• using R Under development (unstable) (2025-12-12 r89161)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘scpoisson/DESCRIPTION’ ... OK
• this is package ‘scpoisson’ version ‘0.0.1’
• package encoding: UTF-8
• 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 ‘scpoisson’ can be installed ... [20s/31s] OK See the install log for details.
• checking package directory ... 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 ... 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 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 ... [29s/83s] OK
• checking Rd files ... [6s/15s] NOTE checkRd: (-1) HclustDepart.Rd:23: Lost braces; missing escapes or markup?     23 | \item{\code{res2}}: {a data frame contains two columns: names (cell names) and clusters (cluster label)}        | ^ checkRd: (-1) HclustDepart.Rd:24-26: Lost braces     24 | \item{\code{sigclust_p}}: {a matrix with cells to cluster as rows, split index as columns,        | ^ checkRd: (-1) HclustDepart.Rd:27-29: Lost braces     27 | \item{\code{sigclust_z}}: {a matrix with cells to cluster as rows, split index as columns,        | ^ checkRd: (-1) LouvainDepart.Rd:38: Lost braces; missing escapes or markup?     38 | \item{\code{sdata}}: {a Seurat object}        | ^ checkRd: (-1) LouvainDepart.Rd:39-40: Lost braces     39 | \item{\code{tsne_data}}: {a matrix containing t-SNE dimension reduction results,        | ^ checkRd: (-1) LouvainDepart.Rd:41-42: Lost braces     41 | \item{\code{umap_data}}: {a matrix containing UMAP dimension reduction results,        | ^ checkRd: (-1) LouvainDepart.Rd:43: Lost braces; missing escapes or markup?     43 | \item{\code{res_clust}}: {a data frame contains two columns: names (cell names) and clusters (cluster label)}        | ^ checkRd: (-1) sigp.Rd:19: Lost braces; missing escapes or markup?     19 | \item{\code{p}}: {p-value for the first split}        | ^ checkRd: (-1) sigp.Rd:20: Lost braces; missing escapes or markup?     20 | \item{\code{z}}: {z-score for the first split}        | ^ checkRd: (-1) sigp.Rd:21: Lost braces     21 | \item{\code{shc_result}}: {a \code{shc} S3-object as defined in sigclust2 package}        | ^ checkRd: (-1) sigp.Rd:22: Lost braces; missing escapes or markup?     22 | \item{\code{clust2}}: {a vector with group index for each cell}        | ^ checkRd: (-1) sigp.Rd:23: Lost braces; missing escapes or markup?     23 | \item{\code{clust_dat}}: {a matrix of data representation used as input for hierarchical clustering}        | ^
• 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 R/sysdata.rda ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [14s/35s] ERROR Running examples in ‘scpoisson-Ex.R’ failed The error most likely occurred in: > ### Name: LouvainDepart > ### Title: Louvain clustering using departure as data representation > ### Aliases: LouvainDepart > > ### ** Examples > > > set.seed(1234) > test_set <- matrix(rpois(500, 2), nrow = 20) > rownames(test_set) <- paste0("gene", 1:nrow(test_set)) > colnames(test_set) <- paste0("cell", 1:ncol(test_set)) > LouvainDepart(test_set) 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. ├─scpoisson::LouvainDepart(test_set)  2. └─scpoisson:::LouvainDepart.matrix(test_set)  3. ├─SeuratObject::SetAssayData(...)  4. └─SeuratObject:::SetAssayData.Assay(...)  5. └─SeuratObject::.Deprecate(...)  6. └─lifecycle::deprecate_stop(...)  7. └─lifecycle:::deprecate_stop0(msg)  8. └─rlang::cnd_signal(...) Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [30s/72s] OK   Running ‘testthat.R’ [29s/71s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [9m/22m] ERROR Error(s) in re-building vignettes: --- re-building ‘scpoissonmodel.Rmd’ using rmarkdown Quitting from scpoissonmodel.Rmd:78-85 [example3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'scpoissonmodel.Rmd' failed with diagnostics: The `slot` argument of `SetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. --- failed re-building ‘scpoissonmodel.Rmd’ SUMMARY: processing the following file failed:   ‘scpoissonmodel.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [8s/19s] 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: 2 ERRORs, 1 NOTE