[Bioc-devel] segfault when building in veracruz2 for BioC 3.5
On 04/07/2017 03:55 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
In general this is the wrong thing to do, since it enables shipping broken code with no possibility of future fixes. Be patient. Martin
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.morgan at 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 at 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 at 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 Aut?noma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdiaz02 at gmail.com ramon.diaz at iib.uam.es http://ligarto.org/rdiaz
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--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Aut?noma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdiaz02 at gmail.com
ramon.diaz at iib.uam.es
http://ligarto.org/rdiaz
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.