[Bioc-devel] Something about time out errors

[Shepherd, Lori]

Thank you for your concern.  There is some conflict on our system that we will look into further. For now, you can ignore this ERROR on mac - the reviewer of your package is aware.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Aimin Yan <aimin.at.work at gmail.com>
Sent: Wednesday, September 27, 2017 12:49:13 PM
To: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Something about time out errors

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
>

        [[alternative HTML version deleted]]

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


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.
	[[alternative HTML version deleted]]