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  • error in GenomicRanges package

    hii everyone,

    i was working with this package so i got some error
    Code:
    > library("GenomicFeatures")
    > testFile <- system.file("bam", "accepted_hits.bam", package = "leeBamViews")
    > aligns <- readBamGappedAlignments(testFile)
    Error: could not find function "readBamGappedAlignments"
    after that i tried to install this package to overcome this problem. but i was not able to do so

    Code:
    > source("http://bioconductor.org/biocLite.R")
    Bioconductor version 3.2 (BiocInstaller 1.19.6), ?biocLite for help
    > biocLite("GenomicRanges")
    BioC_mirror: http://bioconductor.org
    Using Bioconductor 3.2 (BiocInstaller 1.19.6), R 3.2.0 (2015-04-16).
    Installing package(s) ‘GenomicRanges’
    trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicRanges_1.21.16.tar.gz'
    Content type 'application/x-gzip' length 906397 bytes (885 KB)
    ==================================================
    downloaded 885 KB
    
    * installing *source* package ‘GenomicRanges’ ...
    ** libs
    gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib64/R/library/S4Vectors/include" -I"/usr/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
    gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib64/R/library/S4Vectors/include" -I"/usr/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
    gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib64/R/library/S4Vectors/include" -I"/usr/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
    gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib64/R/library/S4Vectors/include" -I"/usr/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c transcript_utils.c -o transcript_utils.o
    gcc -std=gnu99 -shared -L/usr/local/lib64 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o
    installing to /usr/local/lib64/R/library/GenomicRanges/libs
    ** R
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (GenomicRanges)
    
    The downloaded source packages are in
    	‘/tmp/RtmpbPM2YS/downloaded_packages’
    Updating HTML index of packages in '.Library'
    Making 'packages.html' ... done
    Old packages: 'survival'
    Update all/some/none? [a/s/n]: a
    trying URL 'http://cran.fhcrc.org/src/contrib/survival_2.38-3.tar.gz'
    Error in download.file(url, destfile, method, mode = "wb", ...) : 
      cannot open URL 'http://cran.fhcrc.org/src/contrib/survival_2.38-3.tar.gz'
    In addition: Warning message:
    In download.file(url, destfile, method, mode = "wb", ...) :
      cannot open: HTTP status was '0 (null)'
    Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
      download of package ‘survival’ failed
    > install.package("GenomicRanges")
    Error: could not find function "install.package"
    > install.packages("GenomicRanges")
    --- Please select a CRAN mirror for use in this session ---
    Warning message:
    package ‘GenomicRanges’ is not available (for R version 3.2.0)
    so will you please give me some suggestion in this.


    thanks

  • #2
    get resolved

    this problem is also get resolved after i replace the older version of survival package wid the latest one
    Code:
    Old packages: 'survival'
    Update all/some/none? [a/s/n]: a
    trying URL 'http://cran.fhcrc.org/src/contrib/survival_2.38-3.tar.gz'
    Error in download.file(url, destfile, method, mode = "wb", ...) : 
      cannot open URL 'http://cran.fhcrc.org/src/contrib/survival_2.38-3.tar.gz'

    Comment


    • #3
      Hi there,

      I believe that function has been deprecated, and been replaced with readGAlignmentsFromBam() - see here for more details: https://support.bioconductor.org/p/61854/

      Comment

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