Hi Hervé,
On Sat, 15-04-2017, at 05:36:35, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Ramon, > > Good news: looks like a Cairo binary for R 3.4 showed up on CRAN > yesterday: > > https://cran.r-project.org/bin/macosx/el-capitan/contrib/3.4/ > > I installed it on veracruz2, and, according to the logs of the > current builds, ADaCGH2 built and checked successfully on this Great! > machine :-) If everything goes well, this should be reflected > in the next build report (Sat Apr 15). > > Thanks again for your patience, Thank you and Martin for looking into this and letting me know. Best, R. > > Cheers, > H. > > > On 04/08/2017 06:34 AM, Ramon Diaz-Uriarte wrote: >> >> 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) >>>>>> >>>>>> 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=67SOhhQ_xN5IxOZP7n-Vuvtn1Da8u3G6YqpEVI4fTsw&s=yu6OVUP4gT1jkj9xheyXRvn5-tHhTOM1X3QgpWRr4DE&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. >>>>> >>>>> Martin >>>>> >>>>>> >>>>>> >>>>>> At 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=67SOhhQ_xN5IxOZP7n-Vuvtn1Da8u3G6YqpEVI4fTsw&s=c1_EabE3C2Acr74VVb3OyuNuX1EufdNdngH56Qmft2k&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=67SOhhQ_xN5IxOZP7n-Vuvtn1Da8u3G6YqpEVI4fTsw&s=dKDLFLGuh3UsqQmwuRnxOE58wNasCBVVtNJ4cGPPxk4&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=67SOhhQ_xN5IxOZP7n-Vuvtn1Da8u3G6YqpEVI4fTsw&s=xYLVWcIVzsv6htRUVAnOuzcx1AWoyBEih7NAQKyljmg&e= >>>>>> >>>>> >>>>> >>>>> 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 >>>> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__ligarto.org_rdiaz&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=67SOhhQ_xN5IxOZP7n-Vuvtn1Da8u3G6YqpEVI4fTsw&s=dKDLFLGuh3UsqQmwuRnxOE58wNasCBVVtNJ4cGPPxk4&e= >>>> >>> >>> >>> 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 >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__ligarto.org_rdiaz&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=67SOhhQ_xN5IxOZP7n-Vuvtn1Da8u3G6YqpEVI4fTsw&s=dKDLFLGuh3UsqQmwuRnxOE58wNasCBVVtNJ4cGPPxk4&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=67SOhhQ_xN5IxOZP7n-Vuvtn1Da8u3G6YqpEVI4fTsw&s=xYLVWcIVzsv6htRUVAnOuzcx1AWoyBEih7NAQKyljmg&e= >> -- 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
