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

[Andreas Tille <andreas@an3as.eu>]

Hi,

I intend to package r-bioc-complexheatmap.  The Build-Dependency
r-cran-getoptlong is in new as well as the Test-Depends r-cran-gridtext
are in new.  With these packages it is possible it is possible to
reproduce the error of the test suite:


...
---------------------


Attaching package: ‘dendextend’

>.
> The following object is masked from ‘package:stats’:

    cutree

m = matrix(rnorm(100), 10)
> dend1 = as.dendrogram(hclust(dist(m)))
> dend1 = adjust_dend_by_x(dend1, sort(runif(10)))
>.
> m = matrix(rnorm(50), nr = 5)
> dend2 = as.dendrogram(hclust(dist(m)))
>.
> dend3 = as.dendrogram(hclust(dist(m[1:2, ])))
>.
>.
> dend_merge = merge_dendrogram(dend3,.
+ <---->list(set(dend1, "branches_col", "red"),.
+ <----><------> set(dend2, "branches_col", "blue"))
+ )
>.
> grid.dendrogram(dend_merge, test = TRUE, facing = "bottom")
> grid.dendrogram(dend_merge, test = TRUE, facing = "top")
> grid.dendrogram(dend_merge, test = TRUE, facing = "left")
> grid.dendrogram(dend_merge, test = TRUE, facing = "right")
>.
> grid.dendrogram(dend_merge, test = TRUE, facing = "bottom", order = "reverse")
> grid.dendrogram(dend_merge, test = TRUE, facing = "top", order = "reverse")
> grid.dendrogram(dend_merge, test = TRUE, facing = "left", order = "reverse")
> grid.dendrogram(dend_merge, test = TRUE, facing = "right", order = "reverse")
>.
>.
> m = matrix(rnorm(100), 10)
> dend1 = as.dendrogram(hclust(dist(m)))
> dend1 = adjust_dend_by_x(dend1, unit(1:10, "cm"))
> grid.dendrogram(dend1, test = TRUE)
>.
> dl = cut_dendrogram(dend1, k = 3)
> grid.dendrogram(dl$upper, test = TRUE)
>.
>.
> m1 = matrix(rnorm(100), nr = 10)
> m2 = matrix(rnorm(80), nr = 8)
> m3 = matrix(rnorm(50), nr = 5)
> dend1 = as.dendrogram(hclust(dist(m1)))
> dend2 = as.dendrogram(hclust(dist(m2)))
> dend3 = as.dendrogram(hclust(dist(m3)))
> dend_p = as.dendrogram(hclust(dist(rbind(colMeans(m1), colMeans(m2), colMeans(m3)))))
> dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3))
> grid.dendrogram(dend_m, test = T)
>.
> dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3), only_parent = TRUE)
> grid.dendrogram(dend_m, test = T)
>.
> require(dendextend)
> dend1 = color_branches(dend1, k = 1, col = "red")
> dend2 = color_branches(dend2, k = 1, col = "blue")
> dend3 = color_branches(dend3, k = 1, col = "green")
> dend_p = color_branches(dend_p, k = 1, col = "orange")
> dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3))
> grid.dendrogram(dend_m, test = T)
>.
>.
> m = matrix(rnorm(120), nc = 12)
> colnames(m) = letters[1:12]
> fa = rep(c("a", "b", "c"), times = c(2, 4, 6))
> dend = cluster_within_group(m, fa)
> grid.dendrogram(dend, test = TRUE)
>.
>.
> #  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
autopkgtest [20:30:07]: test run-unit-test: -----------------------]


Any idea how to fix this?

Kind regards

       Andreas.


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