CRAN Package Check Results for Maintainer ‘Dorothy Ellis <ddemoreellis at gmail.com>’

Last updated on 2025-03-29 08:53:08 CET.

Package ERROR NOTE OK
jrSiCKLSNMF 1 3 11

Package jrSiCKLSNMF

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