* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/SMDIC.Rcheck’
* using R Under development (unstable) (2023-03-29 r84123)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
    GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
* running under: Fedora 34 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘SMDIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SMDIC’ version ‘0.1.3’
* 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 ‘SMDIC’ can be installed ... [39s/39s] 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [13s/14s] OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [50s/50s] 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] OK
* checking examples with --run-donttest ... [17s/17s] ERROR
Running examples in ‘SMDIC-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotCoocMutex
> ### Title: plotCoocMutex
> ### Aliases: plotCoocMutex
> 
> ### ** Examples
> 
> # get the result of `exp2cell` funtion
> cellmatrix<-GetExampleData("cellmatrix")
> 
> #get the binary mutations matrix,
> mutmatrix<-GetExampleData("mutmatrix")
> 
> # get the result of `mutcorcell` funtion
> mutcell<-GetExampleData("mutcell")
> 
> #perform the function mutcellsummary
> summary<-mutcellsummary(mutcell = mutcell,mutmatrix = mutmatrix,cellmatrix=cellmatrix)
> 
> #dir is the name of mutation annotation file (MAF) format data.
> #It must be an absolute path or the name relatived to the current working directory.
> maf<-"dir"
> #plot the co-occurrence and mutual exclusivity plots for mutation genes which drive immune cells.
> ## No test: 
> plotCoocMutex(maffile = maf,mutcell.summary = summary,cellnumcuoff =0)
-Reading
Error in data.table::fread(file = maf, sep = "\t", stringsAsFactors = FALSE,  : 
  File 'dir' does not exist or is non-readable. getwd()=='/data/blackswan/ripley/R/packages/tests-devel/SMDIC.Rcheck'
Calls: plotCoocMutex -> read.maf -> <Anonymous>
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [25s/25s] 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, 1 NOTE
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/SMDIC.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:57.70, 329.88 + 25.98