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I tried to install package "geneLenDataBase" to run ChAMP. I kept getting message
"Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace 'DelayedArray' 0.24.0 is being loaded, but >= 0.27.1 is required Calls: ... namespaceImport -> loadNamespace -> namespaceImport -> loadNamespace Execution halted ERROR: lazy loading failed for package 'geneLenDataBase'".
But my DelayedArray is in version 0.30. I used to remove the package and re-install, which did not work.
Please share your
sessionInfo()so we can better assistFrom the looks of it, this seems like a typical case where a working version of Bioc & package constellations breaks. Guess we can see more once we will have the full
sessionInfo- meanwhile, please consider reporting also the output ofBiocManager::version()andBiocManager::valid()Here are the output.
R version 4.4.1 Patched (2024-07-31 r86969 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 10 x64 (build 19045)
Matrix products: default
time zone: America/New_York tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] BiocManager_1.30.23 compiler_4.4.1 tools_4.4.1 fs_1.6.4
[1] '3.19'
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org
R version 4.4.1 Patched (2024-07-31 r86969 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 10 x64 (build 19045)
Matrix products: default
time zone: America/New_York tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] BiocManager_1.30.23 compiler_4.4.1 tools_4.4.1 fs_1.6.4
Bioconductor version '3.19'
create a valid installation with
BiocManager::install(c( "Biobase", "GenomicRanges", "GO.db", "IRanges", "org.Hs.eg.db", "org.Mm.eg.db", "S4Vectors", "SummarizedExperiment", "XVector", "zlibbioc" ), update = TRUE, ask = FALSE, force = TRUE)
more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
Warning: 10 packages out-of-date; 0 packages too new
Can you update packages with
BiocManager::install()and choose to update all. Load the DelayedArray package withlibrary(DelayedArray)and then show yoursessionInfo()again. And also the result of.libPaths(). Thank you