Failed to install geneLenDataBase
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Fang • 0
@03dddd2d
Last seen 8 weeks ago
United States

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.

geneLenDataBase ChAMP • 397 views
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Please share your sessionInfo() so we can better assist

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From 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 of BiocManager::version() and BiocManager::valid()

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Here are the output.

sessionInfo()

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

BiocManager::version()

[1] '3.19'

BiocManager::valid()

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org

  • sessionInfo()

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'

  • 10 packages out-of-date
  • 0 packages too new

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

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Can you update packages with BiocManager::install() and choose to update all. Load the DelayedArray package with library(DelayedArray) and then show your sessionInfo() again. And also the result of .libPaths(). Thank you

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