Closed shukwong closed 3 years ago
@shukwong fascinating... r-stringi isn't installed implicitly? it seems to be installed in my plco-analysis
env. adding it is fine w/me, but i'm curious why i'm pulling in a copy and you're not... spells trouble for future issues
not sure why, but now that it's in I am getting a related issue with stringi - trying to update the package and see if it solves the issue...
@cpalmer718 so I am getting the error related to stringi libicui18n.so.64: cannot open shared object file: No such file or directory googling it lead me to doing a manual update.packages() with R and it seems to solve the issue. It's now updated to 1.5.3 from the conda version 1.4.3 but still not sure why it didn't work in the first place
@shukwong so this is a whole chain of dependencies. the first thing: the icu error is known and fixed by pinning icu=58.2 in environment.yaml. as for why it's an issue to begin with: my guess is that the update process you did there has risked breaking SAIGE, which is where a bunch of the R deps come from.
you can proceed as-is for now, but keep an eye out for catastrophic package errors when running SAIGE. if it's broken, try rebuilding the environment from scratch with r-stringr and r-stringi in the environment, along with icu=58.2, and see if that resolves correctly.
i don't understand why r-stringi was absent for you to begin with, i've never had that happen (r-construct.model.matrix should pull it in correctly). i'll try rebuilding on my end and see if the r-construct.model.matrix version update i did this morning somehow broke it.
@shukwong nope, mamba is pulling in r-stringi on its own. i am absolutely flummoxed as to why you didn't end up with r-stringi. is your ~/.condarc different than:
channels:
@cpalmer718 Mine doesn't have r! I think that might be why. Let me rebuild and try it out. Sorry about this could you revert the pull request. Mine currently looks like: channels:
Ah! That'll do it.
I have a question in fact: I feel like... when I look at this repository, it doesn't scream "HERE'S WHERE MY DOCS ARE" lol. do you have any idea how I might lay things out differently to really encourage people to click on the readthedocs link? because there's a section about conda channels in there, but I also feel like... if I just looked at the repo, I'd not necessarily click on it!
maybe I should remove more of the README.md content, to make it clearer that that's not really where people should be looking?
ok all better, except we're technically on alpha.6 now lol. there are still some documentation upgrades in there
Thanks! I think README.md is good as it is, perhaps make it more obvious by instead of "here", use "readthedocs", I would probably be more likely clicking on that :)
excellent idea, will do.
stringi seems to be required by construct.model.matrix