On Thu, 29 Mar 2007, Hin-Tak Leung wrote: > 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?
My belief is that the systems you are considering support visibility attributes (but I don't know for sure about EL4 since Redhat versions of tools do when the standard ones do not). If so, libR.so does not export the zlib entry points. > 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. sensitive _to a particular bug_ There has been such a bug: see the comments in gzfile_fgetc and its history. > 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@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>>> >>> >>> >> > -- Brian D. Ripley, [EMAIL PROTECTED] 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 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
