This information is on the package page (http://www.bioconductor.org/packages...ShortRead.html)

    If you followed this procedure yet:

    library(ShortRead)

    doesn't work, we'll probably need some more information, such as what platform you're trying to install it on.

    Comment


    • #3
      Thanks Bukowski!

      I installed shortread. But when I open R each time and type in "library(ShortRead)", it always repeat this step.

      Loading required package: IRanges

      Attaching package: 'IRanges'


      The following object(s) are masked from package:base :

      cbind,
      duplicated,
      order,
      pmax,
      pmax.int,
      pmin,
      pmin.int,
      rank,
      rbind,
      rep.int,
      sapply,
      sort,
      table,
      unique

      Loading required package: Biostrings
      Loading required package: BSgenome
      Loading required package: lattice

      Comment


      • #4
        I get the same message as well. But everything works fine for me.

        This will explain what "mask" means:

        Comment


        • #5
          Originally posted by Wei-HD View Post
          Thanks Bukowski!

          I installed shortread. But when I open R each time and type in "library(ShortRead)", it always repeat this step.

          Loading required package: IRanges

          Attaching package: 'IRanges'


          The following object(s) are masked from package:base :

          cbind,
          duplicated,
          order,
          pmax,
          pmax.int,
          pmin,
          pmin.int,
          rank,
          rbind,
          rep.int,
          sapply,
          sort,
          table,
          unique

          Loading required package: Biostrings
          Loading required package: BSgenome
          Loading required package: lattice
          That's normal - its just R telling you about what it has just loaded.

          Comment


          • #6
            I-ve tried to install it, but it installs the 1.4 version and I need 1.6.2, does it have to do with the fact that I have installed the 1.4 and am trying to re-install it?

            How can I upgrade?

            Comment


            • #7
              You need to upgrade R to the current version.

              Comment


              • #8
                Hi All,
                I have tried installing the ShortRead package many times now using
                source("http://bioconductor.org/biocLite.R")
                biocLite("ShortRead")
                but everytime I get an error message when I use library(ShortRead).
                My R version is R 3.0.2

                While the installation process is going on I get messages like
                ERROR: configuration failed for package ‘RCurl’
                * removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/RCurl’
                * installing *source* package ‘XML’ ...
                ** package ‘XML’ successfully unpacked and MD5 sums checked
                checking for gcc... gcc
                checking for C compiler default output file name...
                rm: cannot remove `a.out.dSYM': Is a directory
                a.out
                checking whether the C compiler works... yes
                checking whether we are cross compiling... no
                checking for suffix of executables...
                checking for suffix of object files... o
                checking whether we are using the GNU C compiler... yes
                checking whether gcc accepts -g... yes
                checking for gcc option to accept ISO C89... none needed
                checking how to run the C preprocessor... gcc -E
                checking for sed... /bin/sed
                checking for pkg-config... /usr/bin/pkg-config
                checking for xml2-config... no
                Cannot find xml2-config
                ERROR: configuration failed for package ‘XML’
                * removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/XML’
                ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package ‘rtracklayer’
                * removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/rtracklayer’
                ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’
                * removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
                ERROR: dependency ‘Rsamtools’ is not available for package ‘ShortRead’
                * removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/ShortRead’

                The downloaded packages are in
                ‘/tmp/RtmpTluoUe/downloaded_packages’
                Warning messages:
                1: In install.packages(pkgs = pkgs, repos = repos, ...) :
                installation of package ‘RCurl’ had non-zero exit status
                2: In install.packages(pkgs = pkgs, repos = repos, ...) :
                installation of package ‘XML’ had non-zero exit status
                3: In install.packages(pkgs = pkgs, repos = repos, ...) :
                installation of package ‘rtracklayer’ had non-zero exit status
                4: In install.packages(pkgs = pkgs, repos = repos, ...) :
                installation of package ‘Rsamtools’ had non-zero exit status
                5: In install.packages(pkgs = pkgs, repos = repos, ...) :
                installation of package ‘ShortRead’ had non-zero exit status
                6: 'cluster' 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
                'survival' cannot be updated, installed directory
                '/usr/lib/R/library' not writeable
                >

                Kindly suggest something asap.
                thanks in advance.

                Comment


                • #9
                  You are trying to install the library at system level in /usr/lib/R/library so try doing this with sudo (assuming you have admin rights).

                  Comment


                  • #10
                    can u please elaborate??

                    Comment


                    • #11
                      No, that's not the issue.

                      This here is the error you should have paid attention to:

                      Cannot find xml2-config
                      It means that you have not installed the header files for the XML2 systems library. Do so using your package manager. For example, in Ubuntu, use the Software Centre to install the package "libxml2-dev".

                      Comment


                      • #12
                        Also, can u please tell me how to install libcurl on ubuntu for R 3.0.2

                        Comment


                        • #13
                          Originally posted by archi View Post
                          Also, can u please tell me how to install libcurl on ubuntu for R 3.0.2
                          Try:
                          Code:
                          sudo apt-get install libxml2-dev

                          Comment


                          • #14
                            Originally posted by Simon Anders View Post
                            No, that's not the issue.

                            This here is the error you should have paid attention to...
                            Yeah, that was the immediate problem - I missed that.

                            Comment


                            • #15
                              I have installed libxml2-dev but now I'm getting these error.
                              Sorry for asking such basic doubts but please do help
                              Thanks a lot.

                              installing to /home/linux/R/x86_64-pc-linux-gnu-library/2.14/XML/libs
                              ** R
                              ** inst
                              ** preparing package for lazy loading
                              Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’
                              Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) :
                              the supplied generic function definition for ‘xmlClone’ does not seem to call 'standardGeneric'; no methods will be dispatched!
                              in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs”
                              in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs”
                              in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs”
                              ** help
                              *** installing help indices
                              ** building package indices ...
                              ** testing if installed package can be loaded

                              * DONE (XML)
                              ERROR: dependency ‘RCurl’ is not available for package ‘rtracklayer’
                              * removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/rtracklayer’
                              ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’
                              * removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
                              ERROR: dependency ‘Rsamtools’ is not available for package ‘ShortRead’
                              * removing ‘/home/linux/R/x86_64-pc-linux-gnu-library/2.14/ShortRead’

                              The downloaded packages are in
                              ‘/tmp/RtmpTluoUe/downloaded_packages’
                              Warning messages:
                              1: In install.packages(pkgs = pkgs, repos = repos, ...) :
                              installation of package ‘RCurl’ had non-zero exit status
                              2: In install.packages(pkgs = pkgs, repos = repos, ...) :
                              installation of package ‘rtracklayer’ had non-zero exit status
                              3: In install.packages(pkgs = pkgs, repos = repos, ...) :
                              installation of package ‘Rsamtools’ had non-zero exit status
                              4: In install.packages(pkgs = pkgs, repos = repos, ...) :
                              installation of package ‘ShortRead’ had non-zero exit status
                              5: 'cluster' 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
                              'survival' cannot be updated, installed directory
                              '/usr/lib/R/library' not writeable

                              Comment

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