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Failed to install a package from Bioconductor and the library location not writable

I am trying to install a bioconductor package (XVector). Bioconductor version is 3.16, and the package is available for it as the link is confirming that (https://bioconductor.org/packages/release/bioc/html/XVector.html)

BiocManager::install("XVector")

but it pops an error:

Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Installation paths not writeable, unable to update packages
  Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.2/library
  packages:
    boot, foreign, Matrix, nlme, survival
Warning message:
package ‘XVector’ is not available for Bioconductor version '3.16'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

In my library, I have two paths:

.libPaths()
[1] "C:/R"                               "C:/Program Files/R/R-4.2.2/library"

By default my library location is C:/R, which I created on my own and there I was able to install some other packages normally. I also edited the variable name (R_LIBS_USER) and value (C:/R), and edited them to be for the first directory

How can I delete the C/program file location? I observed that R are not able to load the libraries in that user-created folder and tends to reinstall it in the C/program file? But why? The solution would be to delete the C/program location and force R to only install and load libraries in my folder.

Any suggestions?

bioconductor rna-seq r
• 6,862 views • link
updated by Ram Ram • written by mohsamir2016 • mohsamir2016

1 answer

What does BiocManager::version() say? Also, you don't need to remove any entry from .libPaths(), you can simply use the lib.loc argument in both install.packages and BiocManager::install to specify a custom lib path. Plus, given that C:/R is the first lib path, removing the second will probably have no effect. I think you have a version conflict.

• 0 views • link
written by Ram Ram

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