Dear Colleagues,

thank you very much for you comments. Indeed, there was still other R
version "lingering" in the directory I did not expect. After we removed all
versions and did clean install R works beautifully, no errors, no warring :)

All Best,
Monika

On Thu, Aug 1, 2013 at 9:40 AM, Laurent Gatto <lg390@cam.ac.uk> wrote:

> Dear Monika,
>
> In case you could not implement 'the right way', as per Dan's email,
> here are a few hints/clarifications regarding mzR.
>
> The first thing to do when switching back to R 2.15.3 is to run
> biocLite to update (actually downgrade) the Bioconductor packages to
> match the R version. This should also downgrade mzR to version 1.4.6,
> I believe. The matching Rcpp version should then be 0.10.3.
>
> Note that based on your first email, it does not seem that you have an
> actual error but just a warning. When loading the package, mzR checks
> whether the Rcpp version used to build the binary package that you
> have and the actual installed Rcpp version are the same and warns if
> there is a mismatch. This does not mean that things will go wrong
> (although things have gone wrong in the past, resulting in the warning
> message you see): mzR 1.4.6 (originally built using Rcpp 0.10.3) does
> work with 0.10.3 and _might_ also work with the latest Rcpp 0.10.4.
>
> Hope this helps.
>
> Best wishes,
>
> Laurent
>
>
> On 1 August 2013 16:02, Monika Tokmina-Lukaszewska
> <tokminalukas@gmail.com> wrote:
> > Steve, Dan,
> >
> > Thank you guys for your comments. Unfortunately, the problem started when
> > we installed R 3.0.1 version-metaXCMS package is build under lower
> version
> > and does not work at all (our fault, we should have checked that before
> > updating R). So we went back to R (2.15.3) version and to our surprise we
> > got this error after opening the new session. Now, even more packages are
> > not functional and there is no use of the software on this computer at
> the
> > moment.
> > Should we try to install Rcpp 0.10.4, or it works only with 3.0 version?
> We
> > tried Rcpp 0.9.10 but got error....
> >
> > All best, Monika
> >
> > On Wed, Jul 31, 2013 at 6:34 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
> wrote:
> >
> >> On Wed, Jul 31, 2013 at 4:39 PM, Steve Lianoglou
> >> <lianoglou.steve@gene.com> wrote:
> >> > Hi,
> >> >
> >> > On Wed, Jul 31, 2013 at 4:28 PM, Monika Lukaszewska [guest]
> >> > <guest@bioconductor.org> wrote:
> >> >>
> >> >> To whom it may concern:
> >> >> Here I get this error when I open new R session:
> >> >>
> >> >> "During startup - Warning messages:
> >> >> 1: In fun(libname, pkgname) :
> >> >>    mzR has been built against a different Rcpp version
> >> >>  than is installed on your system. This might lead to errors
> >> >>  when loading mzR. If you encounter such issues, please send
> >> >>  a report, including the output of sessionInfo() to the Bioc
> >> >>  mailing list -- http://www.bioconductor.org/help/mailing-list.
> >> >> 2: Class "C++Object" is defined (with package slot ‘Rcpp’) but no
> >> metadata object found to revise subclass information---not exported?
> >>  Making a copy in package ‘.GlobalEnv’"
> >> >>
> >> >> I have installed xcms and metaXCMS packages but I encounter several
> >> errors when I try to run metaXCMS.
> >> >>
> >> >> I installed/uninstall R several times. IS there a way of fixing
> >> mzR/Rcpp problem?
> >> >
> >> > You're installing an old(er) version of R (2.15.3), please install the
> >> > latest version of R (3.0.1) and then reinstall your packages using
> >> > biocLite.
> >> >
> >> > There was some chatter about mzR and Rcpp inconsistencies some time
> >> > ago, which maybe what is biting you now, and I believe has since been
> >> > resolved. The upgrade to R 3.0.1 will likely be all you need.
> >> >
> >> > You'll also get the added bonus of using the latest and greatest (and
> >> > supported) versions of the Bionconductor packages you will be using
> >> > for your analysis.
> >> >
> >>
> >> And when you're done with all that, make sure you have Rcpp 0.10.4
> >> installed.
> >>
> >>
> >>
> >> > HTH,
> >> > -steve
> >> >
> >> > --
> >> > Steve Lianoglou
> >> > Computational Biologist
> >> > Bioinformatics and Computational Biology
> >> > Genentech
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor@r-project.org
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >
> >
> > --
> > Monika Lukaszewska
> >
> > Postdoctoral Fellow
> > Chemistry & Biochemistry Department
> > Montana State University
> > Bozeman MT, 59717
> > lab: (406) 994 5418
> > tokminalukas@chemistry.montana.edu
> >
> >         [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
> --
> Laurent Gatto
> - http://proteome.sysbiol.cam.ac.uk/lgatto/
> Cambridge Centre for Proteomics
> - http://www.bio.cam.ac.uk/proteomics
> Using R/Bioconductor for proteomics data analysis
> - http://lgatto.github.io/RforProteomics/
>



-- 
Monika Lukaszewska

Postdoctoral Fellow
Chemistry & Biochemistry Department
Montana State University
Bozeman MT, 59717
lab: (406) 994 5418
tokminalukas@chemistry.montana.edu

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