[BioC] error when loading mzR

[Dan Tenenbaum]

On Thu, Aug 1, 2013 at 8:02 AM, 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....
>

When you reinstall R you should always do a fresh install; don't
reinstall R and then expect previously installed packages to work.
Similarly, don't mix and match packages from different versions of
Bioconductor.

If you follow these rules and always install packages with biocLite(),
everything should work. So, recommendation: Do a clean install of R
3.0.1 (removing previous installations or installing in a different
directory), then use biocLite() to install all the packages you need.

Dan


> 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