Last updated on 2025-03-29 08:53:08 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| jrSiCKLSNMF | 1 | 3 | 11 |
Current CRAN status: ERROR: 1, NOTE: 3, OK: 11
Version: 1.2.2
Check: installed package size
Result: NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
libs 3.6Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in ‘jrSiCKLSNMF-Ex.R’ failed
The error most likely occurred in:
> ### Name: DetermineDFromIRLBA
> ### Title: Create elbow plots of the singular values derived from IRLBA to
> ### determine D for large datasets
> ### Aliases: DetermineDFromIRLBA
>
> ### ** Examples
>
> SimSickleJrSmall<-DetermineDFromIRLBA(SimSickleJrSmall,d=5)
Calculating IRLBA for all data matrices
Warning in irlba(x, nv = d) :
You're computing too large a percentage of total singular values, use a standard svd instead.
Error in irlba(x, nv = d) :
function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: DetermineDFromIRLBA -> pblapply -> lapply -> FUN -> irlba
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Getting_Started.Rmd’ using rmarkdown
Quitting from Getting_Started.Rmd:50-53 [graphlaplacian]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! function 'as_cholmod_sparse' not provided by package 'Matrix'
---
Backtrace:
▆
1. └─jrSiCKLSNMF::BuildKNNGraphLaplacians(SimSickleJr)
2. └─base::lapply(...)
3. └─jrSiCKLSNMF (local) FUN(X[[i]], ...)
4. ├─igraph::laplacian_matrix(...)
5. │ └─igraph:::ensure_igraph(graph)
6. ├─scran::buildKNNGraph(x, transposed = TRUE, k = k)
7. └─scran::buildKNNGraph(x, transposed = TRUE, k = k)
8. └─scran (local) .local(x, ...)
9. └─scran:::.setup_knn_data(...)
10. └─scran:::.centered_SVD(...)
11. ├─BiocSingular::runSVD(...)
12. └─BiocSingular::runSVD(...)
13. ├─BiocSingular::runSVD(...)
14. └─BiocSingular::runSVD(...)
15. ├─base::do.call(...)
16. └─BiocSingular (local) `<fn>`(...)
17. ├─base::do.call(...)
18. └─irlba (local) `<fn>`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Getting_Started.Rmd' failed with diagnostics:
function 'as_cholmod_sparse' not provided by package 'Matrix'
--- failed re-building ‘Getting_Started.Rmd’
--- re-building ‘Getting_Started_L2_Norm.Rmd’ using rmarkdown
Quitting from Getting_Started_L2_Norm.Rmd:50-53 [graphlaplacian]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! function 'as_cholmod_sparse' not provided by package 'Matrix'
---
Backtrace:
▆
1. └─jrSiCKLSNMF::BuildKNNGraphLaplacians(SimSickleJr)
2. └─base::lapply(...)
3. └─jrSiCKLSNMF (local) FUN(X[[i]], ...)
4. ├─igraph::laplacian_matrix(...)
5. │ └─igraph:::ensure_igraph(graph)
6. ├─scran::buildKNNGraph(x, transposed = TRUE, k = k)
7. └─scran::buildKNNGraph(x, transposed = TRUE, k = k)
8. └─scran (local) .local(x, ...)
9. └─scran:::.setup_knn_data(...)
10. └─scran:::.centered_SVD(...)
11. ├─BiocSingular::runSVD(...)
12. └─BiocSingular::runSVD(...)
13. ├─BiocSingular::runSVD(...)
14. └─BiocSingular::runSVD(...)
15. ├─base::do.call(...)
16. └─BiocSingular (local) `<fn>`(...)
17. ├─base::do.call(...)
18. └─irlba (local) `<fn>`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Getting_Started_L2_Norm.Rmd' failed with diagnostics:
function 'as_cholmod_sparse' not provided by package 'Matrix'
--- failed re-building ‘Getting_Started_L2_Norm.Rmd’
--- re-building ‘Minibatch_jrSiCKLKSNMF.Rmd’ using rmarkdown
Quitting from Minibatch_jrSiCKLKSNMF.Rmd:22-35 [loadjrSiCKLSNMF]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! function 'as_cholmod_sparse' not provided by package 'Matrix'
---
Backtrace:
▆
1. └─jrSiCKLSNMF::BuildKNNGraphLaplacians(SimSickleJr)
2. └─base::lapply(...)
3. └─jrSiCKLSNMF (local) FUN(X[[i]], ...)
4. ├─igraph::laplacian_matrix(...)
5. │ └─igraph:::ensure_igraph(graph)
6. ├─scran::buildKNNGraph(x, transposed = TRUE, k = k)
7. └─scran::buildKNNGraph(x, transposed = TRUE, k = k)
8. └─scran (local) .local(x, ...)
9. └─scran:::.setup_knn_data(...)
10. └─scran:::.centered_SVD(...)
11. ├─BiocSingular::runSVD(...)
12. └─BiocSingular::runSVD(...)
13. ├─BiocSingular::runSVD(...)
14. └─BiocSingular::runSVD(...)
15. ├─base::do.call(...)
16. └─BiocSingular (local) `<fn>`(...)
17. ├─base::do.call(...)
18. └─irlba (local) `<fn>`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Minibatch_jrSiCKLKSNMF.Rmd' failed with diagnostics:
function 'as_cholmod_sparse' not provided by package 'Matrix'
--- failed re-building ‘Minibatch_jrSiCKLKSNMF.Rmd’
SUMMARY: processing the following files failed:
‘Getting_Started.Rmd’ ‘Getting_Started_L2_Norm.Rmd’
‘Minibatch_jrSiCKLKSNMF.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64