Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

failed to load GTF file #53

Closed
byb121 opened this issue Mar 20, 2018 · 3 comments
Closed

failed to load GTF file #53

byb121 opened this issue Mar 20, 2018 · 3 comments
Assignees
@nunofonseca

Comments

@byb121
Copy link

byb121 commented Mar 20, 2018

Because of this issue: Rdatatable/data.table#2272

https://github.com/nunofonseca/irap/blob/master/aux/R/irap_utils.R#L1461 will throw an error for large GTF files while running within a Docker container, which has only 64M for /dev/shm by default for "fread" to use to load GTF.

iRAP should probably use the latest version of data.table, which has the fix.
@nunofonseca
Copy link
Owner

Hi,
Which version of iRAP are you using?
Cheers.

@nunofonseca nunofonseca self-assigned this Mar 20, 2018
@byb121
Copy link
Author

byb121 commented Mar 20, 2018

I was on v0.8.5.p8, didn't see the new release. Will have a go later this week.

@nunofonseca
Copy link
Owner

Great, please let me know if you encounter any issues. Cheers.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@nunofonseca nunofonseca

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@nunofonseca @byb121