[Rcpp-devel] [Bioc-devel] mzR 1.4.0 crashes R at loading

Laurent Gatto lg390 at cam.ac.uk
Thu Nov 22 22:05:51 CET 2012

On 22 November 2012 20:37, Steffen Neumann <sneumann at ipb-halle.de> wrote:
> Hi,
> thanks Dan for fixing this. I can vaguely remember
> we've had such a problem before.

We had this issue 6 months ago, when Rcpp 0.9.12 was released (see [1]
and commit r67124).

> Is there any way to avoid that problem in the future ?
> Is it that BioC needs to recompile packages when
> their dependencies change ?

As far as I understand, Bioc packages are not rebuild if dependencies
are updated. Dan, would it be possible to add an exception and
automatically rebuild mzR whenever a new verion of Rcpp is available?
If not, we will have to do manually bump the version for every Rcpp
update to avoid possible conflict - this should not be too difficult,
as Dirk announces new Rcpp version quite widely.

> Or should we have some *maximum* Rcpp version number
> in the mzR dependencies, so that we're forced
> to bump the mzR version if there are new Rcpp available ?

Forcing a strict Rcpp version in the DESCRIPTION file will break mzR
build at every Rcpp release - this is surely a stringent way to get
the developers react in a timely fashion :-). It does however not
happen with every new Rcpp verions - we had the problem with 0.9.12,
now with 0.10.0, but 0.9.13 to 0.9.15 did not, I believe, require any
package rebuild.

By the way, do other Bioc packages depending on Rcpp not suffer
similar side effects?

Best wishes,


[1] http://stackoverflow.com/questions/11181691/r-bioconductor-mzr-library-load-error/11212115

> I.o.w: how to do this the proper way...
> Sorry for crossposting, I think it is relevant for both sides.
> Yours,
> Steffen

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