Re: r-bioc-complexheatmap: Error: C stack usage in test suite

[Dirk Eddelbuettel <edd@debian.org>]

On 21 July 2020 at 17:13, Andreas Tille wrote:
| 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

You almost surely want the xvfb wrapper here as grid likely opens a device.

| 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
edd@rob:/tmp/downloaded_packages/ComplexHeatmap/tests

Dirk
 
| Kind regards
| 
|          Andreas.
| 
| -- 
| http://fam-tille.de
| 

-- 
https://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org