Skip to content

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

2 messages · Martin, Tiphaine, Dan Tenenbaum

Original
Martin, Tiphaine
# 
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


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.


Regards,

Tiphaine
Dan Tenenbaum
# 
----- Original Message -----
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.
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