Table not instantiated error about pdv HOT 13 CLOSED

Can you share the mzML and the pepXML files with us?

from pdv.

Please reopen this issue if you still have this problem.

from pdv.

I have the problem. I also imported MSFragger (through FragPipe) identification data, and it worked for a little while, until I clicked too much around in the identification list.

from pdv.

One of those error dialogs did say the same message as @proteostasis reports:

Table not instantiated
java.lang.NullPointerException

but that window just disappeared for me (or turned gray), when I tried to take the screenshot.

from pdv.

Thank you for letting us know. Could you please share the data you imported with us? I will take a look.

from pdv.

You can find the files here:
https://nextcloud.sdu.dk/index.php/s/AB88EE3NjPfaTxm

The mzML file is 400 MB. The ZIP file contains the other 2 files in the folder and is 130 MB.

The problem tends to happen, when I start to scroll down in the PSM table. I'm on Ubuntu 18.04 and OpenJDK 1.8.0_242-8u242-b08 (Java 8).

from pdv.

Thanks. I will take a look soon.

from pdv.

Hi there,

Did you use the latest version of PDV? It works well on my side. I did found one bug by testing your data. But it shouldn't generate this problem. I will test it again on Ubuntu later.

Kai

from pdv.

I just tried on my laptop, which is running Ubuntu 20.04 and has OpenJDK 11.0.11. It produces the same problem immediately.

from pdv.

... and I have only been using PDV 1.7.3, which as far as I can see is the newest release.

from pdv.

Thank you for letting me know. I will try it on Ubuntu and release a new version next week.

from pdv.

@phusen, could you please try the new version of PDV (v1.7.4)? I just tested it on a Ubuntu 18.04.5 LTS system with openjdk version "11.0.11" 2021-04-20, it works well as shown below. When I scrolled down in the PSM table, I didn't get any error.

from pdv.

At least from my quick testing, it seems to work reliably now. I didn't reproduce the problem, despite scrolling and clicking around a lot. Before, it would happen almost immediately.

Thanks a lot for the effort!

from pdv.