Closed dpalachan closed 2 years ago
jrobinso
commented
2 years ago Sorry I don't have any insight as I can't reproduce this on MacOS, and don't have a Linux box. Could you try the "development snapshot" build available here? https://software.broadinstitute.org/software/igv/download_snapshot
jrobinso
commented
2 years ago BTW re the "SEVERE" error that is just a logging mis-categorization, this should be an "INFO" message. I would be surprised if logging could cause the issue you see, and it does not on MacOS.
dpalachan
commented
2 years ago Thank you for the swift reaction, I appreciate it! I tried the development snapshot and it didn't give this warning, but it also didn't work. I still get a blank yellow-ish window.
I tried the stable version in an Ubuntu VM and the message appeared on the console, but I had no trouble with it and the IGV window appeared normally and everything worked. So, I guess I'm missing some visualization libraries for CentOS. How could I go about debugging which dependencies I'm missing? Or is there a list of dependencies somewhere? I couldn't find anything with a quick Google search. Thank you in advance.
jrobinso
commented
2 years ago I really couldn't say, we don't do anything special outside of normal Java graphics. If I find anything update this ticket.
On Tue, Dec 28, 2021 at 1:58 AM dpalachan @.***> wrote:
Thank you for the swift reaction, I appreciate it! I tried the development snapshot and it didn't give this warning, but it also didn't work. I still get a blank yellow-ish window.
I tried the stable version in an Ubuntu VM and the message appeared on the console, but I had no trouble with it and the IGV window appeared normally and everything worked. So, I guess I'm missing some visualization libraries for CentOS. How could I go about debugging which dependencies I'm missing? Or is there a list of dependencies somewhere? I couldn't find anything with a quick Google search. Thank you in advance.
— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1078#issuecomment-1001975916, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHD2HBEVS5RFBNW7FFS3XTUTGC3DANCNFSM5K2GS5BA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
You are receiving this because you commented.Message ID: @.***>
dpalachan
commented
2 years ago OK, clear. I would actually close the ticket. On Ubuntu, I got this message on the console, but IGV still worked like a charm. So, my graphics issues on CentOS must be related to missing libraries and not to this message.
davideby
commented
2 years ago Hi @dpalachan,
You mentioned IGV coming up as a yellow screen on CentOS. You might want to have a look at issue 1036 as it sounds like a similar problem.
Sorry, just seeing this after the holidays. Hope it helps.
I tried this with both the bundled Java version and the system version on Linux (Centos 7, openjdk 11.0.13)
This may relate to #1076 , but the solution was not documented, so I'd like to ask for some help on this one.
When I run {{./igv.sh}}, I get:
When I run this with the bundled Java version of IGV, the only difference I get in the output is the Java Vendor, which makes sense.
This results in an empty IGV window with a yellow-ish background and nothing else. The only thing possible is to close the window which displays the "Shutting down" message on the console output.