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Problem running DecontX in sctk-shiny latest docker image #748

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KarlKaise opened this issue Feb 8, 2024 · 2 comments
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Problem running DecontX in sctk-shiny latest docker image #748

KarlKaise opened this issue Feb 8, 2024 · 2 comments

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@KarlKaise
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Hello,

Upon performin DecontX analysis using latest docker image of sctk-shiny app I encountered following issue.

Starting DecontX

Thu Feb 8 14:20:10 2024 .. Analyzing all cells
Thu Feb 8 14:20:11 2024 .... Generating UMAP and estimating cell types
Thu Feb 8 14:20:47 2024 !!! Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters): function 'as_cholmod_sparse' not provided by package 'Matrix'

Would be grateful for any help resolving the issue.
@KarlKaise
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Same problem for SoupX.

@mingl1997 mingl1997 mentioned this issue Jan 14, 2025
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@mingl1997
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Hello,
This was an issue with a particular version of the 'Matrix' R package.
This issue has been addressed in the latest Bioconductor version of singleCellTK.

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@mingl1997 @KarlKaise