Issues with downloading biomaRt - SeqInfo and S4 Vectors
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mgray20 • 0
@22523611
Last seen 3 hours ago
United Kingdom

I need to download biomaRt, however this requires the package "Seqinfo", which in turn requires "S4Vectors". However, I cannot download "Seqinfo", as it states that "namespace 'S4Vectors' 0.47.0 is being loaded, but >= 0.47.6 is required". Specifically updating S4Vectors does not seem to help. How can I download S4Vectors >= 0.47.6? Please see the code used, ad the corresponding error message

#Install BioCManager to install biomaRt
if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(version = "3.22")

# Force reinstall from Bioconductor
BiocManager::install("S4Vectors", ask = FALSE, force = TRUE)

Resulting Error

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace 'S4Vectors' 0.47.0 is being loaded, but >= 0.47.6 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'Seqinfo'
S4Vectors biomaRt Seqinfo • 37 views
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Can you please provide your sessionInfo() after doing library("S4Vectors")

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shepherl 4.2k
@lshep
Last seen just now
United States

Our windows binaries are currently lagging behind as we are currently do not have a windows builder. If you are on windows you can try installing from source install("S4Vectors", type="source") or downloading the source from the landing page and install manually.

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Note that S4Vectors contains source code, so you will also need to install RTools first.

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