Christopher T Gregg
2014-Jan-17 18:47 UTC
[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/labs/gregg/index.html>
[[alternative HTML version deleted]]
Frede Aakmann Tøgersen
2014-Jan-18 09:23 UTC
[R] *** caught segfault *** :: a common problem in 3.0.2
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 T?gersen 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 Company reg. name: Vestas Wind Systems A/S This e-mail is subject to our e-mail disclaimer statement. Please refer to www.vestas.com/legal/notice If you have received this e-mail in error please contact the sender.> -----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> > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.