[BioC] error when loading mzR

[Laurent Gatto]

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 at 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 at fhcrc.org> wrote:
>
>> On Wed, Jul 31, 2013 at 4:39 PM, Steve Lianoglou
>> <lianoglou.steve at gene.com> wrote:
>> > Hi,
>> >
>> > On Wed, Jul 31, 2013 at 4:28 PM, Monika Lukaszewska [guest]
>> > <guest at 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 at 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 at chemistry.montana.edu
>
>         [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at 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/