mm10 is broken

Question

mm10 is broken

Closed this issue 6 years ago · 10 comments

it's giving this error:

::Loading cache::       /mnt/q/shefflab/LOLAweb/databases//LOLACore/mm10/encodeTFBSmm10/encodeTFBSmm10.RData
Timing stopped at: 4.916 0.044 4.984
Warning: Error in combine_CompressedList_objects: the objects to combine must be CompressedList objects (or NULLs)
Stack trace (innermost first):
    96: combine_CompressedList_objects
    95: .local
    94: c
    93: c
    92: readRegionGRL
    91: loadRegionDB
    90: system.time [/srv/shiny-server/LOLAweb/apps/LOLAweb/app.R#578]
    89: eventReactiveHandler [/srv/shiny-server/LOLAweb/apps/LOLAweb/app.R#509]
    69: rawdat_nocache
    68: withCallingHandlers [/srv/shiny-server/LOLAweb/apps/LOLAweb/app.R#385]
    67: observeEventHandler [/srv/shiny-server/LOLAweb/apps/LOLAweb/app.R#382]
     1: runApp
Warning: Error in combine_CompressedList_objects: the objects to combine must be CompressedList objects (or NULLs)
Stack trace (innermost first):
    61: <Anonymous>
    60: stop
    59: rawdat_nocache
    58: observerFunc [/srv/shiny-server/LOLAweb/apps/LOLAweb/app.R#753]
     1: runApp

Answer 1 · 2018-07-06T13:37:06.000Z

Something wrong with that cache, I think...

docker run --rm -it --volume /mnt/q:/mnt/q databio/lolaweb bash
R
LOLA::loadRegionDB("/mnt/q/shefflab/LOLAweb/databases//LOLACore/mm10/")"

Answer 2 · 2018-07-06T13:41:12.000Z

I am trying regenerating the cache now.

Answer 3 · 2018-07-06T13:47:10.000Z

that didn't work. it may be a LOLA version thing. can we try updating the dev container to the latest R/bioconductor/LOLA version?

Answer 4 · 2018-07-06T13:50:31.000Z

turns out it's not a LOLA version problem, but could be a GenomicRanges version problem. I still think we should update...

Answer 5 · 2018-07-06T15:22:17.000Z

ok yeah i think the shinyBase container image we are pulling should include the bioconductor (not github) version of LOLA:

https://github.com/databio/shinyBase/blob/master/Dockerfile#L29

that gets pulled in via the LOLAweb dockerfile ... but i can't remember if that base image gets rebuilt automatically? every time we push a change to databio/shinyBase ? manually?

@nmagee is going to get sick of explaining this to me :)

Answer 6 · 2018-07-06T15:24:33.000Z

it only gets rebuilt if we push a change to databio/shinyBase or trigger it manually.

Answer 7 · 2018-07-06T20:17:09.000Z

Ok, I rebuilt it locally and pushed changes -- can we trigger a re-deploy of the containers @nmagee to see if this solves the problem?

Answer 8 · 2018-07-06T23:30:46.000Z

Hey, just getting home and seeing this message. Yes I’ll go ahead and do a new pull and redeploy.

Answer 9 · 2018-07-06T23:58:05.000Z

Since you rebuilt the shinyBase container and pushed it up to Docker Hub, I just went to the TravisCI page for LOLAweb and triggered the rebuild there. That actually sends an SQS message that will spawn them out onto the servers in a seamless way. I’m seeing the new Dev containers up and running there now. Can one of you guys verify that your fix is in place and working okay?

Answer 10 · 2018-07-07T12:20:24.000Z

Yes, that worked! So, turns out I was right, it was probably some kind GRanges version issue. it's working now on mm10.

@nmagee thanks for redeploy -- at some point can you write down some brief instructions or a link somewhere so that in the future I don't have to bother you to do that? I forgot we were using travis for those builds and that was the way to rebuild it...