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Bioconductor / DelayedArray

A unified framework for working transparently with on-disk and in-memory array-like datasets
https://bioconductor.org/packages/DelayedArray
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Failed to install geneLenDataBase #118

Open fhao2 opened 1 month ago

fhao2 commented 1 month ago

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.

lshep commented 1 month ago

Can you please share your sessionInfo()

fhao2 commented 1 month ago

Sure,

R version 4.4.1 Patched (2024-07-31 r86969 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 10 x64 (build 19045)

lshep commented 1 month ago

Can you provide the full sessionInfo() that includes not only that information but all the loaded packages/version after trying the install/load of the package. It would also be helpful to show your install commands with full output as well. It looks like you also posted on the Support Site; as suggested there trying a BiocManager::valid and BiocManager:install to make sure all packages are up-to-date might also help.

fhao2 commented 1 month ago

Here is the session info

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

And this is the output when I tried to install geneLenDataBase

> BiocManager::install("geneLenDataBase")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 Patched (2024-07-31 r86969
  ucrt)
Installing package(s) 'geneLenDataBase'
Install source package 'geneLenDataBase'

Try to open URL’https://bioconductor.org/packages/3.19/data/experiment/src/contrib/geneLenDataBase_1.40.1.tar.gz'
Content type 'application/x-gzip' length 100438279 bytes (95.8 MB)
downloaded 95.8 MB

* installing *source* package 'geneLenDataBase' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: multiple methods tables found for 'sort'
Warning: multiple methods tables found for 'sort'
Warning: multiple methods tables found for 'sort'
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: <Anonymous> ... namespaceImport -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'geneLenDataBase'
hpages commented 1 month ago

It seems that maybe you have more than one installation of DelayedArray, This can happen if you use more than one package installation path. What's the output of .libPaths()?