* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SingleCellStat.Rcheck’
* using R Under development (unstable) (2025-05-04 r88189)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘SingleCellStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SingleCellStat’ version ‘0.3.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Jun Chen <chen.jun2@mayo.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  Bioinformatics (13:253)
  Omics (3:58)
  Zhang (13:225)
  al (13:235)
  et (13:232)
  omics (13:73)
* 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 ‘SingleCellStat’ can be installed ... [28s/28s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
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* 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 examples ... [2s/2s] ERROR
Running examples in ‘SingleCellStat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DiSC
> ### Title: DiSC: A statistical tool for differential expression analyis of
> ###   individual level single-cell RNA-Seq data
> ### Aliases: DiSC
> 
> ### ** Examples
> 
> set.seed(seed = 1234556)
> data(sim_data)
> 
> count_matrix <- sim_data$count_matrix
> meta_cell <- sim_data$meta_cell
> gene_index <- sim_data$gene_index
> meta_ind <- sim_data$meta_ind
> 
> obj1 <- DiSC(data.mat = count_matrix, cell.ind = meta_cell,
+              metadata = meta_ind, outcome = "phenotype",
+              covariates = "RIN", cell.id = "cell_id",
+              individual.id = "individual", perm.no = 999,
+              features = c('prev', 'm', 'nzsd'), verbose = TRUE,
+              sequencing.data = TRUE)
The data has  24  samples and  1000  genes will be tested!
Permutation testing ...
Error in loadNamespace(name) : there is no package called ‘vegan’
Calls: DiSC ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE