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

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

machine :-) If everything goes well, this should be reflected
in the next build report (Sat Apr 15).

Thanks again for your patience,

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.morgan at 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.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=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 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=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 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

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 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

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 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

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=