CRAN Package Check Results for Maintainer ‘Jan Winter <jan.winter at dkfz-heidelberg.de>’

Last updated on 2022-04-24 03:52:56 CEST.

Package	ERROR	OK
caRpools	4	6

Package caRpools

Current CRAN status: ERROR: 4, OK: 6

Version: 0.83
Check: examples
Result: 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
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 0.83
Check: re-building of vignette outputs
Result: WARN
    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
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64

Version: 0.83
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘CaRpools.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    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
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64