Dear Martin,
Thanks a lot for looking into this. I'll wait then. Best, R. On Mon, 03-04-2017, at 18:34, Martin Morgan <martin.mor...@roswellpark.org> wrote: > 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 >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. -- 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
