[Bioc-devel] Packages with broken unit tests because of sample() change in R 3.6

[Pages, Herve]

Dear developers,

As reported on this list in March (https://stat.ethz.ch/pipermail/bioc-devel/2019-March/014776.html) the sample() function has changed in recent R-devel. This change breaks the 19 following Bioconductor software packages:

  - cicero
  - clipper
  - clusterExperiment
  - CMA
  - CNVPanelizer
  - derfinder
  - derfinderHelper
  - flowQB
  - mAPKLA
  - MCbiclust
  - Melissa
  - metaseqR
  - nucleoSim
  - onlineFDR
  - PathNet
  - phyloseq
  - SPONGE
  - treeio
  - trena


For all these packages (except for the CMA package), the change to sample() breaks the unit tests where sample() is used to generate random data as input to the test. Since sample() generates different random numbers in R 3.6 (compared to R 3.5, with the seed set to the same value), the input to the test now is different and so is its output, so comparison to the old expected result now fails. The fix is to simply modify the expected result to match the new output.

If you maintain one of the above package, please fix your package as soon as possible.

Keep in mind that all Bioconductor packages will need to pass 'R CMD build' and 'R CMD check' with no error in order to be included in the next Bioconductor release, scheduled for Tuesday April 30. Note that Bioconductor 3.9 will be based on R 3.6 (scheduled to be released on Friday April 26) so please make sure to use a recent version of R devel when testing/fixing your package.

See our release schedule:

  https://bioconductor.org/developers/release-schedule/

and this recent announcement on this list:

  https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014832.html

Thank you for your ongoing contribution to Bioconductor.

Cheers,

H.


--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org<mailto:hpages using fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319


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