[BioC] Lumi failed to load

[Dan Tenenbaum]

----- Original Message -----
> From: "Tim Triche, Jr." <tim.triche at gmail.com>
> To: "Pan Du" <dupan.mail at gmail.com>
> Cc: "Hitoshi Okada" <hokada0421 at gmail.com>, bioconductor at r-project.org
> Sent: Friday, October 11, 2013 10:15:22 AM
> Subject: Re: [BioC] Lumi failed to load
> 
> This is presumably my fault.  Will fix and commit.
> 
> --t
> 
> *He that would live in peace and at ease, *
> *Must not speak all he knows, nor judge all he sees.*
> *
> *
> Benjamin Franklin, Poor Richard's
> Almanack<http://archive.org/details/poorrichardsalma00franrich>
> 
> 
> On Fri, Oct 11, 2013 at 4:04 AM, Pan Du <dupan.mail at gmail.com> wrote:
> 
> > Hi Hitoshi
> >
> > Based on the information you provided. I believe the problem
> > happens when
> > you loading the methylumi package. So please check whether
> > methylumi
> > package was properly installed. If the problem still exists, please
> > provide
> > your sessionInfo().
> >

I don't think this is really a methyLumi problem. I think the problem is that we flushed our repositories and then minfi failed to build, We are working on this and it should be fixed by tomorrow morning Seattle time.

Dan


> >
> > Pan
> >
> >
> > On Fri, Oct 11, 2013 at 3:00 AM,
> > <bioconductor-request at r-project.org>
> > wrote:
> >
> > >
> > >
> > > Date: Thu, 10 Oct 2013 19:12:51 -0400
> > > From: Hitoshi Okada <hokada0421 at gmail.com>
> > > To: bioconductor at r-project.org
> > > Subject: [BioC] Lumi failed to load
> > > Message-ID: <CC3D6769-98D2-4705-BD34-59ED0CCB3F1A at gmail.com>
> > > Content-Type: text/plain; charset=windows-1252
> > >
> > > Hi,
> > >
> > > I have installed R version 3.0.2 (Mac version, MacOS is
> > > 10.8.5)and lumi
> > > (2.12), and tried to load but failed with the  message at bottom.
> > >
> > > I appreciate any suggestions to solve this problem. I have
> > > updated
> > > Bioconductor packages are updated.
> > >
> > > Thank you
> > >
> > > Hitoshi
> > >
> > >
> > > > library(lumi)
> > > Loading required package: Biobase
> > > Loading required package: BiocGenerics
> > > Loading required package: parallel
> > >
> > > Attaching package: ?BiocGenerics?
> > >
> > > The following objects are masked from ?package:parallel?:
> > >
> > >     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> > clusterExport,
> > >     clusterMap, parApply, parCapply, parLapply, parLapplyLB,
> > >     parRapply,
> > >     parSapply, parSapplyLB
> > >
> > > The following object is masked from ?package:stats?:
> > >
> > >     xtabs
> > >
> > > The following objects are masked from ?package:base?:
> > >
> > >     anyDuplicated, append, as.data.frame, as.vector, cbind,
> > >     colnames,
> > > duplicated,
> > >     eval, Filter, Find, get, intersect, lapply, Map, mapply,
> > >     match, mget,
> > > order,
> > >     paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
> > Reduce,
> > >     rep.int, rownames, sapply, setdiff, sort, table, tapply,
> > >     union,
> > > unique,
> > >     unlist
> > >
> > > Welcome to Bioconductor
> > >
> > >     Vignettes contain introductory material; view with
> > > 'browseVignettes()'. To
> > >     cite Bioconductor, see 'citation("Biobase")', and for
> > >     packages
> > >     'citation("pkgname")'.
> > >
> > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
> > versionCheck
> > > = vI[[j]]) :
> > >   there is no package called ?minfi?
> > > In addition: Warning message:
> > > replacing previous import by ?graphics::image? when loading
> > > ?methylumi?
> > > Error: package or namespace load failed for ?lumi?
> > >
> > >
> > >
> > >
> >
> >         [[alternative HTML version deleted]]
> >
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