[Bioc-devel] segfault when building in veracruz2 for BioC 3.5

Fri Apr 7 14:55:55 CEST 2017

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 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
>>>
>>> _______________________________________________
>>> Bioc-devel at 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: 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.