- using R version 4.3.3 (2024-02-29)
- using platform: aarch64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘Seurat/DESCRIPTION’ ... OK
- this is package ‘Seurat’ version ‘5.2.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Packages suggested but not available for checking:
'BPCells', 'glmGamPoi', 'monocle', 'presto'
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘Seurat’ can be installed ... [38s/43s] OK
See the install log for details.
- used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
- used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
- used SDK: ‘MacOSX11.3.sdk’
- checking C++ specification ... OK
Not all R platforms support C++17
- checking installed package size ... NOTE
installed size is 11.2Mb
sub-directories of 1Mb or more:
R 2.0Mb
libs 8.3Mb
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [2s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the package can be unloaded cleanly ... [3s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
- checking loading without being on the library search path ... [3s/3s] OK
- checking startup messages can be suppressed ... [3s/3s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [23s/25s] OK
- checking Rd files ... [4s/4s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking compiled code ... OK
- checking examples ... [10s/10s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [99s/107s] 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")
|
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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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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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
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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: 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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[ 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
- checking PDF version of manual ... [9s/9s] OK
- DONE
Status: 1 ERROR, 2 NOTEs
- using check arguments '--no-clean-on-error '