[Bioc-devel] [devteam-bioc] Segfault in Rsamtools when R built with static libz

Martin Morgan martin.morgan at roswellpark.org
Wed Jul 27 15:48:23 CEST 2016

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?


> Thanks,
> ~G
> --
> Gabriel Becker, Ph.D
> Associate Scientist
> Bioinformatics and Computational Biology
> Genentech Research
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