Re: r-bioc-complexheatmap: Error: C stack usage in test suite
Hi Dirk,
On Tue, Jul 21, 2020 at 11:51:05AM -0500, Dirk Eddelbuettel wrote:
> | $ R --no-save < test-dendrogram.R
> | ...
> | > # stack overflow problem
> | > m = matrix(1, nrow = 1000, ncol = 10)
> | > m[1, 2] = 2
> | > dend = as.dendrogram(hclust(dist(m)))
> | > grid.dendrogram(dend, test = T)
> | Error: C stack usage 7969380 is too close to the limit
> | Execution halted
>
> You almost surely want the xvfb wrapper here as grid likely opens a device.
I've tried with xvfb and without - there is no difference. All other
tests are running nicely without xvfb. I even tried the test on the
Linux console where no X server is running on my local machine and there
the error above did not happen.
> | fails. This is not the case if the resulting package is installed on a
> | normal machine - but in the CI environment which is restricted this
> | failure appears reproducibly.
> |
> | Do you have any idea what might cause this issue?
>
> An obvious error in the package is unconditional use in the test file of the
> suggested package:
>
> edd@rob:/tmp/downloaded_packages/ComplexHeatmap/tests$ R --no-save < test-dendrogram.R
>
> [... stuff omitted ...]
>
> R> library(GetoptLong)
> R>
> R> if(!exists("cut_dendrogram")) {
> + cut_dendrogram = ComplexHeatmap:::cut_dendrogram
> + }
> R>
> R> library(dendextend)
> Error in library(dendextend) : there is no package called ‘dendextend’
> Execution halted
This error does not occure since r-cran-dendextend is inside the Test-Depends
and installed inside the minimum chroot. So the problem is not connected
to a lack of the dendextend package.
Kind regards
Andreas.
--
http://fam-tille.de
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