Closed chilampoon closed 11 months ago
for glmmSeq. i solved all those. i will push the changes in 3 hours
@stemangiola sounds good. ^in that commit I hope to avoid install errors in workflow tests, lets see..
@stemangiola sounds good. ^in that commit I hope to avoid install errors in workflow tests, lets see..
This glmmSeq PR should fix things up
@stemangiola There's still this warning in workflow CMD check
❯ checking S3 generic/method consistency ... WARNING
Warning: Warning: declared S3 method 'filter.tidybulk' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
There is one filter.tidybulk in R/dplyr-methods.R and one in dev/dplyr-master-methods.R
.
I added a .Rinsignore
to ignore files in dev/ but it doesn't work. Now I deleted the master methods script to see if this is the source of waning...
Here are the possibilities listed by chatgpt:
I don't get this warning in local check so need to push commits here...
@chilampoon I believe @noriakis solved the same problem in tidySummarizedExperiment
. @noriakis could you please give advise?
Thank you for the mention! The warning in the method lookup could be solved by moving dplyr
to Depends from Imports (https://stat.ethz.ch/pipermail/r-devel/2014-June/069247.html). Also, it may come from R versioning, as I can pass R CMD CHECK without errors and warnings in R 4.3.1 (and Bioc 3.17) based on the commit. So updating check-bioc.yml
to check in R >= 4.3 would also solve the warnings without moving dplyr
to Depends.
Thank you for the mention! The warning in the method lookup could be solved by moving
dplyr
to Depends from Imports (https://stat.ethz.ch/pipermail/r-devel/2014-June/069247.html). Also, it may come from R versioning, as I can pass R CMD CHECK without errors and warnings in R 4.3.1 (and Bioc 3.17) based on the commit. So updatingcheck-bioc.yml
to check in R >= 4.3 would also solve the warnings without movingdplyr
to Depends.
Thanks! lets use the same github action as tidySingleCellExperiment and tidySummarizedExperiment then
@stemangiola there are always new errors/warnings show up after fixing something... I think I better move on clearing up other docs rather than focusing on the RCMDcheck results...
@stemangiola there are always new errors/warnings show up after fixing something... I think I better move on clearing up other docs rather than focusing on the RCMDcheck results...
Yes there are few errors and warnings. I think they are easy to fix, but if you have something in mind feel free to suggest. I think it is better that you run github action on your master branch (so you don't need authorisation) and when they are warning free you can push to the main master.
Yes tidybulk needs some work as it is the biggest and oldest repository of tidy transcriptomics.
@stemangiola there are always new errors/warnings show up after fixing something... I think I better move on clearing up other docs rather than focusing on the RCMDcheck results...
Yes there are few errors and warnings. I think they are easy to fix, but if you have something in mind feel free to suggest. I think it is better that you run github action on your master branch (so you don't need authorisation) and when they are warning free you can push to the main master.
Yes tidybulk needs some work as it is the biggest and oldest repository of tidy transcriptomics.
Sounds good, close this PR for now. Thanks @noriakis and @stemangiola !
Hi @chilampoon, just letting you know I am making some changes from commit #1a0c713 so that we don't duplicate our efforts.
I am hoping to get this passing BiocCheck and R CMD CHECK (currently fixing existing issue in tidybulk as far as I can tell, not related to your improvements) in the next few days so that we can merge before too many changes are made to the main branch.
You can see my changes here https://github.com/william-hutchison/tidybulk/tree/chilampoon-improve-documentation . Let me know if you have any suggestions and thanks for your work!
Hi @william-hutchison looks good to me! Please keep me posted when you finish the updates
dplyr_methods.R
andtidyr_methods.R
and some infuncitons(_se).R
andmethods(_se).R
testthat
due to different adj pvalues . I am not sure if it's because of using a newer version of TMB packageresolve warnings:
TBD: a lot of notes
(right now try to do CI tests to see if any issues pop up)