* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/scPipeline.Rcheck’
* using R Under development (unstable) (2026-01-31 r89360)
* 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 ‘scPipeline/DESCRIPTION’ ... OK
* this is package ‘scPipeline’ version ‘0.2.0.0’
* 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 ‘scPipeline’ can be installed ... [60s/60s] 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 ... [19s/19s] OK
* checking whether the package can be loaded with stated dependencies ... [17s/17s] OK
* checking whether the package can be unloaded cleanly ... [17s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [17s/17s] OK
* checking whether the namespace can be unloaded cleanly ... [20s/20s] OK
* checking loading without being on the library search path ... [21s/21s] 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 ... [76s/77s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
* checking examples with --run-donttest ... [21s/21s] ERROR
Running examples in ‘scPipeline-Ex.R’ failed
The error most likely occurred in:

> ### Name: ConvertGeneIdentifiers
> ### Title: Convert Gene Identifiers in a Seurat Object
> ### Aliases: ConvertGeneIdentifiers
> 
> ### ** Examples
> 
> ## No test: 
> # Read 10X counts data from matrix.mtx, barcodes.tsv and genes.tsv
> library(Seurat)
Loading required package: SeuratObject
Loading required package: sp

Attaching package: ‘SeuratObject’

The following objects are masked from ‘package:base’:

    intersect, t

> counts <- Read10X(data.dir = "../inst/extdata", gene.column = 1)
Error in Read10X(data.dir = "../inst/extdata", gene.column = 1) : 
  Directory provided does not exist
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [62s/63s] OK
* 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/scPipeline.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 9:30.02, 508.83 + 57.39