[Rd] Wrong config check for __libc_stack_end
albapompeo at gmail.com
Mon Feb 1 15:56:00 CET 2016
@Simon. Here's what I did.
I checked out R revision 70059.
Ran export r_cv_libc_stack_end=no. (otherwise it would give that error
we talked about before)
Ran ./configure --without-recommended-packages. (otherwise it would
complain of not finding ./src/library/Recommended/MASS_*.tar.gz)
Ran make check. Log is here - http://pastebin.com/raw/cGJgqB8p
What do you think? Is there anything else I can do to help solve this issue?
On Mon, Feb 1, 2016 at 11:36 AM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
> On Feb 1, 2016, at 4:16 AM, Martin Maechler <maechler at stat.math.ethz.ch> wrote:
>>>>>>> Alba Pompeo <albapompeo at gmail.com>
>>>>>>> on Fri, 29 Jan 2016 08:23:26 -0200 writes:
>>> Here is my log from 'make check' using an Intel i5 64-bit
>>> processor - http://pastebin.com/raw/N6SYAuFX Here is
>>> Isaac's log from 'make check' using an Intel Atom 32-bit
>>> processor - http://pastebin.com/raw/sey6DEk9
>>> We are both on Alpine Linux, which uses the musl
>>> libc. http://www.musl-libc.org/
>>> Thank you very much.
>> It probably would have helped to choose a different subject
>> which I now do.
> Agreed, since there is actually no abuse, case was easily dismissed as bogus given the subject.
>>> On Thu, Jan 28, 2016 at 9:54 AM, Alba Pompeo
>>> <albapompeo at gmail.com> wrote:
>>>> Hello, developers of R.
>>>> I have been unsuccessfully trying to build R on a musl
>>>> libc system for the last days. ./configure works, but
>>>> make fails. The command that errors out is here -
>>>> It was brought to my attention that this is a (very
>>>> longstanding) abuse of a private glibc symbol in R.
>>>> In R 3.2.3, it seems that configure is trying to test for
>>>> it on Linux. It apparently fails to accurately test (as
>>>> demonstrated by the link error), perhaps because the test
>>>> program does not actually *use* __libc_stack_end so it
>>>> gets optimized out. (See line 35500 or so in
>>>> R-3.2.3/configure.) Ideally, the test program would
>>>> check that a pointer to __libc_stack_end is non-null, but
>>>> that's an autoconf bug.
>> So, ideally someone who knows autoconf much better than I do
>> should submit a bug report to the autoconf maintainers.
> @Alba, can you, please, check that your hypothesis actually holds true and the latest R from trunk fixes the check for you?
>> Back to R: I'm not familiar with that part of the code, neither
>> the configuration, nor the usage (in R/src/unix/system.c ).
>> However, that code seems to be using a a glibc "feature" widely
>> available which does help making R startup (a very tiny bit ??)
> No, it's actually very crucial as it is used to detect stack overflows.
>>>> A work around was to 'export r_cv_libc_stack_end=no'
>>>> before configuring R.
>> which *does* solve that problem, right?
>>>> However, there are a couple little issues with non-ASCII
>>>> text and a *lot* of math differences, many of which say
>>>> "*no* convergence: NOTIFY R-core!".
>> Hmm, I may be off, but these would look like entirely unrelated
>> with the libc_stack_end availibility, wouldn't they ?
>> Maybe you / the musl developers should try to make those C
>> libraries more "standard", notably because I would see math
>> differences as something pretty grave for R, and indeed, I would
>> not want to use a platform where R's math functions work
>> incompatibly with all other platforms ... but maybe I
>> misunderstand completely.
>> Hmm... I've found this,
>> which make what you say above more relevant/interesting.
>> Still, from this thread I get that the C source code of R needs
>> considerable configuration patches before R can work with musl.
>> But that needs another thread, something like 'Building R with musl'.
>>>> Until these are resolved, R can't be packaged for
>>>> distributions that use musl, such as Alpine Linux.
>> which I agree would not be ideal.
>> Martin <Maechler at stat.math.ethz.ch> http://stat.ethz.ch/people/maechler
>> Seminar für Statistik, ETH Zürich
>> R-devel at r-project.org mailing list
More information about the R-devel