[R] *** caught segfault *** :: a common problem in 3.0.2

[Christopher T Gregg]

Thank you, Frede.  I will look into these suggestions.  I did not specify the data type carefully…I will assess this and see if it cleans up the problem.

best wishes,
Chris

On Jan 18, 2014, at 2:23 AM, Frede Aakmann Tøgersen <frtog at vestas.com>
 wrote:

> I think you are trying to access memory that you are not allowed to.
> 
> Or did you specify the type of all of your data to be of the right ones?
> 
> The segfault message at least say so.
> 
>> *** caught segfault ***
>> address 0x2464943a08, cause 'memory not mapped'
>> 
>> Traceback:
>> 1: .Call("gyroscope", ncol(Y), nrow(Y), t(Y), as.integer(as.numeric(l) -     1),
>> as.character(lnames), as.integer(perms), as.numeric(coloring),
>> as.integer(useDensity), as.integer(showProfile), as.integer(showPatch))
>> 2: gyro2(data)
> 
> Why don't you have as.integer for ncol(Y), nrow(Y)??
> 
> So are you having ncol(Y), nrow(Y) in the right order when you use t(Y)??
> 
> Why don't you have as.double for t(Y)??
> 
> Is this correct: as.integer(as.numeric(l) -     1)??
> 
> Should as.numeric be as.double?
> 
> Have you checked that all indexes for your arrays in the C/C++ code are defined correctly with the arguments of your  .Call()??
> 
> 
> Yours sincerely / Med venlig hilsen
> 
> 
> Frede Aakmann Tøgersen
> Specialist, M.Sc., Ph.D.
> Plant Performance & Modeling
> 
> Technology & Service Solutions
> T +45 9730 5135
> M +45 2547 6050
> frtog at vestas.com
> http://www.vestas.com
> 
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> 
>> -----Original Message-----
>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
>> On Behalf Of Christopher T Gregg
>> Sent: 17. januar 2014 19:48
>> To: r-help at R-project.org
>> Subject: [R] *** caught segfault *** :: a common problem in 3.0.2
>> 
>> Hi,
>> 
>> I have struggled recently with R crashing with the following error in various
>> contexts.  It has occurred when running the R package RCytoscape, a package
>> we generated internally and when running the base system.  I have seen
>> that this is an issue with the Mavericks OS (http://citizen-
>> statistician.org/2013/10/27/warning-mac-os-10-9-mavericks-and-r-dont-play-
>> nicely/), but I don't run Mavericks.  I have tried reinstalling the latest R
>> version without any improvements and I am seeking a solution for this
>> frustating problem.  The error and sessionInfo() are below.
>> 
>> Thank you very much for any suggestions to overcome this problem.
>> 
>> best wishes,
>> Chris
>> 
>> Here is the error:
>> 
>> *** caught segfault ***
>> address 0x2464943a08, cause 'memory not mapped'
>> 
>> Traceback:
>> 1: .Call("gyroscope", ncol(Y), nrow(Y), t(Y), as.integer(as.numeric(l) -     1),
>> as.character(lnames), as.integer(perms), as.numeric(coloring),
>> as.integer(useDensity), as.integer(showProfile), as.integer(showPatch))
>> 2: gyro2(data)
>> 
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> 
>>> sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] gyroscope_0.9
>>> 
>> 
>> Christopher Gregg, PhD.
>> New York Stem Cell Foundation-Robertson Investigator
>> Assistant Professor, Neurobiology and Anatomy
>> Adjunct Assistant Professor, Human Genetics
>> 323 Wintrobe Bldg 530
>> University of Utah, School of Medicine
>> 20 North 1900 East
>> Salt Lake City, Utah 84132-3401
>> 
>> phone: (801) 581-8212
>> fax: (801) 585-9736
>> ------------------------------------
>> Gregg Lab Website:
>> www.neuro.utah.edu/labs/gregg/index.html<http://www.neuro.utah.edu/l
>> abs/gregg/index.html>
>> 
>> 
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