[Bioc-devel] error about Display environment/ biomart for the build of my package

[Dan Tenenbaum]

----- Original Message -----
> From: "Tiphaine Martin" <tiphaine.martin at kcl.ac.uk>
> To: bioc-devel at r-project.org
> Sent: Thursday, October 16, 2014 10:56:48 AM
> Subject: [Bioc-devel] error about Display environment/ biomart for the build	of my package
> 
> Hi,
> 
> 
> I have a type of warning message by bioconductor package tracker on
> Linux and Mac that I don't have when I did that  on my computers. So
> I don't know to correct or to check it on my computers. I think that
> it is related to the package trackViewer, which need to have tcl/tk
> package.
> 
> 
> Error on Mac OS (check and BiocCheck steps)
> 
> ** testing if installed package can be loaded
> Warning in fun(libname, pkgname) :
>   no display name and no $DISPLAY environment variable
> 
> Error on Linus (BiocCheck step)
> 
> * Installing package...
> Warning in fun(libname, pkgname) :
>   no DISPLAY variable so Tk is not available
> 
> 

This package builder is _supposed_ to run under X11 (using Xvfb, the virtual frame buffer); the message you are seeing indicates that maybe this is not working properly. Anyway, as I look at 

http://bioconductor.org/spb_reports/coMET_0.99.2_buildreport_20141016031739.html#oaxaca_check_anchor

I see that the essage you see is just a warning that comes up when BioCheck tries to install the package, and that warning does not actually increment your RECOMMENDED count. So in other words, if you can fix the R CMD check warnings and the other BiocCheck issues, then you will get a green box for the "CHECK" phase.

> I have an error message on window to connect to Biomart. In my
> package, I create Gviz's annotation tracks that connect to UCSC and
> ENSEMBL via Biomart connection.
> 
> This connection worked on Linux and Mac. So I would like to know if
> other people observed the biomart connection more difficulty under
> windows than under Mac and Linux or if it is just unlucky event.
> 

Biomart is somewhat flaky and almost every day in the nightly build report there are packages that fail (usually on a single platform) because biomart couldn't be reached at that moment in time. The next time you build the package, this will probably not occur.

Dan


> 
> Regards,
> 
> Tiphaine
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>