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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scCB2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scCB2_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scCB2.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘scCB2/DESCRIPTION’ ... OK
* this is package ‘scCB2’ version ‘1.9.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scCB2’ can be installed ... 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 R 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘scCB2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QuickCB2
> ### Title: All-in-one function from raw data to filtered cell matrix
> ### Aliases: QuickCB2
> 
> ### ** Examples
> 
> 
> # simulate 10x output files
> data(mbrainSub)
> mbrainSub <- mbrainSub[,1:10000]
> data_dir <- file.path(tempdir(),"CB2example")
> dir.create(data_dir)
> gene_name <- rownames(mbrainSub)
> 
> # For simplicity, use gene names to generate gene IDs to fit the format.
> gene_id <- paste0("ENSG_fake_",gene_name)
> barcode_id <- colnames(mbrainSub)
> Matrix::writeMM(mbrainSub,file = file.path(data_dir,"matrix.mtx"))
NULL
> write.table(barcode_id,file = file.path(data_dir,"barcodes.tsv"),
+     sep = "\t", quote = FALSE, col.names = FALSE, row.names = FALSE)
> write.table(cbind(gene_id,gene_name),file = file.path(data_dir,"genes.tsv"),
+     sep = "\t", quote = FALSE, col.names = FALSE, row.names = FALSE)
> 
> # Run QuickCB2 on 10x raw data and get cell matrix.
> # Control FDR at 1%. Use 2-core parallel computation.
> 
> RealCell <- QuickCB2(dir = data_dir, 
+                      FDR_threshold = 0.01,
+                      Ncores = 2)
Loading data...
as(<dgTMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead
Done.

Running CB2...
FDR threshold: 0.01
Lower threshold: 100
Cores allocated: 2

(1/5) Filtering empty barcodes and features in raw data...
Detected 0 extra features which won't be used during cell calling.

Upper threshold: 6421
Done.

(2/5) Calculating test statistics for barcodes...
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘scCB2.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘scCB2.Rmd’ using rmarkdown
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/scCB2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scCB2
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘scCB2’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCB2)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scCB2)
> 
> test_check("scCB2")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 25 ]
> 
> proc.time()
   user  system elapsed 
 19.268   1.270  31.823