[Bioc-devel] Error from rmarkdown

[Martin Morgan]

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 r04945002 using ntu.edu.tw" <bioc-devel-bounces using r-project.org on behalf of r04945002 using 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
    
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