Re: Assertion failed when building r-base on Aranym
On Sat, 3 Dec 2016, John Paul Adrian Glaubitz wrote:
> On 11/29/2016 12:39 AM, Andreas Schwab wrote:
> > On Nov 29 2016, John Paul Adrian Glaubitz
> > <glaubitz@physik.fu-berlin.de> wrote:
> >
> >> Are there any m68k-specific patches or build flags which might be
> >> missing in Debian? If possible, could you share your SRPM?
> >
> > It's a bog-standard configure/make/install. Make sure your glibc
> > wasn't miscompiled by the broken qemu.
>
> Ok, I have recompiled glibc on Aranym and tried building r-base with
> that version. The problem is still occurring:
>
> R: malloc.c:2403: sysmalloc: Assertion `(old_top == initial_top (av) &&
> old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse
> (old_top) && ((unsigned long) old_end & (pages ize - 1)) == 0)' failed.
When I googled that assertion failure, I got the impression that whilst
the assertion is in glibc code, the bug usually isn't. The assertion gets
triggered when glibc data structures get clobbered by a program that
overflows an allocated block etc.
> /bin/bash: line 1: 17541 Done echo
> "tools:::data2LazyLoadDB(\"datasets\", compress=3)"
> 17542 Aborted | R_DEFAULT_PACKAGES=NULL LC_ALL=C ../../../bin/R --vanilla --slave > /dev/null
> Makefile:21: recipe for target 'all' failed
>
... which leads me to think the bug is probably in this R binary.
I suppose you or Andreas could try this binary on a system with a
known-good glibc if you wanted to eliminate glibc as a possible cause.
Are there debugging tools or malloc implementations on m68k that could
isolate an out-of-bounds access to heap memory?
--
> The last known successful build on Aranym was with Debian's
> libc6_2.19-16 package with r-base 3.2.2 [1]. Will downgrad glibc to this
> version now and try again.
>
> Adrian
>
> > [1] https://buildd.debian.org/status/fetch.php?pkg=r-base&arch=m68k&ver=3.2.2-1&stamp=1445983541
>
>
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