tests: unknown fitType in DESeqDataSet - estimateDispersions

[smoe]

Hello, I get this error on a problematic fitType when running the pigx-rnaseq tests. Does that ring any bell? Many thanks Steffen

From tests/output/logs/analysis1.report.salmon.transcripts.log:

label: prepare_inputs_import_GTF
^M  |                                                                       ^M  |..............                                                   |  22%
  ordinary text without R code

^M  |                                                                       ^M  |................                                                 |  24%
label: run_deseq2
design formula:~ AnalysisGroup
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
Quitting from lines 145-189 (deseqReport.Rmd)
Error in estimateDispersionsFit(object, fitType = fitType, quiet = quiet) :
  unknown fitType
Calls: runReport ... estimateDispersions -> .local -> estimateDispersionsFit
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors

Execution halted

[smoe]

I came to the conclusion that this happened because of me having missed the locfit R package.