qvalues installation
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jdorgan • 0
@9b684ad3
Last seen 9 weeks ago

I recently installed R 4.0.3. I had to update Bioconductor to 3.12. Following instructions on install page

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.12")

However, this tries to reinstall 295 packages. After a while R stopped responding so I used alt-ctrl-del end task to abort.

I tried installing qvalues using

'BioManager::install("qvalues", lib="H:/R/packages")'

[I use this code all of the time and it works.]

I got the message

Bioconductor version 3.12 (BioManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'qvalues'

It responds with names of many packages followed by

Update all/some/none? [a/s/n]

if I type '''n''' I get message

Warning message:
package 'qvalues' is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see ideas at [URL for installing packages]

if I type '''s''' I get message

ALL:
  Version 1.20.0 installed in H:/R/packages
  Version 1.32.0 available at https://bioconductor.org/packages/3.12/data/experi....

A box appears asking Update? This reiterates to BH bibtex Biobase BiocGenerics BiocParallel etc

I selected some and it started running but then I got message

Error in unpackPkgZip (foundpkgs[okp, 2L], foundpkgs[okp,IL], lib, libs_only, :
   ERROR: failed to lock directory 'H:\R\packages' for modifying [this is where I store all my R packages]
Try removing 'H:\R\packages\00LOCK'
In addition: Warning message
package 'qvalues' is not available for this version of R
A version of this package...
"'> values=list(huntington, mart=ensembl)'''. [this looks like my code in R]
Error unexpected ',' in "values=list(huntington),"

I am at a loss, can someone please help?

Thanks, Joanne

biocViews • 100 views
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Please note that the name of the Bioconductor package is qvalue, and not qvalues (with an s).

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The large number of packages being installed by BiocManager::install(version="3.12") is likely because you are re-using a library (H:/R/packages?) from a previous installation -- BiocManager is updating all of your previously installed packages. It is much better practice to have one library per version of Bioconductor, as outlined in the vignette section "Managing multiple versions" at https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html.

The 00LOCK file / directory is likely left over from your aborted attempt to update these files; you'll need to remove these manually, either using the file browser in Windows or via an R command like unlink("H:/R/Packages/00LOCK", recursive = TRUE).

If you do want to update all the packages in H/R/Packages, then adding the argument BiocManager::install(..., ask = FALSE) will 'just do it' without asking, or responding a to the prompt will update all packages.

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Thank you so much. I installed Bioconductor 3.12 in a new folder and everything worked fine. Joanne

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