[Bioc-devel] Something about time out errors

[Aimin Yan]

I am submitting a R package to bioconductor. but I got the following
warning and errors when I performed R CMD check.

When I perform R CMD check on my local machines, it works.

Is there a possible way that I can set up DISPLAY environment variable?


Here is the link

http://bioconductor.org/spb_reports/PathwaySplice_buildreport_20170925232327.html

Thank you.

Aimin


OS X 10.11.6 El Capitan/x86_64



* checking R code for possible problems ... OK

* checking Rd files ... WARNING

gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL

problem found in gmtGene2Cat.Rd

* checking Rd metadata ... OK





* checking files in vignettes ... WARNING

Files in the 'vignettes' directory newer than all files in 'inst/doc':

  tutorial.html



> # labeling each node by gene set name

> enmap <- enrichmentMap(res,n=10,fixed = FALSE,similarity.threshold=0.3,

+ label.node.by.index = FALSE)

Warning in fun(libname, pkgname) :

  no display name and no $DISPLAY environment variable

Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :

  [tcl] invalid command name "font".

Calls: enrichmentMap ... .tkplot.convert.font -> <Anonymous> -> tcl ->
.Tcl.objv -> structure

Execution halted

* checking for unstated dependencies in tests ... OK

* checking tests ...

  Running testthat.R ERROR

TIMEOUT: R CMD check exceeded 10mins





linux (Ubuntu 16.04.1 LTS)/x86_64



* checking R code for possible problems ... OK

* checking Rd files ... WARNING

gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL

problem found in gmtGene2Cat.Rd

* checking Rd metadata ... OK





* checking files in vignettes ... WARNING

Files in the 'vignettes' directory newer than all files in 'inst/doc':

  tutorial.html





> # labeling each node by gene set name

> enmap <- enrichmentMap(res,n=10,fixed = FALSE,similarity.threshold=0.3,

+ label.node.by.index = FALSE)

Warning in fun(libname, pkgname) :

  couldn't connect to display "localhost:10.0"

Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :

  [tcl] invalid command name "font".

Calls: enrichmentMap ... .tkplot.convert.font -> <Anonymous> -> tcl ->
.Tcl.objv -> structure

Execution halted

* checking for unstated dependencies in tests ... OK

* checking tests ...







Windows Server 2012 R2 Standard/x64



* checking R code for possible problems ... OK

* checking Rd files ... WARNING

gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL

problem found in gmtGene2Cat.Rd

* checking Rd metadata ... OK





* checking files in vignettes ... WARNING

Files in the 'vignettes' directory newer than all files in 'inst/doc':

  tutorial.html








On Mon, Mar 27, 2017 at 12:22 PM, Aimin Yan <aimin.at.work at gmail.com> wrote:

> I am submitting a R package to bioconductor. but I got time out errors
> when I performed R CMD check.
>
>
> Is there a possible way that I can set up time to allow more time for R
> CMD check? Or I have to use examples that they do not cost large time.
>
>
> Thank you for your help
>
> Aimin
>

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