`degCovariates`: breaking change in dplyr filter code

[mjsteinbaugh]

Hi @lpantano , hope you're doing well!

I'm seeing an error in bcbioRNASeq::plotPCACovariates() due to a breaking change in DEGreport::degCovariates(). Here's the traceback:

library(bcbioRNASeq)
data(bcb)
plotPCACovariates(bcb)

> packageVersion("DEGreport")
[1] ‘1.24.1’
> packageVersion("bcbioRNAseq")
[1] ‘0.3.33’

running pca and calculating correlations for:
un-scaled  data in pca;
pve >= 5%;
kendall cor

Error: Problem with `filter()` input `..1`.
x object 'term' not found
ℹ Input `..1` is `!grepl("Intercept", term)`.
Backtrace:
     █
  1. ├─acidgenerics::plotPCACovariates(bcb)
  2. └─bcbioRNASeq::plotPCACovariates(bcb)
  3.   └─bcbioRNASeq:::.local(object, ...)
  4.     ├─base::withCallingHandlers(...) R/plotPCACovariates-methods.R:85:8
  5.     └─DEGreport::degCovariates(...)
  6.       └─DEGreport:::.reduce_covariates(ma, samplepcvals, method)
  7.         └─`%>%`(...)
  8.           ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  9.           └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
 10.             └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
 11.               └─DEGreport:::`_fseq`(`_lhs`)
 12.                 └─magrittr::freduce(value, `_function_list`)
 13.                   ├─base::withVisible(function_list[[k]](value))
 14.                   └─function_list[[k]](value)
 15.                     ├─dplyr::filter(., !grepl("Intercept", !!!sym("term")))
 16.                     └─dplyr:::filter.data.frame(., !grepl("Intercept", !!!sym("term")))
 17.                       └─dplyr:::filter_rows(.data, ...)
 18.                         └─base::tryCatch(...)
 19.                           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 20.                             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 21.                               └─value[[3L]](cond)
 22.                                 └─dplyr:::stop_dplyr(...)

[lpantano]

Hey, Can you let me know the version of dplyr? In Bioconductor seems all alright: https://bioconductor.org/packages/release/bioc/html/DEGreport.html

[mjsteinbaugh]

I have dplyr 1.0.0 installed on my machines. The error will reproduce in my acidgenomics/r-bcbiornaseq Docker image if you want to check it out.

[lpantano]

Hi,

I may have found the error. I push to master, if you can test it and let me know, it would be great.

CC @vbarrera

[mjsteinbaugh]

Will do, thanks @lpantano !

[lpantano]

I think this is fixed now in the latest commit. I will wait for you to test. thanks

[vbarrera]

Working for me.

Thank you very much.