[Bioc-devel] BiocCheck error

[Martin Morgan]

Hi Aimin -- the problem is that your vignette has two VignetteEngine 
commands in it

PathwaySplice/vignettes master$ grep VignetteEngine *
tutorial.Rmd:  %\VignetteEngine{knitr::rmarkdown}
tutorial.Rmd:  %\VignetteEngine{knitr::knitr}

Also, please avoid writing to files in the user system, replace 
'C:/temp' with tempfile() or dir = tempfile(); dir.create(dir) in code 
like the following

PathwaySplice master$ grep -r "C:/" *
man/runPathwaySplice.Rd: 
output.file='C:/temp/test.csv')
man/runPathwaySplice.Rd: 
output.file='C:/temp/test.csv')
man/enrichmentMap.Rd:                      label.node.by.index = TRUE, 
output.file.dir='C:/temp')
man/enrichmentMap.Rd:                      label.node.by.index = FALSE, 
output.file.dir='C:/temp')}
man/compareResults.Rd:compareResults(20, res.adj, res.unadj, 
gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')
R/Run_pathwaysplice.R:#' 
output.file='C:/temp/test.csv')
R/Run_pathwaysplice.R:#' 
output.file='C:/temp/test.csv')
R/Run_pathwaysplice.R:#'                       label.node.by.index = 
TRUE, output.file.dir='C:/temp')
R/Run_pathwaysplice.R:#'                       label.node.by.index = 
FALSE, output.file.dir='C:/temp')}
R/Run_pathwaysplice.R:#' compareResults(20, res.adj, res.unadj, 
gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')

Martin

On 04/10/2018 04:39 PM, Aimin Yan wrote:
> I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed
> without errors and warnings.
> 
> However I get the following error when I use "R CMD BiocCheck
> PathwaySplice_1.3.0.tar.gz"
> 
> R CMD BiocCheck PathwaySplice_1.3.0.tar.gz
> 
> This is BiocCheck version 1.15.8. BiocCheck is a work in progress.
> 
> Output and severity of issues may change. Installing package...
> 
> * Checking for version number mismatch...
> 
> * Checking if other packages can import this one...
> 
> * Checking to see if we understand object initialization...
> 
>      * NOTE: Consider clarifying how 12 object(s) are initialized. Maybe
> 
>        they are part of a data set loaded with data(), or perhaps part
> 
>        of an object referenced in with() or within().
> 
>      object (function)
> 
>        winMenuAddItem (.onAttach)
> 
>        ggplot (compareResults2)
> 
>        aes (compareResults2)
> 
>        random_sampling_200k (compareResults2)
> 
>        PValue (compareResults2)
> 
>        PathwaySplice (compareResults2)
> 
>        geom_point (compareResults2)
> 
>        geom_smooth (compareResults2)
> 
>        labs (compareResults2)
> 
>        scale_colour_manual (compareResults2)
> 
>        scale_shape_manual (compareResults2)
> 
>        get.col.scale (netplot)
> 
> * Checking vignette directory...
> 
>      This is a software package
> 
> Error in vapply(vigdircontents, vigHelper, logical(1), builder = desc) :
> 
>    values must be length 1,
> 
>   but FUN(X[[1]]) result is length 2
> 
> Calls: <Anonymous> ... BiocCheck -> checkVignetteDir -> checkVigBuilder ->
> vapply
> 
> Execution halted
> 
> 
> 
> Any idea about this?
> 
> 
> Here is my sessionInfo()
> 
> https://gist.github.com/aiminy/764718da9b9eeedd6f5eea196ce956b4
> 
> Thank you,
> 
> Aimin
> 
> 	[[alternative HTML version deleted]]
> 
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