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

Gabe Becker becker.gabe at gene.com
Thu Jul 21 18:08:37 CEST 2016

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

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.


Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research

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