• using R Under development (unstable) (2025-12-12 r89161)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.7     flang version 21.1.7
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘DR.SC/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘DR.SC’ version ‘3.6’
• 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 ‘DR.SC’ can be installed ... [228s/247s] OK See the install log for details.
• used C++ compiler: ‘clang version 21.1.7’
• checking C++ specification ... OK
• checking installed package size ... OK
• 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 ... [16s/44s] OK
• checking whether the package can be loaded with stated dependencies ... [17s/45s] OK
• checking whether the package can be unloaded cleanly ... [16s/39s] OK
• checking whether the namespace can be loaded with stated dependencies ... [14s/23s] OK
• checking whether the namespace can be unloaded cleanly ... [16s/40s] OK
• checking loading without being on the library search path ... [16s/39s] OK
• checking whether startup messages can be suppressed ... [16s/42s] 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 ... [75s/191s] OK
• checking Rd files ... 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 ... [8s/18s] 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 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [18s/46s] ERROR Running examples in ‘DR.SC-Ex.R’ failed The error most likely occurred in: > ### Name: DR.SC > ### Title: Joint dimension reduction and spatial clustering > ### Aliases: DR.SC DR.SC.Seurat > ### Keywords: Dimension reduction Spatial clustering > > ### ** Examples > > > ## we generate the spatial transcriptomics data with lattice neighborhood, i.e. ST platform. > data(seu) > library(Seurat) Loading required package: SeuratObject Loading required package: sp Attaching package: ‘SeuratObject’ The following objects are masked from ‘package:base’:     intersect, t > seu <- NormalizeData(seu, verbose=FALSE) > # choose 100 highly variable features > # seu <- FindVariableFeatures(seu, nfeatures = 100) > # maxIter = 2 is only used for illustration, and user can use default. > # seu1 <- DR.SC(seu, K=4, platform = 'ST', maxIter=2,verbose=FALSE) > > # choose spatially variable features (SVGs) > seu <- FindSVGs(seu, nfeatures = 40, verbose=FALSE) 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. └─DR.SC::FindSVGs(seu, nfeatures = 40, verbose = FALSE)  2. ├─SeuratObject::GetAssayData(seu, assay = assay, slot = "counts")  3. └─SeuratObject:::GetAssayData.Seurat(seu, assay = assay, slot = "counts")  4. └─SeuratObject::.Deprecate(...)  5. └─lifecycle::deprecate_stop(...)  6. └─lifecycle:::deprecate_stop0(msg)  7. └─rlang::cnd_signal(...) Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [27s/75s] OK
• checking PDF version of manual ... [8s/18s] 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