[Bioc-devel] mzR 1.4.0 crashes R at loading
sneumann at ipb-halle.de
Thu Nov 22 21:37:11 CET 2012
thanks Dan for fixing this. I can vaguely remember
we've had such a problem before.
Is there any way to avoid that problem in the future ?
Is it that BioC needs to recompile packages when
their dependencies change ?
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 ?
I.o.w: how to do this the proper way...
Sorry for crossposting, I think it is relevant for both sides.
On Thu, 2012-11-22 at 11:07 -0800, Dan Tenenbaum wrote:
> On Thu, Nov 22, 2012 at 5:20 AM, Alvaro Cuadros Inostroza
> <Inostroza at mpimp-golm.mpg.de> wrote:
> > Hi,
> > The last version of mzR crashes R-2.15.2 on windows (both 32 and 64 bit) at loading, i.e., R hangs after running "library(mzR)". I could confirm this in two computers (windows XP and 7).
> > The culprit might be Rcpp 0.10.0. I downgraded it to 0.9.15 (which I got from an old R installation) and now mzR works in both computers.
> > Coincidently, before a user reported me the error on windows, I had got an R crash on linux upon loading TargetSearch (my package which depends on mzR) which I fixed by re-installing both mzR and TargetSearch.
> > I suspect that mzR needs a version bump to force re-compilation. Maybe somebody can confirm this. I don't see any mzR error/warning in http://bioconductor.org/checkResults/2.11/bioc-LATEST/
> I can confirm the crash with the latest version available from the
> website. Also confirmed that it doesn't happen with the latest version
> of mzR built (but not yet propagated) on our windows build machine.
> I've bumped the version number of the release version of mzR so the
> new version will be available after 10AM tomorrow Seattle time.
> The problem does not seem to happen in devel, so I've left it alone.
> > Best regards,
> > --
> > Alvaro
> > # with downgraded Rcpp.
> >> library(mzR)
> > Loading required package: Rcpp
> >> sessionInfo()
> > R version 2.15.2 (2012-10-26)
> > Platform: i386-w64-mingw32/i386 (32-bit)
> > locale:
> >  LC_COLLATE=English_United States.1252
> >  LC_CTYPE=English_United States.1252
> >  LC_MONETARY=English_United States.1252
> >  LC_NUMERIC=C
> >  LC_TIME=English_United States.1252
> > attached base packages:
> >  stats graphics grDevices utils datasets methods base
> > other attached packages:
> >  mzR_1.4.0 Rcpp_0.9.15
> > loaded via a namespace (and not attached):
> >  Biobase_2.18.0 BiocGenerics_0.4.0 codetools_0.2-8
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> Bioc-devel at r-project.org mailing list
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