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  • could not find function "readCufflinks" cummeRbund

    Hi,
    I have used cummeRbund a bit recently with Cuffdiff outputs from runs on Galaxy. It has worked ok but the last few days it does not. I have tried to install the package again but no success. Please see below for my problems, the function "readCufflilnks" does not work, anyone know why? Many thanks!

    Cuffdiff v 0.0.5
    R studio v 0.97.449
    R 2.15.3

    > source("http://bioconductor.org/biocLite.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'
    Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu...s/contrib/2.15
    trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/cummeRbund_2.0.0.zip'
    Content type 'application/zip' length 2607618 bytes (2.5 Mb)
    opened URL
    downloaded 2.5 Mb

    package ‘cummeRbund’ successfully unpacked and MD5 sums checked

    The downloaded binary packages are in
    C:\Users\Johanna\AppData\Local\Temp\RtmpcTUck6\downloaded_packages
    Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu...s/contrib/2.15
    Warning message:
    installed directory not writable, cannot update packages 'cluster', 'foreign', 'KernSmooth',
    'lattice', 'Matrix', 'nnet', 'rpart', 'survival'
    > getwd()
    [1] "C:/Users/Johanna/Documents"
    > setwd("C:/Users/Johanna/Documents/R/at_rt")
    > list.files()
    [1] "CDS_FPKM_differential_expression_testing"
    [2] "CDS_FPKM_tracking"
    [3] "CDS_overloading_diffential_expression_testing"
    [4] "gene_differential_expression_testing"
    [5] "gene_FPKM_tracking"
    [6] "promoters_differential_expression_testing"
    [7] "splicing_differential_expression_testing"
    [8] "transcript_differential_expression_testing"
    [9] "transcript_FPKM_tracking"
    [10] "TSS_groups_differential_expression_testing"
    [11] "TSS_groups_FPKM_tracking"
    > library(cummeRbund)
    Loading required package: BiocGenerics

    Attaching package: ‘BiocGenerics’

    The following object(s) are masked from ‘package:stats’:

    xtabs

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

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect,
    lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position,
    rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique

    Loading required package: RSQLite
    Loading required package: DBI
    Loading required package: ggplot2
    Error in loadNamespace(i, c(lib.loc, .libPaths())) :
    there is no package called ‘colorspace’
    Error: package ‘ggplot2’ could not be loaded
    > cuff= readCufflinks (dbFile = "output_database",
    + geneFPKM = "gene_FPKM_tracking",
    + geneDiff = "gene_differential_expression_testing",
    + isoformFPKM = "transcript_FPKM_tracking",
    + isoformDiff = "transcript_differential_expression_testing",
    + TSSFPKM = "TSS_groups_FPKM_tracking",
    + TSSDiff = "TSS_groups_differential_expression_testing",
    + CDSFPKM = "CDS_FPKM_tracking",
    + CDSExpDiff = "CDS_FPKM_differential_expression_testing",
    + CDSDiff = "CDS_overloading_diffential_expression_testing",
    + promoterFile = "promoters_differential_expression_testing",
    + splicingFile = "splicing_differential_expression_testing",
    + rebuild = T)
    Error: could not find function "readCufflinks"

  • #2
    I have to warn you I am pretty new to R, but I was lucky that mine was workingbut could it be the space between readCufflinks and the parenthesis? readCufflinks(...)

    can you try it without the space and see if it works?

    Comment


    • #3
      yeah, its not the space. sorry.

      Comment


      • #4
        I guess the package is not intalled correctly for some reason, but I do not know why.. It has worked on the same computer until recently.

        Comment


        • #5
          Hi

          I have a similar problem.

          Error in loadNamespace(i, c(lib.loc, .libPaths())) :
          there is no package called ‘colorspace’
          Error: package ‘ggplot2’ could not be loaded

          Error: could not find function "readCufflinks"[/QUOTE]

          This means that ‘ggplot2’ are not installed and cummeRbund needs ggplots
          to work.

          So you should install 'ggplot2' beforehand as follows.

          >install.packages("ggplot2", dependencies=TRUE)

          Comment


          • #6
            Try this

            library(cummeRbund)

            Comment

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