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) 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel