BiocManager upgrade problem
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@alisiavosh-22099
Last seen 23 months ago

Hi, I have installation of R in a server running on redhat 7. I have upgraded R and now to upgrade BiocManager I get error messages as below:

> install.packages("BiocManager")
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.revolutionanalytics.com/src/contrib/BiocManager_1.30.7.tar.gz'
Content type 'application/octet-stream' length 38020 bytes (37 KB)
==================================================
downloaded 37 KB

* installing *source* package ‘BiocManager’ ...
** package ‘BiocManager’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘BiocManager’
    finding HTML links ... done
    BiocManager-pkg                         html  
    available                               html  
    install                                 html  
    repositories                            html  
    valid                                   html  
    version                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocManager)
Making 'packages.html' ... done

The downloaded source packages are in
    ‘/tmp/RtmpgHhwMp/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
> BiocManager::version()
Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
  call: NULL
  error: Bioconductor version '3.8' requires R version '3.5'; see
  https://bioconductor.org/install
> BiocManager::valid()
Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
  call: NULL
  error: Bioconductor version '3.8' requires R version '3.5'; see
  https://bioconductor.org/install
> BiocManager::install(version="3.5")
Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
  call: NULL
  error: Bioconductor version '3.8' requires R version '3.5'; see
  https://bioconductor.org/install
> BiocManager::install(version="3.7")
Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
  call: NULL
  error: Bioconductor version '3.8' requires R version '3.5'; see
  https://bioconductor.org/install

I appreciate any help with regard to this. Thank you

BiocManager • 1.3k views
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Entering edit mode
@martin-morgan-1513
Last seen 9 weeks ago
United States

Likely what you have done is updated your R but reused your installed packages library. A better strategy is to make sure that the .libPaths() are unique to each version of R + Bioconductor; discussed a bit ironically in the BiocManager vignette.

To continue down the path that you're on, in a new R session could try to

remove.packages("BiocVersion")     # repeat until there are no versions to remove
BiocManager::install()
BiocManager::valid()

and then proceed to update packages by cut / paste the output of BiocManager::valid()

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