Hi Elisabeth,

the following worked for me to install and load both libraries in
Bioconductor 2.12.  If you can't install and load hgu133plus2.db in the
usual way, there may be something broken about your local installation.

> library(BiocInstaller)
> biocLite(c("org.Mm.eg.db", "hgu133plus2.db"))
> library(devtools)
> install_url("
http://bioconductor.org/packages/2.6/data/annotation/src/contrib/illuminaMousev2BeadID.db_1.6.1.tar.gz
")
> library(hgu133plus2.db)
> library(illuminaMousev2BeadID.db)
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] illuminaMousev2BeadID.db_1.6.1 org.Mm.eg.db_2.9.0
 [3] hgu133plus2.db_2.9.0           org.Hs.eg.db_2.9.0
 [5] RSQLite_0.11.4                 DBI_0.2-7
 [7] AnnotationDbi_1.22.6           Biobase_2.20.1
 [9] BiocGenerics_0.6.0             BiocInstaller_1.10.3
[11] devtools_1.3

loaded via a namespace (and not attached):
 [1] digest_0.6.3   evaluate_0.4.7 httr_0.2       IRanges_1.18.3
 [5] memoise_0.1    RCurl_1.95-4.1 stats4_3.0.1   stringr_0.6.2
 [9] tools_3.0.1    whisker_0.3-2
>




On Thu, Sep 5, 2013 at 8:28 AM, E.M. Lodder <e.m.lodder@amc.uva.nl> wrote:

> Hi Diego,
>
> Sorry I didn't copy that in the example, but I did install it first, it
> gives exactly the same error message.
>
> Does anyone know the reason for not allowing these packages in newer
> versions of BioC?
> I guess many people like me will have older datasets they may want to
> reanalyse.
> The contents of these kind of reference packages is not code which I can
> understand may refer to obsolete functions etc. but just reference data,
> for the annotation of the probe names so I don't really understand why they
> would not just be taken along.
>
> Elisabeth
>
> -----Original Message-----
> From: kurai.yousei@gmail.com [mailto:kurai.yousei@gmail.com] On Behalf Of
> Diego Diez
> Sent: donderdag 5 september 2013 10:51
> To: E.M. Lodder
> Cc: Marc Carlson; bioconductor@r-project.org
> Subject: Re: [BioC] package availability for R3.01
>
> The link you include with illuminaMousev2BeadID.db is for bioconductor
> 2.6 (i.e. a release several years old). It seems that package does not
> exist anymore in Bioconductor (since version 2.9, now we are in 2.12).
> As for hgu133plus2.db, you have to install it first (you only tried to
> install illuminaMousev2BeadID.db in your example code). Try:
>
> biocLite("hgu133plus2.db")
> library(hgu133plus2.db)
>
> HTH,
>
> Diego
>
>
> On Thu, Sep 5, 2013 at 5:29 PM, E.M. Lodder <e.m.lodder@amc.uva.nl> wrote:
> >
> > Hi all,
> >
> > I'm afraid that doesn't answer my question, both packages are available
> through the bioconductor website:
> >
> > http://bioconductor.org/packages/2.6/data/annotation/html/illuminaMous
> > ev2BeadID.db.html
> > and
> > http://bioconductor.org/packages/release/data/annotation/html/hgu133pl
> > us2.db.html
> >
> > but give this same error message when installing:
> >
> > > Warning message:
> > > package 'illuminaMousev2BeadID.db' is not available (for R version
> > > 3.0.1)
> >
> > any more ideas?
> >
> > Elisabeth
> >
> >
> > -----Original Message-----
> > From: bioconductor-bounces@r-project.org
> > [mailto:bioconductor-bounces@r-project.org] On Behalf Of Marc Carlson
> > Sent: woensdag 4 september 2013 22:21
> > To: bioconductor@r-project.org
> > Subject: Re: [BioC] package availability for R3.01
> >
> > Hi Elisabeth,
> >
> > That package "illuminaMousev2BeadID.db"  is not a bioconductor package
> and I don't think it ever has been a bioconductor package.  Perhaps someone
> in the past made a custom package for you and then named it that?  In any
> case, you can look at this vignette if you need to repeat that process:
> >
> > http://www.bioconductor.org/packages/release/bioc/vignettes/Annotation
> > Forge/inst/doc/SQLForge.pdf
> >
> >
> > As for the "hgu133plus2.db" package, you can get that package using
> > biocLite() as it is a bioconductor package.  If you want to see a list
> of all the annotation packages for the latest release you can find it here:
> >
> > http://www.bioconductor.org/packages/release/BiocViews.html#___Annotat
> > ionData
> >
> >
> >
> >    Marc
> >
> >
> >
> >
> > On 09/04/2013 12:39 PM, E.M. Lodder wrote:
> > > Hi All,
> > >
> > > Just a quick question I just updated my R to 3.01 and wanted to
> reinstall some of the packages I was using.
> > > Now I do get the following error message:
> > >
> > >>      source("http://bioconductor.org/biocLite.R")
> > >>      biocLite("illuminaMousev2BeadID.db")
> > > BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12
> > > (BiocInstaller 1.10.3), R version 3.0.1.
> > > Installing package(s) 'illuminaMousev2BeadID.db'
> > > Warning message:
> > > package 'illuminaMousev2BeadID.db' is not available (for R version
> > > 3.0.1)
> > >> library("hgu133plus2.db",character.only = TRUE)
> > > Error in library("hgu133plus2.db", character.only = TRUE) :
> > >    there is no package called 'hgu133plus2.db'
> > >> library("illuminaMousev2BeadID.db", character.only = TRUE)
> > > Error in library("illuminaMousev2BeadID.db", character.only = TRUE) :
> > >    there is no package called 'illuminaMousev2BeadID.db'
> > > Any ideas on how to fix this? Or should I just operate with two
> different versions of R in parallel for the moment?
> > >
> > > Thanks!
> > >
> > > Elisabeth
> > > ________________________________
> > >
> > > AMC Disclaimer : http://www.amc.nl/disclaimer
> > >
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> >
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-- 
Levi Waldron
Assistant Professor
Epidemiology and Biostatistics Program
CUNY School of Public Health at Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003

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