Flashier compatibility

[brandon-wenz]

Hi,
I am trying to use the eQTL workflow but am running into an issue that I haven't seen mentioned. When running the mashr_flashr_workflow.ipynb I am getting an error :
"INFO: Running flash: Perform FLASH analysis with non-negative factor constraint (time estimate: 20min)
ERROR: flash (id=e5206fa16d7663ef) returns an error.
INFO: Running flash_nonneg: Perform FLASH analysis with non-negative factor constraint (time estimate: 20min)
ERROR: flash_nonneg (id=cbc617a36edccad1) returns an error."
In the stderr file it says : "Error: 'flash.init' is not an exported object from 'namespace:flashier'". I belive this is because it appears the flashier package has changed their function names (https://github.com/willwerscheid/flashier) so perhaps flash.init now needs to be flash_init. I think there are a few other examples that likely have changed. If this is indeed an issue, hopefully it can help someone else who is having an issue. I have been trying to figure out a workaround, but have been unsuccessful so far.
Thanks!

[stephens999]

One solution would be to install an older version of flashier, from before the name changes.

[Similar issues have been encountered by other users with other packages breaking with the flashier changes. Perhaps @pcarbo has comments or pointers.]

[pcarbo]

@brandon-wenz This should be fixed now with the latest versions of flashier and mashr available on GitHub.

[brandon-wenz]

Thank you both very much! This fixed the issue. I did attempt to install an older version of flashier, but perhaps due to my inexperience with these things, was unable to figure out how to install a previous version from github. Thanks!