On Feb 1, 2016, at 9:56 AM, Alba Pompeo <albapom...@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.urba...@r-project.org> wrote: >> >> On Feb 1, 2016, at 4:16 AM, Martin Maechler <maech...@stat.math.ethz.ch> >> wrote: >> >>>>>>>> Alba Pompeo <albapom...@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 >>>> <albapom...@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 <maech...@stat.math.ethz.ch> http://stat.ethz.ch/people/maechler >>> Seminar für Statistik, ETH Zürich >>> >>> ______________________________________________ >>> R-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
