[Bioc-devel] segfault when building in veracruz2 for BioC 3.5
Ramon Diaz-Uriarte
rdiaz02 at gmail.com
Fri Apr 7 10:59:25 CEST 2017
Dear Hervé,
Thanks for your answer. I'll ignore those segfaults then.
Best,
R.
On Fri, 07-04-2017, at 08:36:40, Hervé Pagès <hpages at fredhutch.org> wrote:
> 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.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)
>>>>
>>>> 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 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:
>>>>
>>>> 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: rdiaz02 at gmail.com
>>>> ramon.diaz at 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=
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>>
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>>
>>
>> --
>> 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: rdiaz02 at gmail.com
>> ramon.diaz at 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 at 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=
>>
--
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: rdiaz02 at gmail.com
ramon.diaz at iib.uam.es
http://ligarto.org/rdiaz
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