Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-11 Thread Martin Maechler
Fantastic. Thanks a lot, Luke! I can close the thread just to say the finalit wasn't Matrix after all! ;-) On Fri, Apr 8, 2011 at 20:48, luke-tier...@uiowa.edu wrote: Fixed in R-devel by 55385 and R-2-113-branch by 55386. The problem was a call to install() in the C srouce code

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-11 Thread luke-tierney
Given the configure settings this looks like its probably an issue in regexpr's internals rather than in Matrix per se. I can confirm that with gctorture() for (i in 1:100) regexpr(package:, package:lattice, fixed = TRUE) Error in regexpr(package:, package:lattice, fixed = TRUE) :

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-11 Thread Hin-Tak Leung
--- On Fri, 8/4/11, Martin Maechler maech...@stat.math.ethz.ch wrote: Fantastic.  Thanks a lot, Luke! I can close the thread just to say the final    it wasn't Matrix after all! ;-) I am glad it is all working out - I have spent way too much time on this, having gone through about

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-11 Thread luke-tierney
Fixed in R-devel by 55385 and R-2-113-branch by 55386. The problem was a call to install() in the C srouce code without protecting another value before the install call. This particular issue was very unlikely to cause a problem outside of a gctorture context, but in that context with the memory

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-08 Thread peter dalgaard
(Resending with fewer recipients...) On Apr 8, 2011, at 07:09 , Hin-Tak Leung wrote: --- On Fri, 8/4/11, peter dalgaard pda...@gmail.com wrote: On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: Oh, I am tracking both R and Matrix via git-svn and retrieves all revisions to all branches

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-08 Thread Prof Brian Ripley
On Fri, 8 Apr 2011, peter dalgaard wrote: (Resending with fewer recipients...) On Apr 8, 2011, at 07:09 , Hin-Tak Leung wrote: --- On Fri, 8/4/11, peter dalgaard pda...@gmail.com wrote: On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: Oh, I am tracking both R and Matrix via git-svn and

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-08 Thread Hin-Tak Leung
--- On Fri, 8/4/11, peter dalgaard pda...@gmail.com wrote: On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: Oh, I am tracking both R and Matrix via git-svn and retrieves all revisions to all branches daily (or at least, regularly). I.e. R svn head.  2.13.0 only forked off recently and

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-08 Thread peter dalgaard
On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: Oh, I am tracking both R and Matrix via git-svn and retrieves all revisions to all branches daily (or at least, regularly). I.e. R svn head. 2.13.0 only forked off recently and most of the trunk-2.13.0rc differences are so far mostly

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Hin-Tak Leung
Douglas Bates wrote: I isolated the problem and tested then committed a fix. I am going to ask Martin to upload the new release as I have gotten out of sync with some of his recent changes and he will, I hope, reconcile the branches and trunk. If you need the fixed version immediately, say for

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Martin Maechler
HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 7 Apr 2011 07:51:44 +0100 writes: HL Douglas Bates wrote: I isolated the problem and tested then committed a fix. I am going to ask Martin to upload the new release as I have gotten out of sync with some of his

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Martin Maechler
Martin Maechler maech...@stat.math.ethz.ch on Thu, 7 Apr 2011 12:24:32 +0200 writes: HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 7 Apr 2011 07:51:44 +0100 writes: HL Douglas Bates wrote: I isolated the problem and tested then committed a fix. I am going to

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Hin-Tak Leung
Martin Maechler wrote: Martin Maechler maech...@stat.math.ethz.ch on Thu, 7 Apr 2011 12:24:32 +0200 writes: HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 7 Apr 2011 07:51:44 +0100 writes: HL Douglas Bates wrote: I isolated the problem and tested then committed a

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Martin Maechler
HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 07 Apr 2011 19:31:35 +0100 writes: HL Martin Maechler wrote: Martin Maechler maech...@stat.math.ethz.ch on Thu, 7 Apr 2011 12:24:32 +0200 writes: HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 7

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Hin-Tak Leung
--- On Thu, 7/4/11, Martin Maechler maech...@stat.math.ethz.ch wrote: ???  But  the prerelease version of R-2.13.0 *contains* already Matrix_0.999375-49  the one you claim has the bug. [[and you still haven't told use the exact R version you were using]] Oh, I am tracking both R and

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Hin-Tak Leung
Hin-Tak Leung wrote: Martin Maechler wrote: Martin Maechler maech...@stat.math.ethz.ch on Thu, 7 Apr 2011 12:24:32 +0200 writes: HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 7 Apr 2011 07:51:44 +0100 writes: HL Douglas Bates wrote: I isolated the problem and

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-30 Thread Douglas Bates
On Tue, Mar 29, 2011 at 2:17 PM, Douglas Bates ba...@stat.wisc.edu wrote: On Tue, Mar 29, 2011 at 5:34 AM, Hin-Tak Leung ht...@users.sourceforge.net wrote: Martin Maechler wrote: Douglas Bates ba...@stat.wisc.edu    on Mon, 28 Mar 2011 09:24:39 -0500 writes:     Can you provide the output

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-29 Thread Hin-Tak Leung
Martin Maechler wrote: Douglas Bates ba...@stat.wisc.edu on Mon, 28 Mar 2011 09:24:39 -0500 writes: Can you provide the output from sessionInfo() so we can know the platform? Also, did you configure R with --enable-strict-barrier or set the C compilation flag

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-28 Thread Martin Maechler
Douglas Bates ba...@stat.wisc.edu on Mon, 28 Mar 2011 09:24:39 -0500 writes: Can you provide the output from sessionInfo() so we can know the platform? Also, did you configure R with --enable-strict-barrier or set the C compilation flag -DTESTING_WRITE_BARRIER? I

[Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-26 Thread Hin-Tak Leung
Current core/Recommended Matrix package (0.999375-48) has been segfaulting against R 2.13-alpha/2.14-trunk for the last week or so (since R-2.13 was branched, when I started trying) when run with R CMD check --use-gct: -- pkgname - Matrix source(file.path(R.home(share), R,