Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5
Hi Hervé,
On Sat, 15-04-2017, at 05:36:35, Hervé Pagès 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
>> 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
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,
Re: [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
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
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", "
Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5
Dear Martin,
On Fri, 07-04-2017, at 12:55:55, Martin Morgan
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
>> 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("Chr
Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5
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
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 bes
Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5
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 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
>> 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@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", "o
Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5
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
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@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
Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5
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
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 a
Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5
Dear Martin,
Thanks a lot for looking into this. I'll wait then.
Best,
R.
On Mon, 03-04-2017, at 18:34, Martin Morgan
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 = r
Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5
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 Bi
