From albapompeo at gmail.com  Mon Feb  1 18:33:11 2016
From: albapompeo at gmail.com (Alba Pompeo)
Date: Mon, 1 Feb 2016 15:33:11 -0200
Subject: [Rd] Wrong config check for __libc_stack_end
In-Reply-To: <5A694E77-F32F-41C4-8D6D-1E1119ABFCB1@r-project.org>
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Here's what I did.

svn checkout https://svn.r-project.org/R/trunk/
cd ./trunk
aclocal -I m4 && autoconf
tools/rsync-recommended
cd ..
mkdir build
cd build
../trunk/configure
make
make check

On make check it gives an error.
Here's the log.
http://pastebin.com/raw/1qfjqQY2


On Mon, Feb 1, 2016 at 1:53 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
> On Feb 1, 2016, at 9:56 AM, Alba Pompeo <albapompeo at gmail.com> wrote:
>
>> @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)
>
> No, the whole point was to test this behavior. I see that the fix is in configure.ac but not configure so you'll need to run something like
> aclocal -I m4 && autoconf
> to update it.
>
> Also please don't build in the sources - you'll have trouble making sure they are clean. It is recommended to build in a separate directory (see the docs).
>
>
>> Ran ./configure --without-recommended-packages. (otherwise it would
>> complain of not finding ./src/library/Recommended/MASS_*.tar.gz)
>
> I guess you forgot to run
> tools/rsync-recommended
> perhaps? It doesn't matter either way for the above issues, but it's probably better to build with recommended packages.
>
> Cheers,
> Simon
>
>
>> Ran make.
>> 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 -
>>>>>> http://pastebin.com/raw/UwFRsiqT
>>>>>>
>>>>>> 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 ??)
>>>> faster.
>>>>
>>>
>>> No, it's actually very crucial as it is used to detect stack overflows.
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>
>>>>>> 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,
>>>>
>>>> http://wiki.musl-libc.org/wiki/Functional_differences_from_glibc#Floating-point_and_mathematical_library
>>>>
>>>> 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
>>>>
>>>> --
>>>> Martin <Maechler at stat.math.ethz.ch>  http://stat.ethz.ch/people/maechler
>>>> Seminar f?r Statistik, ETH Z?rich
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>>
>



[Rd] Wrong config check for __libc_stack_end
Alba Pompeo