Error in question ("Error: segfault from C stack overflow") appears to be associated with long "date" vectors, and is addressed in the R project's PR #14267, incorporated in R 2.11.1, announcement of the release of which may be found at <http://article.gmane.org/gmane.comp.lang.r.general/191995>, dated 2010-05-31 09:16:36 GMT. I was running R 2.11.0_1. Fix: It is believed that upgrading the port to R 2.11.1 will resolve this error. How-To-Repeat: Ensure the existence of a suitable file to read; the one I use in the following example (/tmp/individual_allocations) has 169199 lines: > I <- read.table("/tmp/individual_allocations", header = TRUE, colClasses = c("Date", "numeric", "numeric", "numeric", "numeric")) > png("/tmp/Space_Date.png", width = 700, height = 700) > Is <- subset(I, as.numeric(I$Tag) %% 7 == 6) > xlist <- as.numeric(unique(Is$Tag)) - as.numeric(min(Is$Tag)) > boxplot( GB_total ~ Tag, data = Is, varwidth = TRUE, notch = TRUE, col = "lightblue", medcol = "darkblue", xlab = "Date", ylab = "Allocation size (GB)", main = "Local Disk Space Allocation Distributions by Date", at = (xlist/7), xlim = c(0, max(xlist/7 ))) Error: segfault from C stack overflow
Maintainer of math/R, Please note that PR ports/148264 has just been submitted. If it contains a patch for an upgrade, an enhancement or a bug fix you agree on, reply to this email stating that you approve the patch and a committer will take care of it. The full text of the PR can be found at: http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/148264 -- Edwin Groothuis via the GNATS Auto Assign Tool edwin@FreeBSD.org
State Changed From-To: open->feedback Awaiting maintainers feedback (via the GNATS Auto Assign Tool)
I believe this update may be of interest. After applying the following patch: diff -ru R/Makefile R/Makefile --- R/Makefile 2010-05-31 05:31:45.000000000 -0700 +++ R/Makefile 2010-06-30 15:09:30.000000000 -0700 @@ -11,8 +11,7 @@ .else PORTNAME= R .endif -PORTVERSION= 2.11.0 -PORTREVISION= 1 +PORTVERSION= 2.11.1 CATEGORIES= math lang MASTER_SITES= http://cran.r-project.org/src/base/R-2/ \ ftp://cran.r-project.org/pub/R/src/base/R-2/ \ diff -ru R/distinfo R/distinfo --- R/distinfo 2010-04-27 12:51:30.000000000 -0700 +++ R/distinfo 2010-06-30 15:12:30.000000000 -0700 @@ -1,3 +1,3 @@ -MD5 (R-2.11.0.tar.gz) = c6c1e866299f533617750889c729bfb3 -SHA256 (R-2.11.0.tar.gz) = 9b2a1769cdf21ad00500cbc0a1f7e09c872681d2ca0ea592e7692f15ff980a43 -SIZE (R-2.11.0.tar.gz) = 19779908 +MD5 (R-2.11.1.tar.gz) = 7421108ade3e9223263394b9bbe277ce +SHA256 (R-2.11.1.tar.gz) = 48c1b96426f5b588763652b0b633cadccf410bae34300c22fd40524662bc23bb +SIZE (R-2.11.1.tar.gz) = 19729300 and rebuilding math/R, using the just-built R 2.11.1 did, in fact, avoid the "Error: segfault from C stack overflow" condition; I was able to create all of the plots without incident. There may be other issues with 2.11.1, or there may be issues with environments other than FreeBSD/i386 stable/7; I have not tested that. But the above patch does appear to be sufficient to update the port from 2.11.0_1 to 2.11.1, and the resulting executable and associated libraries appear to work. Peace, david -- David H. Wolfskill david@catwhisker.org Depriving a girl or boy of an opportunity for education is evil. See http://www.catwhisker.org/~david/publickey.gpg for my public key.
On 6/30/10, David Wolfskill <david@catwhisker.org> wrote: > First, thanks for maintaining the math/R port -- I find it very useful. > > Lately, I've been getting the rather infamous "Error: segfault from C > stack overflow" message during attempts to plot large datasets with date > vectors. > > Per <http://article.gmane.org/gmane.comp.lang.r.general/191995>, R > 2.11.1 was released on 31 May 2010, and it is alleged to resolve the > issue. > > I'm using R 2.11.0_1 -- I upgrade the ports installe don my laptop > daily. > > Is there a problem that I might be able to help with for upgrading the > port to 2.11.1? > I had meant to update the port earlier, when the bugfix release first came out, but I was preoccupied by some other matters. I will try to submit an update soon. I am glad that you find it useful, and I am sorry that you have been -- er -- bugged by the problem with the earlier release. If you're updating all of your ports daily, and you're still using the M-Tech 30W described on your website, you're a brave soul -- or a patient one. b.
Responsible Changed From-To: freebsd-ports-bugs->bf I'll take it.
bf 2010-07-31 15:05:25 UTC FreeBSD ports repository Modified files: math/R Makefile distinfo Log: Update to 2.11.1 PR: 148264 Prodded by: David Wolfskill <david@catwhisker.org> Approved by: makc (co-mentor) Revision Changes Path 1.91 +1 -2 ports/math/R/Makefile 1.43 +3 -3 ports/math/R/distinfo _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
State Changed From-To: feedback->closed Committed. Thanks!