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CummeRbund installation failing

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  • #46
    Thanks GenoMax!

    Originally posted by GenoMax View Post
    Have you installed libxml2 library (this is ubuntu I assume)?
    Thank you very much for your kindly response! I have installed libxml2 library and also tried to install XML-3.98 alone but get Error2/3. My 64bit-PC is lying on Ubuntu 12.04 LTS system.

    Error2: install XML alone
    $ cd XML
    $ sh ./configure --host=x86_64
    ......
    Minor 9, Patch 1 for 2.9.1
    Located parser file -I/usr/local/include/libxml2/parser.h
    Checking for 1.8: -I/usr/local/include/libxml2
    Using libxml2.*
    checking for gzopen in -lz... no
    checking for xmlParseFile in -lxml2... no
    checking for xmlParseFile in -lxml... no
    configure: error: "libxml not found"

    Error3: install XML in R
    >install.package("XML")
    .......
    /usr/bin/ld: /usr/local/lib/libxml2.a(error.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
    /usr/local/lib/libxml2.a: could not read symbols: Bad value
    collect2: ld returned 1 exit status
    make: *** [XML.so] Error 1
    ERROR: compilation failed for package ‘XML’
    * removing ‘/usr/local/lib64/R/library/XML’
    The downloaded source packages are in
    ‘/tmp/RtmpsOfYSc/downloaded_packages’
    Updating HTML index of packages in '.Library'
    Making packages.html ... done
    Warning message:
    In install.packages("XML") :
    installation of package ‘XML’ had non-zero exit status

    Libxml2:
    $ sudo apt-get install libxml2
    Reading package lists... Done
    Building dependency tree
    Reading state information... Done
    libxml2 is already the newest version.
    The following packages were automatically installed and are no longer required:
    natefoo-taxonomy python-numexpr tk-table python-gnuplot libhdf5-serial-1.8.4
    liblzo2-2 natefoo-add-scores galaxy-server-test python-tables macs14
    Use 'apt-get autoremove' to remove them.
    0 upgraded, 0 newly installed, 0 to remove and 569 not upgraded.
    $ which xml2-config
    /usr/local/bin/xml2-config
    Last edited by yincf; 10-31-2013, 03:20 AM.

    Comment


    • #47
      Do you have zlib1g and zlib1g-dev installed?

      Comment


      • #48
        Originally posted by GenoMax View Post
        Do you have zlib1g and zlib1g-dev installed?
        I have installed them, but the error changed nothing!

        Thank you!

        Comment


        • #49
          error installing cummerbund on windows7

          Hello all,
          I am also having issues finishing the cummerbund installation too, but I'm using a windows7 starter netbook computer.

          These first 2 commands work fine:
          > source('http://www.bioconductor.org/biocLite.R')
          Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help

          > biocLite("cummeRbund")
          BioC_mirror: http://bioconductor.org
          Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
          Installing package(s) 'cummeRbund'
          trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/cummeRbund_2.4.0.zip'
          Content type 'application/zip' length 2601827 bytes (2.5 Mb)
          opened URL
          downloaded 2.5 Mb

          package ‘cummeRbund’ successfully unpacked and MD5 sums checked

          But when I try to load the cummerbund library I get the following errors
          > library(cummeRbund)
          Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
          there is no package called ‘biomaRt’
          Error: package ‘Gviz’ could not be loaded

          I've tried installing these packages alone but that does not work either and cummerbund does not work without them. (see below)
          > install.packages('biomaRt')
          package ‘biomaRt’ is not available (for R version 3.0.2)
          > install.packages('Gviz')
          Warning message:
          package ‘Gviz’ is not available (for R version 3.0.2)

          > cuff<-readCufflinks()
          Error: could not find function "readCufflinks"

          Please help me if you know how to fix this issue.
          Thanks

          Comment


          • #50
            Originally posted by yincf View Post
            I have installed them, but the error changed nothing!

            Thank you!

            Looking at your last message it appears that you only posted error 2 and 3. What was error 1? Can you post that?

            Comment


            • #51
              Originally posted by Kerah View Post
              Hello all,
              I am also having issues finishing the cummerbund installation too, but I'm using a windows7 starter netbook computer.

