CRAN Check Failure for Upcoming broom Release

[simonpcouch]

Hi there! The broom dev team just ran reverse dependency checks on the upcoming broom 0.7.0 release and found new errors/test failures for the CRAN version of this package. I've pasted the results below, which result from changes to the default conf.int argument in tidy.coxph.

Newly broken

• checking examples ... ERROR

  Running examples in ‘survminer-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: ggforest
  > ### Title: Forest Plot for Cox Proportional Hazards Model
  > ### Aliases: ggforest
  > 
  > ### ** Examples
  > 
  > require("survival")
  Loading required package: survival
  > model <- coxph( Surv(time, status) ~ sex + rx + adhere,
  +                 data = colon )
  > ggforest(model)
  Warning in .get_data(model, data = data) :
    The `data` argument is not provided. Data will be extracted from model fit.
  Error in `[.data.frame`(cbind(allTermsDF, coef[inds, ]), , c("var", "level",  : 
    undefined columns selected
  Calls: ggforest -> [ -> [.data.frame
  Execution halted
  

In both

• checking installed package size ... NOTE

    installed size is  5.2Mb
    sub-directories of 1Mb or more:
      doc   4.8Mb
  

The changes in this PR correct the new errors by explicitly setting conf.int = TRUE in the call to tidy.coxph.

We hope to submit this new version of the package to CRAN in the coming weeks. Hopeful that these fixes make getting a new version up on CRAN in the meantime easier. :-)

By the way, super neat package! Really interesting graphic coming out of that ggforest() function.

[mblue9]

Hello, would be great it this PR could be accepted if it fixes the ggforest error here

[kassambara]

Thank you, merged now!

[eugeniozoni]

Hi there,
I made sure to have the last updated packages, both Survmier and Broom, however, upon calling

res.cox <- coxph(Surv(BONE_PROGR_TIME, BONE_MET.x) ~ X2.Oxoisovaleric.acid + Dehydroepiandrosterone.sulfate + L.Lactic.acid + Pyruvic.acid + Hypoxanthine, id = PID, data = df3)

summary(res.cox)

and then

ggforest(res.cox, data=df3)

I still get that erro related to the column

ggforest(res.cox, data=df3)
Error in [.data.frame(data, , var) : undefined columns selected

What am I missing?
thank you for the help!

[mghahrem]

Hi all,
I just updated R to version 4.2.2 and RStudio to version 2022.12.0+353 and now when I run ggforest() on my Cox model, I get the following error:

cx1 <- coxph(Surv(surv_time, surv_status) ~ mygrp + age + sex + educ, data =mydata)
ggforest(cx1, data = mydata)

Error in match.names(clabs, names(xi)) :
names do not match previous names

This is while this exact code was working perfectly prior to the updates. Has anyone else faced such error or know how to fix it?

Thank you,
Mary

[hm828721]

Hi all,

I am facing the same issue as @mghahrem. Has anyone found a workaround (or, ideally, a fix :) ) yet?
Thanks so much!

Hannah

[mghahrem]

Hi @hm828721,

Please refer to the following page:
https://stackoverflow.com/questions/75152731/r-ggforest-error-in-match-namesclabs-namesxi-names-do-not-match-previou

The proposed solution on converting the data table from a tibble to standard R data.frame using the as.data.frame() function, is what worked for me. I hope it works out for you too!

Best,
Mary