* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/SCdeconR.Rcheck’
* using R Under development (unstable) (2025-12-20 r89211)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘SCdeconR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SCdeconR’ version ‘1.0.0’
* 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 ‘SCdeconR’ can be installed ... [45s/45s] OK
* 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 ... [13s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/14s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/14s] OK
* checking loading without being on the library search path ... [14s/14s] 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 ... [57s/57s] 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 examples ... [13s/13s] OK
* checking examples with --run-donttest ... [40s/40s] ERROR
Running examples in ‘SCdeconR-Ex.R’ failed
The error most likely occurred in:

> ### Name: bulk_generator
> ### Title: Generate artificial bulk RNA-seq samples based on simulation
> ### Aliases: bulk_generator
> 
> ### ** Examples
> 
> ## No test: 
> ref_list <- c(paste0(system.file("extdata", package = "SCdeconR"), "/refdata/sample1"),
+               paste0(system.file("extdata", package = "SCdeconR"), "/refdata/sample2"))
> phenopath1 <- paste0(system.file("extdata", package = "SCdeconR"),
+ "/refdata/phenodata_sample1.txt")
> phenopath2 <- paste0(system.file("extdata", package = "SCdeconR"),
+ "/refdata/phenodata_sample2.txt")
> phenodata_list <- c(phenopath1,phenopath2)
> 
> # construct integrated reference using harmony algorithm
> refdata <- construct_ref(ref_list = ref_list,
+                       phenodata_list = phenodata_list,
+                       data_type = "cellranger",
+                       method = "harmony",
+                       group_var = "subjectid",
+                       nfeature_rna = 50,
+                       vars_to_regress = "percent_mt", verbose = FALSE)
Warning: executing %dopar% sequentially: no parallel backend registered
Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
> phenodata <- data.frame(cellid = colnames(refdata),
+                         celltypes = refdata$celltype,
+                         subjectid = refdata$subjectid)
> prop <- data.frame(celltypes = unique(refdata$celltype), 
+ proportion = rep(1/length(unique(refdata$celltype)), length(unique(refdata$celltype))))
> bulk_sim <- bulk_generator(ref = GetAssayData(refdata, slot = "data", assay = "SCT"),
+                            phenodata = phenodata,
+                            num_mixtures = 20,
+                            prop = prop,
+                            num_mixtures_sprop = 1)
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
     ▆
  1. ├─SCdeconR::bulk_generator(...)
  2. │ ├─generics::intersect(colnames(ref), phenodata$cellid)
  3. │ └─base::colnames(ref)
  4. │   └─base::is.data.frame(x)
  5. ├─SeuratObject::GetAssayData(refdata, slot = "data", assay = "SCT")
  6. └─SeuratObject:::GetAssayData.Seurat(refdata, slot = "data", assay = "SCT")
  7.   └─SeuratObject::.Deprecate(...)
  8.     └─lifecycle::deprecate_stop(...)
  9.       └─lifecycle:::deprecate_stop0(msg)
 10.         └─rlang::cnd_signal(...)
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/SCdeconR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 6:33.28, 354.38 + 36.37