Dear Martin,
On Fri, 07-04-2017, at 12:55:55, Martin Morgan <martin.mor...@roswellpark.org> wrote: > 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 Thanks for your answer. I'll be patient :-) (Just to clarify: I understand that what I was proposing was an ugly kludge; I think I have misunderstood the issue; apologies for the noise) Best, R. > >> 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) >>>> >>>> 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 >> > > > 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
