(issue was accidentically closed by specifying wrong issue id in commit)
wmwTest(eset, gmt, valType="p.greater") does work (see https://github.com/Accio/BioQC-example/blob/master/bioqc-kidney.Rnw#L94)
whereas
wmwTest(mat, tissueInds, valType="p.greater") does not (see https://github.com/Accio/BioQC-example/blob/master/bioqc-simulation.Rnw#L149)