[Rd] zlib+shlib issue with the official EL4 R binary
Prof Brian Ripley
ripley at stats.ox.ac.uk
Thu Mar 29 16:24:28 CEST 2007
I presume you are talking about RPMs built with --with-system-zlib?
That's not recommended in the R-admin manual, and perhaps you can persuade
Martyn Plummer not to do it.
On Thu, 29 Mar 2007, Hin-Tak Leung wrote:
> I have got a curious issue with an R package which uses zlib, against
> the official binary here:
> on a Redhat EL4 i686 system.
> The problem is that at the end of reading a gzip'ed file within my
> C code, gzgetc() returns -1 (no more to read or error) but
> gzeof() doesn't return true. Now one can probably jump to conclusion
> that this is a zlib problem (or mine), but it is not. Here is
> the summary table (my package binary is the same one on the four
> 2.4.1 cases below - built against the official EL4 binary on EL4)
> Rver shlib buildhost runhost status of zlib code in mypackage
> 2.3.1 no EL4 EL4 ok
> 2.4.1 no EL4 EL4 ok
> 2.4.1 yes EL4 EL4 broken
> 2.4.1 yes EL4 FC6 ok
> 2.4.1 yes FC6 FC6 ok
> The most curious part is entry 3 vs 4 - if I just transplant
> the official R binary for EL4 and run it on FC6 (x86_64 and
> loading the same mypackage i686 binary), then it works.
> The dynamic linker on FC6 is very different from all the earlier
> redhat releases [and supposedly a lot faster...].
> so it looks like an issue due to a bad interaction for the
> combination of both the shlib compile-time option and the EL4
> runtime environment. (e.g. R 2.4.1 is shipped and bundled with
> zlib 1.2.3 but EL4 is only equiped with zlib 18.104.22.168...).
> For the moment I'll just recommend anybody who needs to run my
> package (snpMatrix in http://www-gene.cimr.cam.ac.uk/clayton/software/)
> on Redhat EL4 to just build and install R from source, since shlib=no
> is the default for compiling from source.
> Anybody has any idea how this strange brokenness of zlib might happen?
> Hin-Tak Leung
> R-devel at r-project.org mailing list
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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