Last updated on 2017-09-26 01:47:11.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.83 | 1.52 | 29.04 | 30.56 | OK | --no-examples --no-tests --no-vignettes |
| r-devel-linux-x86_64-debian-gcc | 0.83 | 1.40 | 28.83 | 30.23 | OK | --no-examples --no-tests --no-vignettes |
| r-devel-windows-ix86+x86_64 | 0.83 | 4.00 | 57.00 | 61.00 | OK | --install=fake |
| r-patched-linux-x86_64 | 0.83 | 1.58 | 29.39 | 30.97 | OK | --no-examples --no-tests --no-vignettes |
| r-release-linux-x86_64 | 0.83 | 1.49 | 29.60 | 31.09 | OK | --no-examples --no-tests --no-vignettes |
| r-release-windows-ix86+x86_64 | 0.83 | 5.00 | 64.00 | 69.00 | OK | --install=fake |
| r-release-osx-x86_64 | 0.83 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 0.83 | 6.00 | 53.00 | 59.00 | OK | --install=fake |
| r-oldrel-osx-x86_64 | 0.83 | ERROR |
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