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-boun...@r-project.org> on behalf of Aimin Yan
<aimin.at.w...@gmail.com>
Sent: Wednesday, September 27, 2017 12:49:13 PM
To: bioc-devel@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.w...@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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