• using R Under development (unstable) (2026-02-02 r89367)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-12) 15.2.0     GNU Fortran (Debian 15.2.0-12) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-02-03 18:13:24Z
• checking for file ‘tidyseurat/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘tidyseurat’ version ‘0.8.7’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• 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 ‘tidyseurat’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ 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 ... [6s/6s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/6s] OK
• checking whether the package can be unloaded cleanly ... [5s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/6s] OK
• checking loading without being on the library search path ... [6s/7s] OK
• checking whether startup messages can be suppressed ... [6s/6s] 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 ... [25s/30s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [12s/13s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [15s/16s] ERROR   Running ‘testthat.R’ [15s/16s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(tidyseurat)   Loading required package: ttservice   Loading required package: SeuratObject   Loading required package: sp      Attaching package: 'SeuratObject'      The following objects are masked from 'package:base':          intersect, t      ========================================   tidyseurat version 0.8.7   If you use TIDYSEURAT in published research, please cite:      Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.      This message can be suppressed by:     suppressPackageStartupMessages(library(tidyseurat))        To restore the Seurat default display use options("restore_Seurat_show" = TRUE)   ========================================         Attaching package: 'tidyseurat'      The following object is masked from 'package:ttservice':          plot_ly      >   > test_check("tidyseurat")   Saving _problems/test-dplyr-208.R   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%   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%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   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%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   Performing log-normalization   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|        |     | | 0%     |     |======================================================================| 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%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   [ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-dplyr.R:205:3'): add_count ─────────────────────────────────────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and   is now defunct.   Backtrace:        ▆     1. ├─testthat::expect_equal(nrow(add_count(pbmc_small, groups)), length(rownames(pbmc_small))) at test-dplyr.R:205:3     2. │ └─testthat::quasi_label(enquo(object), label)     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))     4. ├─base::nrow(add_count(pbmc_small, groups))     5. ├─dplyr::add_count(pbmc_small, groups)     6. ├─tidyseurat:::add_count.Seurat(pbmc_small, groups)     7. │ └─... %>% as_meta_data(x)     8. ├─tidyseurat:::as_meta_data(., x)     9. │ └─... %>% column_to_rownames(c_(seurat_object)$name)    10. ├─tibble::column_to_rownames(., c_(seurat_object)$name)    11. │ ├─base::stopifnot(is.data.frame(.data))    12. │ └─base::is.data.frame(.data)    13. ├─dplyr::select_if(., !colnames(.) %in% col_to_exclude)    14. │ └─rlang::is_logical(.predicate)    15. ├─colnames(.) %in% col_to_exclude    16. ├─base::colnames(.)    17. │ └─base::is.data.frame(x)    18. ├─dplyr::add_count(...)    19. └─dplyr:::add_count.data.frame(...)    20. └─dplyr:::add_count_impl(...)    21. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call)    22. └─lifecycle:::deprecate_stop0(msg)    23. └─rlang::cnd_signal(...)      [ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [22s/25s] OK
• checking PDF version of manual ... [6s/8s] OK
• checking HTML version of manual ... [4s/6s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR