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GenABEL-Project / ProbABEL

Tool for genome-wide association analysis of imputed genetic data.
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The R checks for CoxPH fail with survival package 2.39.2 #27

Open lckarssen opened 8 years ago

lckarssen commented 8 years ago

The R checks for Cox' proportional hazards model (run_R_test_pacoxph) fail with version 2.39.2 of the R survival package:

./run_R_test_pacox.sh 
Checking Cox PH regression...
Loading required package: survival
Dose: check consistency of names                  OK
Prob: check consistency of names                  OK
Check consistency dose <-> prob gtdata            OK
Running ProbABEL...                               OK
Comparing R output with ProbABEL output:
 additive (dosages)                               OK
 additive (probabilities)                         OK
 dominant                                         OK
 recessive                                        OK
 overdominant                                     OK
 2df                                              OK

Run the same checks, but without any covariates (see bug #1266)
Running ProbABEL...                               OK
Comparing R output with ProbABEL output:
 additive (dosages)                               OK
 additive (probabilities)                         OK
 dominant                                         Error in summary(model[[1]])$coefficients : 
  $ operator is invalid for atomic vectors
Calls: run.model
Execution halted

This is on the current HEAD of master (commit 6d23885), but also for ProbABEL v0.4.5. On the Jenkins server the tests pass, the version number of the survival package there is 2.38.3.

lckarssen commented 8 years ago

Since the checks pass with Survival v2.38.3, I have moved the milestone from v0.5.0 to v1.0.0, so that this issue doesn't delay the release of v0.5.0.

lckarssen commented 8 years ago

The differences between v2.38-3 and v2.29-2 of the Survival package can be found here on GitHub