Last updated on 2025-01-15 02:49:54 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 5.1.0 | 113.71 | 613.20 | 726.91 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 5.1.0 | 80.87 | 395.17 | 476.04 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 5.2.0 | 1345.25 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 5.2.0 | 1314.90 | OK | |||
| r-devel-windows-x86_64 | 5.1.0 | 115.00 | 763.00 | 878.00 | NOTE | |
| r-patched-linux-x86_64 | 5.1.0 | 125.43 | 578.01 | 703.44 | NOTE | |
| r-release-linux-x86_64 | 5.1.0 | 112.37 | 583.77 | 696.14 | NOTE | |
| r-release-macos-arm64 | 5.2.0 | 293.00 | NOTE | |||
| r-release-macos-x86_64 | 5.2.0 | 363.00 | NOTE | |||
| r-release-windows-x86_64 | 5.1.0 | 115.00 | 870.00 | 985.00 | NOTE | |
| r-oldrel-macos-arm64 | 5.2.0 | 264.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 5.2.0 | 505.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 5.1.0 | 148.00 | 961.00 | 1109.00 | NOTE |
Version: 5.1.0
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
CCAIntegration.Rd: DimReduc
FindNeighbors.Rd: Neighbor, Graph, Graphs
FindTransferAnchors.Rd: RANN, RcppAnnoy
IntegrateData.Rd: DimReduc, RANN, Assay
IntegrateEmbeddings.Rd: DimReduc
JointPCAIntegration.Rd: DimReduc
PrepSCTIntegration.Rd: Assay
RPCAIntegration.Rd: DimReduc
RunCCA.Rd: merge.Seurat
SCTAssay-class.Rd: Assay
TopNeighbors.Rd: Neighbor
TransferData.Rd: DimReduc, RANN
fortify-Spatial.Rd: Segmentation-class, Centroids-class,
Molecules-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 5.1.0
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: 5.2.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'BPCells', 'presto'
Flavor: r-release-macos-arm64
Version: 5.2.0
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, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 5.2.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'BPCells', 'monocle', 'presto'
Flavor: r-release-macos-x86_64
Version: 5.1.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'BPCells', 'presto'
Flavors: r-release-windows-x86_64, r-oldrel-windows-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: tests
Result: ERROR
Running ‘testthat.R’ [81s/84s]
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")
|
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|
|======================================================================| 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
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|======================================================================| 100%
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|======================================================================| 100%
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|======================================================================| 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
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|
|======================================================================| 100%
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|======================================================================| 100%
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|======================================================================| 100%
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|======================================================================| 100%
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|======================================================================| 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