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waldronlab / lefser

R implementation of the LEfSe method
https://waldronlab.io/lefser/
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Revert "update code in fillPmatZmat" #50

Closed shbrief closed 3 days ago

shbrief commented 3 days ago

Reverts waldronlab/lefser#43

LiNk-NY commented 3 days ago

@shbrief was there a problem?

shbrief commented 3 days ago

It seems like your pull request has no problem, but somehow the unit test is failing depending on where I run the test (I thought it might be from the pull request, so reverted it).

shbrief commented 3 days ago

I'm trying to 1) merge your pull request again and 2) find out why the unit test fails sometimes, but having problems. ;(

LiNk-NY commented 3 days ago

@shbrief I saw that these failures were present at the upstream/devel checkout f48c761: 

* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  15/15 mismatches (average diff: 0.704)
  [1] -3.34 - -3.80 ==  0.459
  [2] -3.26 - -3.70 ==  0.438
  [3] -3.13 - -3.52 ==  0.388
  [4] -2.92 - -3.36 ==  0.440
  [5] -2.79 - -3.13 ==  0.339
  [6] -2.63 - -3.08 ==  0.453
  [7] -2.51 - -3.07 ==  0.560
  [8] -2.14 -  2.14 == -4.283
  [9]  3.08 -  2.49 ==  0.590
  ...

  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 16 ]
  Error: Test failures
  Execution halted

and also present in the devel report: https://bioconductor.org/checkResults/devel/bioc-LATEST/lefser/nebbiolo2-checksrc.html