CRAN Package Check Results for Maintainer Rahul Satija <seurat at nygenome.org>

CRAN Package Check Results for Maintainer ‘Rahul Satija <seurat at nygenome.org>’

Last updated on 2025-12-14 04:50:30 CET.

Package	ERROR	NOTE	OK
Seurat	4	3	6
SeuratObject		3	10

Package Seurat

Current CRAN status: ERROR: 4, NOTE: 3, OK: 6

Version: 5.3.1
Check: examples
Result: ERROR Running examples in ‘Seurat-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CustomDistance > ### Title: Run a custom distance function on an input data matrix > ### Aliases: CustomDistance > > ### ** Examples > > data("pbmc_small") > # Define custom distance matrix > manhattan.distance <- function(x, y) return(sum(abs(x-y))) > > input.data <- GetAssayData(pbmc_small, assay.type = "RNA", slot = "scale.data") Warning: The following arguments are not used: assay.type Error: ! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. Backtrace: ▆ 1. ├─SeuratObject::GetAssayData(pbmc_small, assay.type = "RNA", slot = "scale.data") 2. └─SeuratObject:::GetAssayData.Seurat(...) 3. └─SeuratObject::.Deprecate(...) 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 5.3.1
Check: tests
Result: ERROR Running ‘testthat.R’ [189s/237s] 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 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Saving _problems/test_preprocessing-197.R 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% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] ══ Skipped tests (24) ══════════════════════════════════════════════════════════ • On CRAN (24): 'test_differential_expression.R:307:3', 'test_differential_expression.R:349:3', 'test_differential_expression.R:455:3', '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_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_preprocessing.R:192:1'): (code run outside of `test_that()`) ─── <lifecycle_error_deprecated/defunctError/rlang_error/error/condition> Error: The `slot` argument of `SetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. Backtrace: ▆ 1. ├─SeuratObject::SetAssayData(...) at test_preprocessing.R:192:1 2. └─SeuratObject:::SetAssayData.Seurat(...) 3. └─SeuratObject::.Deprecate(...) 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 5.3.1
Check: examples
Result: ERROR Running examples in ‘Seurat-Ex.R’ failed The error most likely occurred in: > ### Name: CustomDistance > ### Title: Run a custom distance function on an input data matrix > ### Aliases: CustomDistance > > ### ** Examples > > data("pbmc_small") > # Define custom distance matrix > manhattan.distance <- function(x, y) return(sum(abs(x-y))) > > input.data <- GetAssayData(pbmc_small, assay.type = "RNA", slot = "scale.data") Warning: The following arguments are not used: assay.type Error: ! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. Backtrace: ▆ 1. ├─SeuratObject::GetAssayData(pbmc_small, assay.type = "RNA", slot = "scale.data") 2. └─SeuratObject:::GetAssayData.Seurat(...) 3. └─SeuratObject::.Deprecate(...) 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 5.3.1
Check: tests
Result: ERROR Running ‘testthat.R’ [8m/15m] 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 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Saving _problems/test_preprocessing-197.R 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% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] ══ Skipped tests (24) ══════════════════════════════════════════════════════════ • On CRAN (24): 'test_differential_expression.R:307:3', 'test_differential_expression.R:349:3', 'test_differential_expression.R:455:3', '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_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_preprocessing.R:192:1'): (code run outside of `test_that()`) ─── <lifecycle_error_deprecated/defunctError/rlang_error/error/condition> Error: The `slot` argument of `SetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. Backtrace: ▆ 1. ├─SeuratObject::SetAssayData(...) at test_preprocessing.R:192:1 2. └─SeuratObject:::SetAssayData.Seurat(...) 3. └─SeuratObject::.Deprecate(...) 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 5.3.1
Check: tests
Result: ERROR Running ‘testthat.R’ [249s/251s] 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 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Saving _problems/test_preprocessing-197.R 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% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% 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|======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] ══ Skipped tests (24) ══════════════════════════════════════════════════════════ • On CRAN (24): 'test_differential_expression.R:307:3', 'test_differential_expression.R:349:3', 'test_differential_expression.R:455:3', '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_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_preprocessing.R:192:1'): (code run outside of `test_that()`) ─── <lifecycle_error_deprecated/defunctError/rlang_error/error/condition> Error: The `slot` argument of `SetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. Backtrace: ▆ 1. ├─SeuratObject::SetAssayData(...) at test_preprocessing.R:192:1 2. └─SeuratObject:::SetAssayData.Seurat(...) 3. └─SeuratObject::.Deprecate(...) 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 5.3.1
Check: tests
Result: ERROR Running ‘testthat.R’ [291s/402s] 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 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Saving _problems/test_preprocessing-197.R 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% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] ══ Skipped tests (24) ══════════════════════════════════════════════════════════ • On CRAN (24): 'test_differential_expression.R:307:3', 'test_differential_expression.R:349:3', 'test_differential_expression.R:455:3', '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_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_preprocessing.R:192:1'): (code run outside of `test_that()`) ─── <lifecycle_error_deprecated/defunctError/rlang_error/error/condition> Error: The `slot` argument of `SetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. Backtrace: ▆ 1. ├─SeuratObject::SetAssayData(...) at test_preprocessing.R:192:1 2. └─SeuratObject:::SetAssayData.Seurat(...) 3. └─SeuratObject::.Deprecate(...) 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] Error: ! Test failures. Execution halted Flavor: r-release-linux-x86_64

Version: 5.3.1
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'BPCells', 'presto' Flavors: r-oldrel-macos-arm64, r-oldrel-windows-x86_64

Version: 5.3.1
Check: installed package size
Result: NOTE installed size is 11.3Mb sub-directories of 1Mb or more: R 2.1Mb libs 8.3Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 5.3.1
Check: Rd cross-references
Result: NOTE Package unavailable to check Rd xrefs: ‘BPCells’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 5.3.1
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'BPCells', 'monocle', 'presto' Flavor: r-oldrel-macos-x86_64

Package SeuratObject

Current CRAN status: NOTE: 3, OK: 10

Version: 5.3.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘BPCells’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 5.2.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: 'BPCells' Flavor: r-oldrel-windows-x86_64