Maybe Gabe could share the linker line. I think (from the man page) as long as the directory with the static lib comes first with -L, it should find the static lib, not the shared object.
On Wed, Jul 27, 2016 at 6:48 AM, Martin Morgan <martin.mor...@roswellpark.org> wrote: > Hi Gabe -- > > On 07/21/2016 12:08 PM, Maintainer wrote: >> >> Hi all, >> >> I build the R installations on our research cluster. Unfortunately we >> are running an older OS so the system versions of various libraries >> (libz, bz2, pcre and libcurl, specifically) are not modern enough to >> build R with. >> >> For protection from ABI incompatability when R is interacting with other >> programs on the system, I have built static versions of those libraries >> and linked them directly into R. This works fine once a few gotchas are >> taken care of. >> >> After an inordinant amount of work, I have tracked an intermittent >> segfault we have been getting to Rsamtools, and specifically the version >> of libz that it grabs during linking. >> >> The problem is that Rsamtools is hardcoded to have -lz in it's PKG_LIBS >> variable by Makevars (I believe this is because the embedded version of >> samtools needs libz). Because there is no way (that I know of) to take >> the system libz out of the path, and it is an so, it will ALWAYS be used >> instead of the static one I want it to use instead. Furthermore, AFAICS >> there is no way to override the PKG_LIBS construction with an >> environment variable. >> >> Can someone please make Rsamtools' Makevars a bit more polite for those >> of us stuck in old OSes? >> Barring that (and until that lands) I am stuck downloading and modifying >> the package locally, which I really don't like doing. > > > Sorry to be slow at this. I guess this could be done 'elegantly' via > configure.ac, but that introduces some complexity. I was wondering... > > Other packages hard-code -lz, including e.g., rtracklayer, > VariantAnnotation, Rsubread, and R itself (including grDevices). So I guess > this is a general problem? > > Can you build R with static linkage, and set LDFLAGS to include a 'custom' > location before the system-wide location? > > Martin > >> >> Thanks, >> ~G >> >> >> -- >> Gabriel Becker, Ph.D >> Associate Scientist >> Bioinformatics and Computational Biology >> Genentech Research >> >> >> ________________________________________________________________________ >> devteam-bioc mailing list >> To unsubscribe from this mailing list send a blank email to >> devteam-bioc-le...@lists.fhcrc.org >> You can also unsubscribe or change your personal options at >> https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >> > > > This email message may contain legally privileged and/or...{{dropped:2}} > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel