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GenABEL-Project / ProbABEL

Tool for genome-wide association analysis of imputed genetic data.
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probabel 0.5.0 fails two checks #47

Open tillea opened 3 years ago

tillea commented 3 years ago

Hi,

when trying to rebuild the Debian package of probabel I get

FAIL: run_R_test_palinear.sh
============================

Checking linear regression...
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                                              Error: prob.2df.PA and prob.2df.R are not equal:
  Component "beta_SNP_A1A2": Mean relative difference: 0.122881
  Component "sebeta_SNP_A1A2": Mean relative difference: 0.9999318
  Component "beta_SNP_A1A1": 'is.NA' value mismatch: 2 in current 1 in target
  ....
Execution halted
FAIL run_R_test_palinear.sh (exit status: 1)

XFAIL: run_R_test_palogist.sh
=============================

Checking logistic regression...
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)                               Error: dose.add.PA and dose.add.R are not equal:
  Component "beta_SNP_addA1": Mean relative difference: 0.01649978
  Component "sebeta_SNP_addA1": Mean relative difference: 0.5609667
Execution halted
XFAIL run_R_test_palogist.sh (exit status: 1)

I've added the according test file Kind regards, Andreas.

test-suite.log

maarten-k commented 3 years ago

@lckarssen Shall we ask if they remove Probabel from the Debian project as a package? Since there is no workforce to maintain the software, it is better not to use it. ( so also distribution and installing is not a good idea)