Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5

[Martin Morgan]

On 03/31/2017 04:19 AM, Ramon Diaz-Uriarte wrote:

Dear All,

A package I maintain, ADaCGH2, is failing to build in veracruz2 with a
segfault that seems to happen when plotting (in a call to plotting that
happens inside a mclapply)

http://bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/veracruz2-buildsrc.html


these are some of the lines of the traceback:

Traceback:
 1: dev.hold()
 2: plot.default(c(2925836, 5135683.5, 6415674.5, 7169722, 9715199, 13220514.5, 15307852, 41589471, 44534348, 47975338, 52729020, 54225865, 54970734, 55406435.5, 57169693.5, 57359284.5, 66362289.5, 69947314.5, 72243027.5, 75218239, 75268559.5, 75683700, 76272391, 76901797, 77282738, 83724180, 88707195.5, 89536816.5, 102463647.5, 104082964, 107610854, 108945724, 120577571, 122947762.5, 124680401, 129086592, 144839226, 148940008.5, 154240128.5, 155887373.5, 178034441.5, 184199138, 184552484), c(0.397, 0.002, -0.179, -0.1385, -0.095, 
-0.611, -0.165, -0.54, -0.358, 0.172, -0.2435, -0.044, -0.048, 0.078, -0.344, -0.139, -0.513, -0.681, -0.406, 0.083, -0.325, -0.186, -0.138, 0.393, -0.075, -0.655, 0.123, -0.346, -0.099, -0.3465, 0.463, -0.18, -0.101, -0.175, -0.101, 0.371, -0.642, -0.13, -0.33, -0.491, 0.138, -0.187, 0.21), ylab = "log ratio",     xlab = quote("Chromosomal location"), col = c("orange", "orange",     "orange", "orange", "orange", "orange", "orange", 
"orange",     "orange", "orange", "orange", "orange", "orange", "orange",     "orange", "orange", "orange", "orange", "orange", "orange",     "orange", "orange", "orange", "orange", "orange", "orange",     "orange", "orange", "orange", "orange", "orange", "orange",     "orange", 
"orange", "orange", "orange", "orange", "orange",     "orange", "orange", "orange", "orange", "orange"), cex = 1,     axes = FALSE, main = quote("Chr4@L.1"), pch = 20)
 3: plot(c(2925836, 5135683.5, 6415674.5, 7169722, 9715199, 13220514.5, 15307852, 41589471, 44534348, 47975338, 52729020, 54225865, 54970734, 55406435.5, 57169693.5, 57359284.5, 66362289.5, 69947314.5, 72243027.5, 75218239, 75268559.5, 75683700, 76272391, 76901797, 77282738, 83724180, 88707195.5, 89536816.5, 102463647.5, 104082964, 107610854, 108945724, 120577571, 122947762.5, 124680401, 129086592, 144839226, 148940008.5, 154240128.5, 155887373.5, 178034441.5, 184199138, 184552484), c(0.397, 0.002, -0.179, -0.1385, -0.095, -0.611, 
-0.165, -0.54, -0.358, 0.172, -0.2435, -0.044, -0.048, 0.078, -0.344, -0.139, -0.513, -0.681, -0.406, 0.083, -0.325, -0.186, -0.138, 0.393, -0.075, -0.655, 0.123, -0.346, -0.099, -0.3465, 0.463, -0.18, -0.101, -0.175, -0.101, 0.371, -0.642, -0.13, -0.33, -0.491, 0.138, -0.187, 0.21), ylab = "log ratio", xlab = quote("Chromosomal location"),     col = c("orange", "orange", "orange", "orange", "orange",     "orange", "orange", "orange", 
"orange", "orange", "orange",     "orange", "orange", "orange", "orange", "orange", "orange",     "orange", "orange", "orange", "orange", "orange", "orange",     "orange", "orange", "orange", "orange", "orange", "orange",     "orange", "orange", "orange", "orange", "orange", 
"orange",     "orange", "orange", "orange", "orange", "orange", "orange",     "orange", "orange"), cex = 1, axes = FALSE, main = quote("Chr4@L.1"),     pch = 20)
 4: do.call(funname, c(list(mf[[i]], y, ylab = yl, xlab = xl), dots))



It seems that what triggers the problem is an innocuous plot.default
followed by dev.hold? (none of which I call explicitly in my code)

I was able to reproduce this with

$ cat segfault-test.R
xx <- parallel::mclapply(1:2, function(i) {
    Cairo::CairoPNG(filename = paste("plt", i, ".png", sep=''))
    dev.hold()
})

$ R -f segfault-test.R

The El-Capitain builds are still in a great deal of flux, and in 
particular the Cairo package requires a binary installation that is not 
yet available (the Cairo package is used is actually from Mavericks). 
The best strategy is probably to wait until binaries become available.

Martin



At least another package, arrayQualityMetrics seems to experience a
somewhat similar problem:

http://bioconductor.org/checkResults/devel/bioc-LATEST/arrayQualityMetrics/veracruz2-buildsrc.html

where, again, an apparently innocuous plot.default followed by dev.hold
triggers a segfault (and there is no mclapply here)

Traceback:
 1: dev.hold()
 2: plot.default(-2, -1, pch = "", xlim = range(-1, (dim(mns)[2])),     ylim = range(min(as.vector(mns)) 
- 1, max(as.vector(mns)) +         1), xlab = "5' <-----> 3'\n Probe Number ", ylab = ylab,     
axes = FALSE, main = "RNA degradation plot", ...)
 3: plot(-2, -1, pch = "", xlim = range(-1, (dim(mns)[2])), ylim = range(min(as.vector(mns)) -     1, 
max(as.vector(mns)) + 1), xlab = "5' <-----> 3'\n Probe Number ",     ylab = ylab, axes = FALSE, 
main = "RNA degradation plot",     ...)
 4: plotAffyRNAdeg(AffyRNAdeg(expressionset, log.it = TRUE), lwd = 1,     cols 
= x$arrayColors)




I am not sure how to proceed here. Any suggestions?


Thanks,


R.

--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
       ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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