[Bioc-devel] BiocCheck error

[Aimin Yan]

Martin,

Thank you. yes, you are right.
Now it works, I also changed outputs to tempfile() or tempdir().

Aimin


On Tue, Apr 10, 2018 at 6:07 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

> 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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>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
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