I checked out your package git clone https://git.bioconductor.org/packages/anamiR
and then, on R-devel (since that is the version being used in the current Bioconductor 'devel' release) and with BiocManager::version() returning 3.11 and BiocManager::valid() returning TRUE, I did cd anamiR/vignettes R -f Stangle IntroductionToanamiR.Rmd This gave me the R file IntroductinoToanamiR.R, which I then 'source'd' in R with R > source("IntroductionToanamiR.R", echo = TRUE, max = Inf) This lead to > mrna_d <- differExp_discrete(se = mrna_se, + class = "ER", method = "t.test", + t_test.var = FALSE, log2 = FALSE, + p_value.cutoff = 0.05, logratio = 0.5 + ) Error in t.test.default(da[gp_1], da[gp_2], var.equal = t_test.var) : not enough 'x' observations While the error comes from t.test > traceback() 10: stop("not enough 'x' observations") 9: t.test.default(da[gp_1], da[gp_2], var.equal = t_test.var) 8: stats::t.test(da[gp_1], da[gp_2], var.equal = t_test.var) 7: FUN(newX[, i], ...) 6: apply(data, 1, t_test, gp1, gp2) 5: differExp_discrete(se = mrna_se, class = "ER", method = "t.test", t_test.var = FALSE, log2 = FALSE, p_value.cutoff = 0.05, logratio = 0.5) at IntroductionToanamiR.R#47 4: eval(ei, envir) 3: eval(ei, envir) 2: withVisible(eval(ei, envir)) 1: source("IntroductionToanamiR.R", echo = TRUE, max = Inf) It seems likely that the problem is somewhere else in your code. Since the error is reproducible outside the build system and using a standard bioc-devel installation, further troubleshooting is really the maintainer's responsibility. If the above isn't enough, respond here and I'll work on this further. Martin On 12/21/19, 12:48 AM, "Bioc-devel on behalf of r04945...@ntu.edu.tw" <bioc-devel-boun...@r-project.org on behalf of r04945...@ntu.edu.tw> wrote: Hi all, I am the maintainer of anamiR. I keep getting this error on build report, which I don't get it on my local environment. Also, the weird part is that it did not show up until this September. Does anyone how to fix this? it looks like something went wrong with t.test from stats, and I don't think this package has been changed... Quitting from lines 187-198 (IntroductionToanamiR.Rmd) Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics: not enough 'x' observations --- failed re-building ‘IntroductionToanamiR.Rmd’ Any suggestion would be helpful, Thank you! Ti-Tai _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel