warning messages and meanings

[chiwwong]

I always get the following warning messages while running the GSEA using the package, but not sure what is the meaning.

1.'package:stats' may not be available when loading 2. All values in the stats vector are greater than zero and scoreType is "std", maybe you should switch to scoreType = "pos". 3. There were 2 pathways for which P-values were not calculated properly due to unbalanced (positive and negative) gene-level statistic values. For such pathways pval, padj, NES, log2err are set to NA. You can try to increase the value of the argument nPermSimple (for example set it nPermSimple = 10000) 4. number of items to replace is not a multiple of replacement length

For the second point, I have also tried to add the scoreType = "pos" as one of the parameters, but the warning message is still there at the rerun.

Thanks!

Prerequisites

• [ ] Have you read Feedback and follow the guide?
  • [ ] make sure your are using the latest release version
  • [ ] read the documents
  • [ ] google your quesion/issue

Describe you issue

• [ ] Make a reproducible example (e.g. 1)
• [ ] your code should contain comments to describe the problem (e.g. what expected and actually happened?)

Ask in right place

• [ ] for bugs or feature requests, post here (github issue)
• [ ] for questions, please post to Bioconductor or Biostars with tag clusterProfiler

[grimwoo]

I also have the warning message "'package:stats' may not be available when loading" while using gseGO() function, which did not produce result object. And I could successfully load stat library (library(stats)).