[BioC] sma package moved to archived status (was Re: failure to install: aCGH depends on unavailable package)

[Patrick Aboyoun]

I've been informed by Ben Bolstad (package maintainer) that sma has been 
retired/archived and so BioC developers will need to remove dependency 
on sma for BioC 2.5. The following 6 packages will be directly affected:

aCGH, BiocCaseStudies, GeneSelector, limma, limmaGUI, MLInterfaces

For those looking for alternatives for particular functionality, we can 
open up a discussion on the BioC-devel mailing list.


Cheers,
Patrick



Ramon Diaz-Uriarte wrote:
> Dear Patrick,
>
> Thanks a lot!
>
>
> Best,
>
> R.
>
>
> On Friday 25 September 2009 19:10:03 Patrick Aboyoun wrote:
>   
>> Ramon,
>> I am not sure what happened to the sma package on CRAN. It must have
>> been removed from the repository over the past week since our build
>> system had fresh installations last week and sma was still available. I
>> e-mailed the package author and CRAN maintainer to find out why this
>> change happened. I'll e-mail back my findings and what if any actions we
>> in BioC will have to take.
>>
>>
>> Patrick
>>
>> Ramon Diaz-Uriarte wrote:
>>     
>>> Dear All,
>>>
>>> I just noticed (failures installing a bunch of BioC packages in new R
>>> installations) that aCGH depends on "sma", but sma is no longer
>>> available. Thus, the recommended procedure
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("aCGH")
>>> will fail. And any package which depends on aCGH (e.g., snapCGH) will
>>> fail to install too.
>>>
>>> I guess this is a bug in sma but, if I understand correctly, it should
>>> not be possible for a package to fail the standard installation procedure
>>> for the stable release?
>>>
>>>
>>>
>>> Best,
>>>
>>> R.
>>>
>>> P.D. sma used to be available in CRAN, so it is possible to get an old
>>> version from
>>> http://cran.r-project.org/src/contrib/Archive/sma/
>>> install that, and then install aCGH.
>>>
>>>
>>> ### this is one example; it fails on at least two other different systems
>>> too.
>>>
>>>       
>>>> version
>>>>         
>>>                _
>>> platform       x86_64-pc-linux-gnu
>>> arch           x86_64
>>> os             linux-gnu
>>> system         x86_64, linux-gnu
>>> status
>>> major          2
>>> minor          9.2
>>> year           2009
>>> month          08
>>> day            24
>>> svn rev        49384
>>> language       R
>>> version.string R version 2.9.2 (2009-08-24)
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
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>
>