Skip to content

[Bioc-devel] BiocCheck error

3 messages · Aimin Yan, Martin Morgan

Original
Aimin Yan
# 
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
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:
This email message may contain legally privileged and/or...{{dropped:2}}
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: