CRAN Package Check Results for Package caRpools

Last updated on 2018-02-23 00:47:28 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.83 6.19 42.17 48.36 OK --no-examples --no-tests --no-vignettes
r-devel-linux-x86_64-debian-gcc 0.83 5.34 36.16 41.50 OK --no-examples --no-tests --no-vignettes
r-devel-windows-ix86+x86_64 0.83 15.00 54.00 69.00 OK --install=fake
r-patched-linux-x86_64 0.83 2.32 46.52 48.84 OK --no-examples --no-tests --no-vignettes
r-release-linux-x86_64 0.83 2.13 47.62 49.75 OK --no-examples --no-tests --no-vignettes
r-release-windows-ix86+x86_64 0.83 8.00 51.00 59.00 OK --install=fake
r-release-osx-x86_64 0.83 ERROR
r-oldrel-windows-ix86+x86_64 0.83 5.00 54.00 59.00 OK --install=fake
r-oldrel-osx-x86_64 0.83 ERROR

Check Details

Version: 0.83
Check: package dependencies
Result: ERROR
    Packages required but not available: ‘DESeq2’ ‘biomaRt’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

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")
    Error in `rownames<-`(`*tmp*`, value = c("CTRL", "CTRL", "TREAT", "TREAT" :
     duplicate rownames not allowed
    Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
    Execution halted
Flavor: r-oldrel-osx-x86_64

Version: 0.83
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in readLines(con) :
     incomplete final line found on 'CaRpools.Rmd'
    Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", :
     It seems you should call rmarkdown::render() instead of knitr::knit2html() because CaRpools.Rmd appears to be an R Markdown v2 document.
    Quitting from lines 1875-1881 (CaRpools.Rmd)
    Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
    duplicate rownames not allowed
    Execution halted
Flavor: r-oldrel-osx-x86_64