[Bioc-devel] Something about time out errors

[Hervé Pagès]

Hi Aimin,

Yes, this seems to be a problem on our side. It seems to happen
intermittently on the Mac builder. We'll take a look at it.

Note that the link you provided is to a build that was triggered 4 days
ago. As you can see on the issue page for your submission, 6 more
builds have been triggered since then and none of them has this problem.

If you see this problem again in the future, as Lori said, please
ignore it.

Thanks,
H.


On 09/29/2017 12:45 PM, Shepherd, Lori wrote:
> 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
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_PathwaySplice-5Fbuildreport-5F20170925232327.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=T9VcuKoIUH0EOVHTE1RBvmKHdiAnPL2PObqOxtT-5iw&s=KBtlWH67KrvXeU4Cx8ainxufjL4HBSsvdG2ZSKSMvgM&e=
>
> 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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