Hi Ramon, It doesn't seem that this segfault occurs in ADaCGH2 so you can ignore it. I can't be 100% sure but I actually expect it to go away when things are sorted out with the new El Capitan binaries. Unfortunately it's not something we fully control so let's wait and see...
Cheers, H. On 04/07/2017 12:55 AM, Ramon Diaz-Uriarte wrote:
Dear Martin and Valerie, I am not sure how to proceed here since the 14th is approaching and I still see this error (in both my package and at least one other package ---arrayQualityMetrics). I could comment out the plotting code for the vignette and examples when running on El Capitan. Is this a possible workaround that I should implement? If this is reasonable, what is the recommended way to find out the code is running in El Capitan and not Mavericks? (For instance, can I tell from Sys.info()["sysname"]? --I do not have access to a Mac). Martin mentioned that the Cairo package requires a binary installation that is not yet available. Should I continue to wait? There is not a lot of margin for changing the code, uploading to BioC, waiting for the build, and making sure it works. What if it continues to fail on El Capitan by the 14th? Best, R. On Mon, 03-04-2017, at 18:34:26, 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) https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ADaCGH2_veracruz2-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LUd6DHmjoVArzVDFUEtSRfMSN_AiOXqmmqFV_4As46k&s=se3QJrNKC3kMzGsf88z7nuqgS_X7o08nzTQ8K7uvai4&e= 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. MartinAt least another package, arrayQualityMetrics seems to experience a somewhat similar problem: https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_arrayQualityMetrics_veracruz2-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LUd6DHmjoVArzVDFUEtSRfMSN_AiOXqmmqFV_4As46k&s=s7ZpqOndpOhYWVbIGj-Ih8XraT1i9EyvtPExPWojz6M&e= 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__ligarto.org_rdiaz&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LUd6DHmjoVArzVDFUEtSRfMSN_AiOXqmmqFV_4As46k&s=2xbtlQH33eoT53i8vluEoB_10V59Wi3_ePQC0uzrQ_Q&e= _______________________________________________ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LUd6DHmjoVArzVDFUEtSRfMSN_AiOXqmmqFV_4As46k&s=hNVkbl1RyrBo2RW_tbZQNZbyiwDK_Xf3J1gGnmS8AQU&e=This email message may contain legally privileged and/or confidential information. 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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 https://urldefense.proofpoint.com/v2/url?u=http-3A__ligarto.org_rdiaz&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LUd6DHmjoVArzVDFUEtSRfMSN_AiOXqmmqFV_4As46k&s=2xbtlQH33eoT53i8vluEoB_10V59Wi3_ePQC0uzrQ_Q&e= _______________________________________________ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LUd6DHmjoVArzVDFUEtSRfMSN_AiOXqmmqFV_4As46k&s=hNVkbl1RyrBo2RW_tbZQNZbyiwDK_Xf3J1gGnmS8AQU&e=
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