Can´t install GenomicRanges and rtracklayer
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Entering edit mode
Johanna • 0
@b6b69938
Last seen 22 months ago
Germany

Hi everyone,

I am trying to install the two packages GenomicRanges and rtracklayer for a while now and it doesn´t work. I have the most recent version of R 4.2.0 and installing all other packages works. Heres the output, that comesup no matter what I try: Can someone help me?

 BiocManager::install()

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22)

**Installation paths not writeable, unable to update packages**

  path: /usr/lib/R/library
  packages:
    nlme, spatial, survival




I also tried two other codes, but they also didnt work: 

remove.packages(c("GenomicRanges", "rtracklayer"), lib = ("/home/xxx/R/x86_64-pc-linux-gnu-library/4.2"))
.libPaths()

biocLite(pkgs = c("rtracklayer", "IRanges", "GenomicRanges", type = "binary"))



> sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
rtracklayer GenomicRanges Installation • 954 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 11 hours ago
United States

You can't just call BiocManager::install() and expect it to know what you want to install! You need to specify the packages you want as a character vector, like BiocManager::install(c("GenomicRanges","rtracklayer"))

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