From hin-tak.leung at cimr.cam.ac.uk  Thu Mar 29 16:59:30 2007
From: hin-tak.leung at cimr.cam.ac.uk (Hin-Tak Leung)
Date: Thu, 29 Mar 2007 15:59:30 +0100
Subject: [Rd] zlib+shlib issue with the official EL4 R binary
In-Reply-To: <Pine.LNX.4.64.0703291539130.17915@gannet.stats.ox.ac.uk>
References: <460BC6EB.3010502@cimr.cam.ac.uk>
	<Pine.LNX.4.64.0703291522480.24561@auk.stats>
	<Pine.LNX.4.64.0703291539130.17915@gannet.stats.ox.ac.uk>
Message-ID: <460BD452.2030705@cimr.cam.ac.uk>

Prof Brian Ripley wrote:
> On Thu, 29 Mar 2007, Prof Brian Ripley wrote:
> 
>> 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.
> 
> I've checked, and he no longer does so, sorry.  So there is a zlib 
> inside R, and its entry points will be visible to a packages' .so when R 
> is built as a binary, but not when it is built as a shared library.  In 
> that case it depends on the fine details (including of what you did) 
> whether
> mypackage.so resolved against R.bin or libz.so in the first two lines of 
> your table.  But it is entirely possible that it links against R.bin in 
> line 2 and libz.so in line 3.
> 
> If your program is that sensitive to the version of libz I think you 
> should statically link against your own copy (which is R's solution for 
> its own purposes).

Hmm, I have always thought it is the reverse - i.e. when R is built
with shlib, the internal version of zlib is exposed to packages' so?

gzeof() is just for detecting end of file - I don't think it is
a "sensitive" use of zlib. It is just better to be able to tell when
read failed, whether one has *actually* reach end of file or not.

I'll try bundling the latest zlib with my package and see if it
makes any differences... thanks!

Hin-Tak

>> 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
>>>
>>
>>
>



[Rd] zlib+shlib issue with the official EL4 R binary
Hin-Tak Leung