* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/Seurat.Rcheck’ * using R Under development (unstable) (2026-10-28 r90786) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-10-29 16:55:22 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘Seurat/DESCRIPTION’ ... OK * this is package ‘Seurat’ version ‘5.6.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'BPCells' * 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 ... [135s/94s] OK * used C compiler: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’ * used C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’ * checking C++ specification ... INFO specified C++17 * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... 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 ... [68s/70s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... INFO Package unavailable to check Rd xrefs: ‘BPCells’ * 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 ... 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 ... INFO GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [21s/22s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [128s/132s] [128s/132s] ERROR 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 v5.6 adds significant improvements in speed and efficiency, particularly for large datasets. For more information, see https://satijalab.org/seurat/articles/announcements. > # > # # 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") Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 822 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.6740 Number of communities: 5 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: 822 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.6740 Number of communities: 5 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: 822 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.6740 Number of communities: 5 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: 822 Running smart local moving algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.6740 Number of communities: 5 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| Saving _problems/test_preprocessing-365.R Saving _problems/test_preprocessing-374.R Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene means and variances 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| 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% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| 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|=============================================== | 67% | |======================================================================| 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| [ FAIL 2 | WARN 0 | SKIP 5 | PASS 699 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test_objects.R:6:3', 'test_spatial.R:355:3', 'test_spatial.R:447:3', 'test_spatial.R:500:3' • {BPCells} is not installed (1): 'test_utilities.R:447:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_preprocessing.R:365:3'): VST variable feature ordering is stable with multiple layers ── Expected `VariableFeatures(object = object.single.thread)` to be identical to `VariableFeatures(object = object.multi.thread.4)`. Differences: 17/230 mismatches x[90]: "BLVRA" y[90]: "NRGN" x[91]: "CD3E" y[91]: "BLVRA" x[92]: "HVCN1" y[92]: "CD3E" x[93]: "LINC00936" y[93]: "HVCN1" x[94]: "NRGN" y[94]: "LINC00936" ── Failure ('test_preprocessing.R:371:3'): VST variable feature ordering is stable with multiple layers ── Expected `VariableFeatures(...)` to be identical to `VariableFeatures(...)`. Differences: Component "counts.4": 6 string mismatches [ FAIL 2 | WARN 0 | SKIP 5 | PASS 699 ] Error: ! Test failures. Execution halted * checking PDF version of manual ... [11s/12s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-MKL/Seurat.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 8:03.34, 476.63 + 30.32