[BioC] package availability for R3.01

Fri Sep 6 19:49:08 CEST 2013

Hi Elisabeth,

So to answer your questions it is first important to understand that 
these annotation packages contain real databases, and that sometimes the 
code in a release can rely on certain fields in those databases having 
certain information present in order to work.  So they are not simply 
immutable data stores that always look the same between releases, things 
are actually quite a bit more complicated than that.

Having explained that, we do try to always carry over our packages from 
one release to the next.  In fact we update many hundreds of them every 
6 months to contain the latest data available.  We do that because 
annotations change all the time and it's important that people can have 
a current snapshot.  But some of the annotation packages are contributed 
voluntarily from the outside and sometimes these package authors need to 
either pass the responsibilty on to another person or (even more rarely) 
they may decide that they need to deprecate their packages.  This 
doesn't actually happen very often (this is why I was surprised that you 
found that package in that old release), but it did happen for the 
package called illuminaMousev2BeadID.db.

We also maintain tools (like the one that I mentioned in my 1st post) to 
allow you to re-create a modernized version of the 
illuminaMousev2BeadID.db package (or to create new packages).  So if you 
wanted to create an updated version of that package you can do so 
without too much effort.  You could even (if you felt ambitious) become 
a package contributor yourself and help to maintain it for the world.  
But before you do anything like that, I would recommend that you talk to 
Mark Dunning (the original contributor) and find out why he discontinued it.

As for why you are not able to install the latest version of 
hgu133plus2.db, I don't think anyone else is able to reproduce that 
problem right now.  This makes it very hard to troubleshoot. But for 
that question I see that Martin has already given some very helpful 
suggestions.

Finally, I wanted to encourage you to please not use really old 
annotation packages from so many years ago.  Annotations change 
constantly.  And while it's true that most of the change is caused 
simply by additional information being added, you still don't want to 
miss out on that if you can avoid it.

Hope this helps you,

   Marc

On 09/05/2013 05:28 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.
>
> 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 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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