From ripley at stats.ox.ac.uk  Thu Mar 29 16:24:28 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Thu, 29 Mar 2007 15:24:28 +0100 (BST)
Subject: [Rd] zlib+shlib issue with the official EL4 R binary
In-Reply-To: <460BC6EB.3010502@cimr.cam.ac.uk>
References: <460BC6EB.3010502@cimr.cam.ac.uk>
Message-ID: <Pine.LNX.4.64.0703291522480.24561@auk.stats>

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:

> Hi,
>
> I have got a curious issue with an R package which uses zlib, against
> the official binary here:
> http://cran.r-project.org/bin/linux/redhat/el4/i386/R-2.4.1-1.rh4AS.i386.rpm
> 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...].
> (http://docs.fedoraproject.org/release-notes/fc6/en_US/sn-Devel.html#id2956225)
>
> 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 1.2.1.2...).
>
> 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
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
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



[Rd] zlib+shlib issue with the official EL4 R binary
Prof Brian Ripley