I've added the newer actions here so you can test against R 4.1 & Bioc 3.13

FYI the Mac error here is due to homebrew & looks like we have to just wait for a fix, reported here r-lib/actions#280
The Linux & Windows errors are tidybulk-related I think.

The Linux & Windows errors are tidybulk-related I think.

Thanks. Sorry I have not extensive tests of tidybulk for SE, I am a bit overwhelmed at the moment.

The tests would have avoided this whole wrong reduce dimension behaviour.

The Linux & Windows errors are tidybulk-related I think.

Thanks. Sorry I have not extensive tests of tidybulk for SE, I am a bit overwhelmed at the moment.

The tests would have avoided this whole wrong reduce dimension behaviour.

I have fixed few things, now vignette is failing because of the introduction of feature. Is tidybulk being checked against 3_13?

Thanks. Sorry I have not extensive tests of tidybulk for SE, I am a bit overwhelmed at the moment.

The tests would have avoided this whole wrong reduce dimension behaviour.

No worries, totally understand!

I have fixed few things, now vignette is failing because of the introduction of feature. Is tidybulk being checked against 3_13?

Yes definitely being checked against 3.13, can see in the actions here

I think it's because it's using tidySumarizedExperiment version 1.1.3 and feature is in 1.1.4?

As it's pulling from Bioc devel which only has 1.1.3
https://www.bioconductor.org/packages/devel/bioc/html/tidySummarizedExperiment.html

I think it's because it's using tidySumarizedExperiment version 1.1.3 and feature is in 1.1.4?

True. I pushed the version 1.1.4 couple of days ago. Anyway now I pushed the 1.1.5. It should be online in couple of days.

Getting there!

I think it's because it's using tidySumarizedExperiment version 1.1.3 and feature is in 1.1.4?

True. I pushed the version 1.1.4 couple of days ago. Anyway now I pushed the 1.1.5. It should be online in couple of days.

Getting there!

In the website

https://www.bioconductor.org/packages/devel/bioc/html/tidySummarizedExperiment.html

I can see

That's what I see too 1.1.3 in devel but we need 1.1.4 or 1.1.5 to appear there. Did you push to bioconductor repo? Their build report from Monday is showing it's still 1.1.3 https://www.bioconductor.org/checkResults/3.13/bioc-LATEST/#T

Did you push to bioconductor repo?

I did for 1.1.4

1.1.5 is there now https://www.bioconductor.org/packages/devel/bioc/html/tidySummarizedExperiment.html
so I’ve restarted the jobs here

1.1.5 is there now https://www.bioconductor.org/packages/devel/bioc/html/tidySummarizedExperiment.html
so I’ve restarted the jobs here

Now locally checks pass, but here I get

Warning in tools::parse_Rd(infile) :
  /tmp/RtmpEjiKR1/filec9e04525abd5/tidybulk/man/keep_abundant-methods.Rd:105: unknown macro '\lifecycle'
    * ERROR: Avoid references to external hosting platforms
      Found in files:
        functions.R (line 2434, column 50)

I can't understand why, I have redone the lifecycle import..

Warning in tools::parse_Rd(infile) :
/tmp/RtmpEjiKR1/filec9e04525abd5/tidybulk/man/keep_abundant-methods.Rd:105: unknown macro '\lifecycle'
* ERROR: Avoid references to external hosting platforms
Found in files:
functions.R (line 2434, column 50)
I can't understand why, I have redone the lifecycle import..

It's not due to lifecycle that's just a warning. It was this line 2434

if("EPIC" %in% .packages() %>% not) stop("tidybulk says: Please attach the apckage EPIC manually (i.e. library(EPIC)). This is because EPIC is only available on GitHub and it is not possible to seemlessy make EPIC part of the dependencies.")

I get the error locally with BiocCheck 1.27.9 (same version as used in the actions here). Seems to be mention of Github triggers the error from this new check Bioconductor/BiocCheck@60cef89#diff-6cd987920443d42098a4963d43b2e0efec9fd16f9198d66705e6d95094e3b87a

I've edited that line to remove the mention of Github to see if it passes here.

Yeeeee

Woo hoo 🎉finally 😅