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

[Gabe Becker]

Martin and Michael,

It looks like I have been conflating two issues when trying to deal with
these things. The problem of grabbing the system libz seems to have gone
away in the Rsamtools case earlier than in the libR.so case during my
process. wwI will check back in if something raises it's head again, but
Michael appears to be correct that just -L is sufficient (it didn't seem to
be for a long time but I think that's because libR.so wasn't getting my -L
when I thought it was).

So lets just leave it at I'm sorry for the noise and I'll be really happy
when I'm not elbow-deep in linker calls for days on end anymore...

Best,
~G



On Wed, Jul 27, 2016 at 8:05 AM, Michael Lawrence <lawrence.michael at gene.com
> wrote:

> 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.morgan at 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
> >>
> >>
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>



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

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