Re: r-bioc-complexheatmap: Error: C stack usage in test suite
Hi Andreas,
Thanks for your email!
Yes, that was a bug and I think I have fixed it in the recent versions. You can see all the tests are passed in the following links:
https://travis-ci.org/github/jokergoo/ComplexHeatmap
http://bioconductor.org/checkResults/devel/bioc-LATEST/ComplexHeatmap/
A recent feedback from users says the error of "Error: C stack usage" still occurs for huge matrix where the values are all identical (this is a very rare case), which means this bug might have not been completely fixed yet.
What should I do now? Should I just comment these lines that cause errors in the script? Which version of the package are you testing? The Bioconductor release version or development version?
Regards,
Zuguang Gu
________________________________________
From: Andreas Tille <andreas@an3as.eu>
Sent: 21 July 2020 17:13
To: debian-r@lists.debian.org; Gu, Zuguang
Subject: r-bioc-complexheatmap: Error: C stack usage in test suite
Hi Zuguang,
the Debian R team is trying to package ComplexHeatmap for Debian. When
we run the test suite in a restricted environment (no remote access, no
X server only the packages specified in DESCRIPTION available) it turns
out that the test
$ 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
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?
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: