[BioC] package availability for R3.01

James W. MacDonald jmacdon at uw.edu
Thu Sep 5 15:49:11 CEST 2013 

Hi Elisabeth,

On Thursday, September 05, 2013 8:28:34 AM, E.M. Lodder 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.

You must not have installed the hgu133plus2.db package, because it is 
available, and can be installed. As an example, here is my R-3.0.1 
sessionInfo after installing the package:

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] hgu133plus2.db_2.9.0 org.Hs.eg.db_2.9.0   RSQLite_0.11.4
[4] DBI_0.2-7            AnnotationDbi_1.22.6 Biobase_2.20.1
[7] BiocGenerics_0.6.0   BiocInstaller_1.10.3

loaded via a namespace (and not attached):
[1] IRanges_1.18.3 stats4_3.0.1   tools_3.0.1


>
> 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.

The Illumina package you are wanting to install was made by Mark 
Dunning, who contributed it to BioC. He has evidently stopped creating 
this package for us (which has to happen each release), although he is 
still making other packages. You might contact him directly, or look on 
the website he cites 
(http://compbio.sysbiol.cam.ac.uk/Resources/Annotation/index.html) to 
see what the deal is with that package.

Or you could just install the 'regular' illuminaMousev2.db' package and 
use that instead.

We cannot arbitrarily take annotation packages along, because the 
underlying infrastructure can and does change with each successive 
release. Unless the package is rebuilt using the newest versions of R 
and requisite BioC packages, there is no guarantee that a given old 
package will continue to work correctly.

That said, there is nothing preventing you from installing the old 
package version into your new version of R. In addition, there is 
nothing preventing you from installing an old version of R and then 
installing the old annotation package using biocLite(). Except that you 
will then be on your own, and should not expect anybody to give you 
support, as we only support current versions of packages, and certainly 
don't support old versions of packages installed in current BioC 
installations.

Best,

Jim


>
> Elisabeth
>
> -----Original Message-----
> From: kurai.yousei at gmail.com [mailto:kurai.yousei at gmail.com] On Behalf Of Diego Diez
> Sent: donderdag 5 september 2013 10:51
> To: E.M. Lodder
> Cc: Marc Carlson; bioconductor at 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 at 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 at r-project.org
>> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Marc Carlson
>> Sent: woensdag 4 september 2013 22:21
>> To: bioconductor at 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
>>> ________________________________
>>>
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>>
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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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