Fix integration tests

[Melkiades]

We get the following to fix:

  ✖ | 3      31 | summarize_glm_count [0.5s]                                      
  ────────────────────────────────────────────────────────────────────────────────
  Failure (test-summarize_glm_count.R:60:3): h_glm_poisson emmeans-fit works with healthy input
  mat1$statistic not equal to expected$statistic.
  target is NULL, current is numeric
  
  Failure (test-summarize_glm_count.R:157:3): h_glm_quasipoisson emmeans-fit works with healthy input
  mat1$statistic not equal to expected$statistic.
  target is NULL, current is numeric
  
  Failure (test-summarize_glm_count.R:240:3): h_glm_count emmeans-fit works with healthy input
  mat1$statistic not equal to expected$statistic.
  target is NULL, current is numeric
  ────────────────────────────────────────────────────────────────────────────────

  ✖ |  14 1     | coxph [0.3 s]                                                   
  ────────────────────────────────────────────────────────────────────────────────
  Failure (test-coxph.R:59:3): try_car_anova works correctly
  result$warn_text not identical to NULL.
  Types not compatible: character is not NULL

[Melkiades]

I cannot reproduce this locally, unfortunately. Could it be a version problem? Tests are run under the following version:

* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘tern/DESCRIPTION’ ... OK
* this is package ‘tern’ version ‘0.7.10.9009’

[ayogasekaram]

I also cannot reproduce these failures locally.

[Melkiades]

@arkadiuszbeer do you have any idea why this could happen only on the integration side of things?

[arkadiuszbeer]

@Melkiades I am on it.
I am testing on bee docker image, but now it is stuck on Running ‘testthat.R’ for 2 hours - I am also investigating it.

[arkadiuszbeer]

I was able to reproduce this error on bee server.

x | 3      31 | summarize_glm_count [0.7s]                                      
────────────────────────────────────────────────────────────────────────────────
Failure (test-summarize_glm_count.R:60:3): h_glm_poisson emmeans-fit works with healthy input
mat1$statistic not equal to expected$statistic.
target is NULL, current is numeric

Failure (test-summarize_glm_count.R:157:3): h_glm_quasipoisson emmeans-fit works with healthy input
mat1$statistic not equal to expected$statistic.
target is NULL, current is numeric

Failure (test-summarize_glm_count.R:240:3): h_glm_count emmeans-fit works with healthy input
mat1$statistic not equal to expected$statistic.
target is NULL, current is numeric
────────────────────────────────────────────────────────────────────────────────                                                                             
✓ |        18 | summarize_num_patients [0.6s]                                   

[Melkiades]

blocked by https://github.com/insightsengineering/idr-tasks/issues/443