- using R version 4.2.0 (2022-04-22)
- using platform: x86_64-apple-darwin17.0 (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 ... [4s/4s] 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 ... 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 ... [6s/6s] OK
- checking Rd files ... [1s/1s] 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 ... [16s/16s] 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 ... [42s/66s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
sh: mageck: command not found
Quitting from lines 1956-1959 [HT-method-MAGeCK] (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: 2 ERRORs
- using check arguments '--no-clean-on-error '