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waldronlab / curatedMetagenomicDataAnalyses

Analyses in R and Python Using curatedMetagenomicData
https://waldronlab.io/curatedMetagenomicDataAnalyses/
Creative Commons Attribution 4.0 International
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Age and Sex metaanalysis vignettes broken in cMD 3 #41

Closed lwaldron closed 2 years ago

lwaldron commented 2 years ago

See the following after upgrading GHA to Bioconductor 3.14 https://github.com/waldronlab/curatedMetagenomicAnalyses/runs/5558310146?check_suite_focus=true#step:18:258 :

Quitting from lines 120-122 (Age_metaanalysis_vignette.Rmd) 
Error: processing vignette 'Age_metaanalysis_vignette.Rmd' failed with diagnostics:
'ranks' must contain values from 'taxonomyRanks()'
--- failed re-building ‘Age_metaanalysis_vignette.Rmd’
lwaldron commented 2 years ago

Also Sex_metaanalysis_vignette.Rmd, likely the same problem (https://github.com/waldronlab/curatedMetagenomicAnalyses/runs/5558310146?check_suite_focus=true#step:18:976):

Quitting from lines 121-123 (Sex_metaanalysis_vignette.Rmd) 
Error: processing vignette 'Sex_metaanalysis_vignette.Rmd' failed with diagnostics:
'ranks' must contain values from 'taxonomyRanks()'
--- failed re-building ‘Sex_metaanalysis_vignette.Rmd’