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]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
