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@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
