• using R version 4.1.1 Patched (2021-09-05 r80862)
• using platform: aarch64-apple-darwin20 (64-bit)
• using session charset: UTF-8
• checking for file ‘caRpools/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘caRpools’ version ‘0.83’
• 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 ‘caRpools’ can be installed ... [3s/3s] 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 loading without being on the library search path ... 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 ... [4s/4s] OK
• checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [13s/14s] ERROR
  Running examples in ‘caRpools-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: carpools.hit.overview
  > ### Title: Analysis: Analysis of pooled CRISPR screening data using a
  > ### Wilcoxon Test
  > ### Aliases: carpools.hit.overview
  > ### Keywords: ~Analysis
  >
  > ### ** Examples
  >
  > data(caRpools)
  >
  > data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
  + treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
  + normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
  + control.picks=NULL)
  >
  >
  > data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
  + treated.list = list(TREAT1,TREAT2), namecolumn=1,
  + fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
  + sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
  + fitType="parametric")
  converting counts to integer mode
  Warning in DESeqDataSet(se, design = design, ignoreRank) :
    some variables in design formula are characters, converting to factors
  gene-wise dispersion estimates
  mean-dispersion relationship
  final dispersion estimates
  Warning in DESeqDataSet(se, design = design, ignoreRank) :
    some variables in design formula are characters, converting to factors
  gene-wise dispersion estimates
  mean-dispersion relationship
  final dispersion estimates
  >
  > data.mageck = stat.mageck(untreated.list = list(CONTROL1, CONTROL2),
  + treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
  + norm.fun="median", extractpattern=expression("^(.+?)(_.+)"),
  + mageckfolder=NULL, sort.criteria="neg", adjust.method="fdr", filename = "TEST" , fdr.pval = 0.05)
  sh: mageck: command not found
  Warning in system(mageckstring) : error in running command
  Warning in file(file, "rt") :
    cannot open file 'TEST.gene_summary.txt': No such file or directory
  Error in file(file, "rt") : cannot open the connection
  Calls: stat.mageck -> load.file -> read.table -> file
  Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [0s/0s] NONE
    ‘CaRpools.Rmd’ using ‘UTF-8’... [0s/0s] OK
• checking re-building of vignette outputs ... [33s/75s] WARNING
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘CaRpools.Rmd’ using rmarkdown
  converting counts to integer mode
  Warning in DESeqDataSet(se, design = design, ignoreRank) :
    some variables in design formula are characters, converting to factors
  gene-wise dispersion estimates
  mean-dispersion relationship
  final dispersion estimates
  Warning in DESeqDataSet(se, design = design, ignoreRank) :
    some variables in design formula are characters, converting to factors
  gene-wise dispersion estimates
  mean-dispersion relationship
  final dispersion estimates
  sh: mageck: command not found
  Quitting from lines 1956-1959 (CaRpools.Rmd)
  Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
  cannot open the connection
  --- failed re-building ‘CaRpools.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘CaRpools.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted
  
• checking PDF version of manual ... OK
• DONE
  Status: 1 ERROR, 1 WARNING
• using check arguments '--no-clean-on-error '