CRAN Package Check Results for Package Seurat

Last updated on 2025-02-02 07:50:25 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	5.2.1	112.05	659.51	771.56	OK
r-devel-linux-x86_64-debian-gcc	5.2.1	78.12	430.08	508.20	OK
r-devel-linux-x86_64-fedora-clang	5.2.1			1278.74	OK
r-devel-linux-x86_64-fedora-gcc	5.2.1			1268.11	OK
r-devel-windows-x86_64	5.2.1	112.00	756.00	868.00	OK
r-patched-linux-x86_64	5.2.1	122.55	614.02	736.57	NOTE
r-release-linux-x86_64	5.2.1	105.74	618.63	724.37	NOTE
r-release-macos-arm64	5.2.1			315.00	NOTE
r-release-macos-x86_64	5.2.1			571.00	NOTE
r-release-windows-x86_64	5.2.1	108.00	761.00	869.00	NOTE
r-oldrel-macos-arm64	5.2.0			288.00	ERROR
r-oldrel-macos-x86_64	5.2.0			505.00	NOTE
r-oldrel-windows-x86_64	5.2.1	142.00	1015.00	1157.00	NOTE

Check Details

Version: 5.2.1
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'BPCells', 'enrichR', 'presto' Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 5.2.1
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'BPCells', 'presto' Flavors: r-release-macos-arm64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 5.2.1
Check: installed package size
Result: NOTE installed size is 11.3Mb sub-directories of 1Mb or more: R 2.0Mb libs 8.3Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64

Version: 5.2.1
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'BPCells', 'monocle', 'presto' Flavor: r-release-macos-x86_64

Version: 5.2.0
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'BPCells', 'glmGamPoi', 'monocle', 'presto' Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 5.2.0
Check: installed package size
Result: NOTE installed size is 11.2Mb sub-directories of 1Mb or more: R 2.0Mb libs 8.3Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 5.2.0
Check: tests
Result: ERROR Running ‘testthat.R’ [99s/107s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Seurat) Loading required package: SeuratObject Loading required package: sp Attaching package: 'SeuratObject' The following objects are masked from 'package:base': intersect, t > # > # # Run tests for 'v3' > # message('Run tests for v3 assay') > # options(Seurat.object.assay.version = 'v3') > # test_check("Seurat") > > # Run tests for 'v5' > message('Run tests for v5 assay') Run tests for v5 assay > options(Seurat.object.assay.version = 'v5') > test_check("Seurat") | | | 0% | |======================================================================| 100% Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running smart local moving algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 2045 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: -0.0613 Number of communities: 64 Elapsed time: 0 seconds Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [ FAIL 6 | WARN 1 | SKIP 29 | PASS 708 ] ══ Skipped tests (29) ══════════════════════════════════════════════════════════ • On CRAN (29): 'test_differential_expression.R:307:3', 'test_differential_expression.R:349:3', 'test_differential_expression.R:455:3', 'test_dimensional_reduction.R:55:3', 'test_integratedata.R:111:3', 'test_integration.R:74:3', 'test_integration.R:105:3', 'test_integration.R:136:3', 'test_integration.R:170:3', 'test_integration.R:202:3', 'test_integration.R:234:3', 'test_integration.R:264:3', 'test_integration.R:306:3', 'test_integration.R:335:3', 'test_integration.R:365:3', 'test_integration5.R:38:3', 'test_integration5.R:331:3', 'test_objects.R:6:3', 'test_preprocessing.R:140:3', 'test_preprocessing.R:158:3', 'test_preprocessing.R:433:3', 'test_preprocessing.R:554:3', 'test_read_mtx.R:4:3', 'test_read_mtx.R:18:3', 'test_transferdata.R:65:3', 'test_transferdata.R:88:3', 'test_transferdata.R:100:3', 'test_transferdata.R:112:3', 'test_transferdata.R:128:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_sketching.R:41:3'): SketchData defaults work ─────────────────── Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test_sketching.R:41:3 2. │ └─base::withCallingHandlers(...) 3. └─Seurat::SketchData(...) 4. ├─Seurat::LeverageScore(...) 5. └─Seurat:::LeverageScore.Seurat(...) 6. ├─Seurat::LeverageScore(...) 7. └─Seurat:::LeverageScore.StdAssay(...) 8. ├─Seurat::LeverageScore(...) 9. └─Seurat:::LeverageScore.default(...) 10. └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE) ── Error ('test_sketching.R:92:3'): SketchData with multiple layers works ────── Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test_sketching.R:92:3 2. │ └─base::withCallingHandlers(...) 3. └─Seurat::SketchData(...) 4. ├─Seurat::LeverageScore(...) 5. └─Seurat:::LeverageScore.Seurat(...) 6. ├─Seurat::LeverageScore(...) 7. └─Seurat:::LeverageScore.StdAssay(...) 8. ├─Seurat::LeverageScore(...) 9. └─Seurat:::LeverageScore.default(...) 10. └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE) ── Error ('test_sketching.R:124:3'): SketchData with a different number of cells per layer works ── Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test_sketching.R:124:3 2. │ └─base::withCallingHandlers(...) 3. └─Seurat::SketchData(...) 4. ├─Seurat::LeverageScore(...) 5. └─Seurat:::LeverageScore.Seurat(...) 6. ├─Seurat::LeverageScore(...) 7. └─Seurat:::LeverageScore.StdAssay(...) 8. ├─Seurat::LeverageScore(...) 9. └─Seurat:::LeverageScore.default(...) 10. └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE) ── Error ('test_sketching.R:184:3'): SketchData with specified features works ── Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test_sketching.R:184:3 2. │ └─base::withCallingHandlers(...) 3. └─Seurat::SketchData(...) 4. ├─Seurat::LeverageScore(...) 5. └─Seurat:::LeverageScore.Seurat(...) 6. ├─Seurat::LeverageScore(...) 7. └─Seurat:::LeverageScore.StdAssay(...) 8. ├─Seurat::LeverageScore(...) 9. └─Seurat:::LeverageScore.default(...) 10. └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE) ── Error ('test_sketching.R:212:3'): SketchData with specified features and multiple layers works ── Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test_sketching.R:212:3 2. │ └─base::withCallingHandlers(...) 3. └─Seurat::SketchData(...) 4. ├─Seurat::LeverageScore(...) 5. └─Seurat:::LeverageScore.Seurat(...) 6. ├─Seurat::LeverageScore(...) 7. └─Seurat:::LeverageScore.StdAssay(...) 8. ├─Seurat::LeverageScore(...) 9. └─Seurat:::LeverageScore.default(...) 10. └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE) ── Error ('test_sketching.R:247:3'): SketchData when setting your own variable features and specifying features works ── Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix' Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test_sketching.R:247:3 2. │ └─base::withCallingHandlers(...) 3. └─Seurat::SketchData(...) 4. ├─Seurat::LeverageScore(...) 5. └─Seurat:::LeverageScore.Seurat(...) 6. ├─Seurat::LeverageScore(...) 7. └─Seurat:::LeverageScore.StdAssay(...) 8. ├─Seurat::LeverageScore(...) 9. └─Seurat:::LeverageScore.default(...) 10. └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE) [ FAIL 6 | WARN 1 | SKIP 29 | PASS 708 ] Error: Test failures Execution halted Flavor: r-oldrel-macos-arm64