Help on errors in UCSC genome browser mirror
Kun Sun
Dear Madam/Sir,
Thanks very much for your great genome browser and the kindness of allowing us to mirror it.
I have successfully built a mirror which functions well in most scenarios, but I have encounters
several issues that I would like to seek your help:
In hg38, you browser could visualization the gene expression in GTEx project as following:
But I could not see this figure in my mirror. I have checked the logs, and there are errors:
Error in .External2(C_X11, paste0("png::", filename), g$width, g$height,
unable to start device PNG,
Calls: png,
In addition: Warning message:,
In png(file = outFile, width = 1070, height = 600) :
unable to open connection to X11 display '',
Execution halted
I have searched such errors for a while, and it seems that this is an error from R software.
I wonder does hgc program calls R to do this plotting? Indeed, I can see some R programs
under hgcData directory. But when I call R myself, I find that there is no such problem and
my R do support png. And all the other figures in the genome browser are correct. Could you
please tell me what happened and how could I fix this issue?
Another thing is that, I have downloaded the “encodeCcreCombined.bb” and table data of
“encodeCcreCombined” via the table browser. I have loaded the table data into mysql and
put the “.bb” file in the correct directory, but my mirror still does not show this track. This track
is different from others (e.g., refGene) and could you please tell me how could I load this
kind of tracks (and other encode3 tracks are similar) into the mirror?
Thanks very much and looking forward to hearing from you soon.
Best Regards,
Kun Sun
Ph.D. (CUHK) B.Sci. (USTC)
Assistant Professor/Investigator,
Institute of Cancer Research,
Shenzhen Bay Laboratory,
E-mail: sun...@szbl.ac.cn
Tel: +86-0755-2641-9310
Website: https://hellosunking.github.io/
Address: Rm B505, No. 9 Duxue Road,
Nanshan District, Shenzhen, China
Daniel Schmelter
Hello Kun,
Thank you for your questions and for reporting that unexpected behavior with GTEx on your GBiB or GBiC.
The issue with GTEx appears to be a bug. This bug has been reported and will be investigated by our engineers. Our program does call R for the plotting and that error appears to be associated with an inability to detect framesize. A search returns the idea that you may be able to set this manually as suggested here:
https://unix.stackexchange.com/questions/31283/error-in-r-unable-to-open-connection-to-x11
It will take a bit more time to come to a systemic diagnosis and solution. In the meantime, similar functionality can be obtained by clicking "View in GTEx Portal". We apologize for any inconvenience this may have caused and thank you again for reporting that bug.
In mirroring Encode3 data, if you are connected to the internet and your mirror is updated, the cCRE track should be displaying. This may be something an update would help with. Could you please tell us a little more about your mirror, whether it is a GBiB, GBiC, or custom installation? Is it operating mostly offline and with downloaded data or downloading data on-the-fly? If it is an offline GBiB, you can download and mirror the track with the mirror tracks download UI referenced here:
https://genome.ucsc.edu/goldenpath/help/gbib.html#GbibMirroring
You may also want to update your mirror manually or turn on auto-updates:
https://genome.ucsc.edu/goldenpath/help/gbib.html#UpdatingGbib
If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Warm wishes,
Daniel Schmelter
UCSC Genomics Institute
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