• using R version 4.3.0 beta (2023-04-10 r84212)
• using platform: aarch64-apple-darwin20 (64-bit)
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 12.2.0
• running under: macOS Big Sur 11.6.7
• 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 See the install log for details.
• 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 ... [0s/0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/0s] 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/5s] 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 ... [0s/0s] OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [11s/13s] 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 ... [26s/39s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘CaRpools.Rmd’ using rmarkdown 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 ... [4s/5s] OK
• DONE Status: 2 ERRORs
• using check arguments '--no-clean-on-error '