              These first 2 commands work fine:
              > source('http://www.bioconductor.org/biocLite.R')
              Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help

              > biocLite("cummeRbund")
              BioC_mirror: http://bioconductor.org
              Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
              Installing package(s) 'cummeRbund'
              trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/cummeRbund_2.4.0.zip'
              Content type 'application/zip' length 2601827 bytes (2.5 Mb)
              opened URL
              downloaded 2.5 Mb

              package ‘cummeRbund’ successfully unpacked and MD5 sums checked

              But when I try to load the cummerbund library I get the following errors
              > library(cummeRbund)
              Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
              there is no package called ‘biomaRt’
              Error: package ‘Gviz’ could not be loaded

              I've tried installing these packages alone but that does not work either and cummerbund does not work without them. (see below)
              > install.packages('biomaRt')
              package ‘biomaRt’ is not available (for R version 3.0.2)
              > install.packages('Gviz')
              Warning message:
              package ‘Gviz’ is not available (for R version 3.0.2)

              > cuff<-readCufflinks()
              Error: could not find function "readCufflinks"

              Please help me if you know how to fix this issue.
              Thanks
              Did you try?
              Code:
              source("http://bioconductor.org/biocLite.R")
              biocLite("Gviz")
              biocLite("biomaRt")
              Are you installing in cygwin?

              Comment


              • #52
                Originally posted by GenoMax View Post
                Did you try?
                Code:
                source("http://bioconductor.org/biocLite.R")
                biocLite("Gviz")
                biocLite("biomaRt")
                Are you installing in cygwin?
                Wow thank you so much GenoMax that worked like a charm!
                CummeRbund is up and running and I can make plots from the data.
                Many thanks

                Comment


                • #53
                  Originally posted by GenoMax View Post
                  Looking at your last message it appears that you only posted error 2 and 3. What was error 1? Can you post that?
                  Thanks again!
                  I am sorry the number of errors may not be exact. Error 1 is the first information I have posted in this topic.
                  Now I guess that my problem is XML installation, but I can not fix it.

                  Comment


                  • #54
                    Originally posted by yincf View Post
                    Thanks again!
                    I am sorry the number of errors may not be exact. Error 1 is the first information I have posted in this topic.
                    Now I guess that my problem is XML installation, but I can not fix it.
                    Can you tell me what version of R you are using?

                    One of the things that may be useful to try is to upgrade R to the latest version using the directions at this link: http://korolevbin.blogspot.com/2013/...on-ubuntu.html

                    Comment


                    • #55
                      Thankyou

                      Originally posted by GenoMax View Post
                      Can you tell me what version of R you are using?

                      One of the things that may be useful to try is to upgrade R to the latest version using the directions at this link: http://korolevbin.blogspot.com/2013/...on-ubuntu.html
                      Thank you very much GenoMax, you are realy my god!
                      My cummeRbund is ok now! I reinstalled R-3.0.2 and libxml2 with source.

                      Comment


                      • #56
                        Hmisc installation error when installing cummeRbund

                        I am receiving this error while installing cummeRbund on Ubuntu 12.04 LTS using the biocLite. The following error makes little sense to me, only that it should be something to do with the compilation of Hmisc source. Running as a root didn't solve my problem; the trail is also given below.

                        /usr/bin/ld: cannot find -lgfortran
                        collect2: error: ld returned 1 exit status
                        make: *** [Hmisc.so] Error 1
                        ERROR: compilation failed for package ‘Hmisc’


                        Trail:

                        [email protected]:~$ sudo -s
                        [email protected]:~# R

                        R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
                        Copyright (C) 2013 The R Foundation for Statistical Computing
                        Platform: x86_64-pc-linux-gnu (64-bit)

                        R is free software and comes with ABSOLUTELY NO WARRANTY.
                        You are welcome to redistribute it under certain conditions.
                        Type 'license()' or 'licence()' for distribution details.

                        Natural language support but running in an English locale

                        R is a collaborative project with many contributors.
                        Type 'contributors()' for more information and
                        'citation()' on how to cite R or R packages in publications.

                        Type 'demo()' for some demos, 'help()' for on-line help, or
                        'help.start()' for an HTML browser interface to help.
                        Type 'q()' to quit R.

