[Bioc-devel] BiocCheck error

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]]

This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited.  If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.