[Bioc-devel] Help needed to reproduce my crash report

[Martin Morgan]

On 11/16/2016 02:44 AM, Ted Wong wrote:
> Hi,
>
> I need help to reproduce a crash in my crash report.
>
> The crash report is: http://master.bioconductor.org/checkResults/3.4/bioc-LATEST/Anaquin/malbec1-buildsrc.html
>
> This is what I did:
>
> 1. svn co --username ... --password .... https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Anaquin
>
> to create a new directory
>
> 2. svn update -r 123975
>
> because this is the reversion stated in the crash report
>
> 3. cd ../ and R CMD build --keep-empty-dirs --no-resave-data Anaquin
>
> to run the tests.
>
> That's what I got:
>
> * checking for file ‘Anaquin/DESCRIPTION’ ... OK
> * preparing ‘Anaquin’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * looking to see if a ‘data/datalist’ file should be added
> * building ‘Anaquin_1.1.2.tar.gz’
>
> I tried the command on:
>
>   *   Ubuntu, Bioconductor 3.3, R 3.3.1
>   *   Mac OS-X, Bioconductor 3.4, R 3.3.2

The builds are of the current Bioconductor, so version 3.4. Check that 
this is the case, and that your packages are current

    BiocInstaller::biocVersion()
    BiocInstaller::biocValid()

FWIW, I did

   cd Anaquin
   R CMD INSTALL .
   cd vignettes
   R CMD Stangle Anaquin.Rmd
   R
   > source("Anaquin.R", echo=TRUE, max=Inf)

and then got

 > plotLinear(anaquin, title=title, xlab=xlab, ylab=ylab)
Error in unit(aspect_ratio, "null") :
   'x' and 'units' must have length > 0
 > traceback()
17: stop("'x' and 'units' must have length > 0")
16: unit(aspect_ratio, "null")
15: unit.c(grobHeight(axis_h$top), unit(aspect_ratio, "null"), 
grobHeight(axis_h$bottom))
14: f(...)
13: self$draw_panels(panels, layout, x_scales, y_scales, ranges,
         coord, data, theme, self$params)
12: f(..., self = self)
11: self$facet$render_panels(panels, self$panel_layout, 
self$panel_scales$x,
         self$panel_scales$y, self$panel_ranges, coord, data, theme,
         labels)
10: f(..., self = self)
9: layout$render(geom_grobs, data, plot$coordinates, theme, plot$labels)
8: ggplot_gtable(data)
7: print.ggplot(p)
6: print(p)
5: plotLinear(anaquin, title = title, xlab = xlab, ylab = ylab) at 
Anaquin.R#26
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("Anaquin.R", echo = TRUE, max = Inf)
 > BiocInstaller::biocVersion()
[1] '3.4'
 > BiocInstaller::biocValid()
[1] TRUE

Martin

>
> Both worked.
>
> Ted,
>
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