                        > source("http://bioconductor.org/biocLite.R")
                        Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
                        > biocLite("cummeRbund")
                        BioC_mirror: http://bioconductor.org
                        Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
                        Installing package(s) 'cummeRbund'
                        also installing the dependencies ‘Hmisc’, ‘biovizBase’, ‘Gviz’

                        trying URL 'http://cran.fhcrc.org/src/contrib/Hmisc_3.13-0.tar.gz'
                        Content type 'application/x-gzip' length 587751 bytes (573 Kb)
                        opened URL
                        ==================================================
                        downloaded 573 Kb

                        trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/biovizBase_1.10.5.tar.gz'
                        Content type 'application/x-gzip' length 1036027 bytes (1011 Kb)
                        opened URL
                        ==================================================
                        downloaded 1011 Kb

                        trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/Gviz_1.6.0.tar.gz'
                        Content type 'application/x-gzip' length 1965136 bytes (1.9 Mb)
                        opened URL
                        ==================================================
                        downloaded 1.9 Mb

                        trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/cummeRbund_2.4.0.tar.gz'
                        Content type 'application/x-gzip' length 2273576 bytes (2.2 Mb)
                        opened URL
                        ==================================================
                        downloaded 2.2 Mb

                        * installing *source* package ‘Hmisc’ ...
                        ** package ‘Hmisc’ successfully unpacked and MD5 sums checked
                        ** libs
                        gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c Hmisc.c -o Hmisc.o
                        gfortran -fpic -O3 -pipe -g -c cidxcn.f -o cidxcn.o
                        gfortran -fpic -O3 -pipe -g -c cidxcp.f -o cidxcp.o
                        gfortran -fpic -O3 -pipe -g -c hoeffd.f -o hoeffd.o
                        gfortran -fpic -O3 -pipe -g -c jacklins.f -o jacklins.o
                        gfortran -fpic -O3 -pipe -g -c largrec.f -o largrec.o
                        gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c mChoice.c -o mChoice.o
                        gfortran -fpic -O3 -pipe -g -c maxempr.f -o maxempr.o
                        gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c nstr.c -o nstr.o
                        gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c ranksort.c -o ranksort.o
                        gfortran -fpic -O3 -pipe -g -c rcorr.f -o rcorr.o
                        gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c string_box.c -o string_box.o
                        gfortran -fpic -O3 -pipe -g -c wclosest.f -o wclosest.o
                        gcc -std=gnu99 -shared -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
                        /usr/bin/ld: cannot find -lgfortran
                        collect2: error: ld returned 1 exit status
                        make: *** [Hmisc.so] Error 1
                        ERROR: compilation failed for package ‘Hmisc’
                        * removing ‘/home/s/R/x86_64-pc-linux-gnu-library/3.0/Hmisc’
                        ERROR: dependency ‘Hmisc’ is not available for package ‘biovizBase’
                        * removing ‘/home/s/R/x86_64-pc-linux-gnu-library/3.0/biovizBase’
                        ERROR: dependency ‘biovizBase’ is not available for package ‘Gviz’
                        * removing ‘/home/s/R/x86_64-pc-linux-gnu-library/3.0/Gviz’
                        ERROR: dependency ‘Gviz’ is not available for package ‘cummeRbund’
                        * removing ‘/home/s/R/x86_64-pc-linux-gnu-library/3.0/cummeRbund’

                        The downloaded source packages are in
                        ‘/tmp/Rtmpt64xmr/downloaded_packages’
                        Warning messages:
                        1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                        installation of package ‘Hmisc’ had non-zero exit status
                        2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                        installation of package ‘biovizBase’ had non-zero exit status
                        3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                        installation of package ‘Gviz’ had non-zero exit status
                        4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
                        installation of package ‘cummeRbund’ had non-zero exit status

                        Please help. Thanks.

                        Comment


                        • #57
                          See answer #2 or 3 in this thread: http://stackoverflow.com/questions/6...find-lgfortran

                          One of those should work for you.

                          Comment


                          • #58
                            Originally posted by GenoMax View Post
                            See answer #2 or 3 in this thread: http://stackoverflow.com/questions/6...find-lgfortran

                            One of those should work for you.
                            GenoMax, this solved the problem. Thank you.

                            The problem was due to the missing link in /usr/lib/libfortran.so on my Ubuntu 12.04 LTS.

                            So this corrected it,

                            sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/libgfortran.so

                            Comment


                            • #59
                              I have got my results from cuffdiff and just wondering that what would be the best option to visualize the data?

                              Comment


                              • #60
                                library(cummeRbund)

                                good luck
                                jp.


                                Originally posted by mhkiani View Post
                                I have got my results from cuffdiff and just wondering that what would be the best option to visualize the data?

                                Comment

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