Trouble with GenomicFeatures Package

Question

[MarjoryMollusc]

I have installed GenomicRanges, the dependency before-hand and then have tried to install GenomicFeatures. Both appear to say that they have successfully been installed however RStudio does not recognise any of them.

Below are the commands and outputs I have used:

> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("GenomicRanges")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘GenomicRanges’

  There is a binary version available but the source version is later:
              binary source needs_compilation
GenomicRanges 1.30.0 1.30.3              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/GenomicRanges_1.30.0.zip'
Content type 'application/zip' length 3223041 bytes (3.1 MB)
downloaded 3.1 MB

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘GenomicRanges’

The downloaded binary packages are in
        Z:\Users\Marjory\AppData\Local\Temp\Rtmp8CRT7c\downloaded_packages

Then when attempting to install GenomicFeatures:

> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("GenomicFeatures")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘GenomicFeatures’
also installing the dependency ‘GenomicRanges’


  There is a binary version available but the source version is later:
              binary source needs_compilation
GenomicRanges 1.30.0 1.30.3              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/GenomicRanges_1.30.0.zip'
Content type 'application/zip' length 3223041 bytes (3.1 MB)
downloaded 3.1 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/GenomicFeatures_1.30.3.zip'
Content type 'application/zip' length 2737145 bytes (2.6 MB)
downloaded 2.6 MB

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘GenomicRanges’
package ‘GenomicFeatures’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        Z:\Users\Marjory\AppData\Local\Temp\Rtmp8CRT7c\downloaded_packages

I have tried installing through both RStudio and the RGui, tried opening and closing, tried the clearing of the envrionment too, but it is still telling me that there is no package called GenomicRanges or GenomicFeatures etc.

Answer 1

[Kevin Blighe]

Please take a look at the comment by Martin Morgan, here: https://support.bioconductor.org/p/77688/#77693

I suggest that as administrator you start R and run the command .libPaths(). Then quit R, remove the version of R that you have installed, and remove the directories reported by .libPaths().

[MarjoryMollusc]

Thanks Kevin, that worked!