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

[Vincent Carey]

MLInterfaces used sma::stat.diag.da
As the package was GPL2 I believe I can just move the relevant sources to
MLInterfaces for now; will include attribution in the man page.

However, the package does not seem to be too far from being checkable
with R 2.10, so perhaps biocore can take on the maintenance, and just distribute
via Bioconductor.  I would volunteer to do the first set of patches to
get it past
check, if we want to go that route.

On Fri, Sep 25, 2009 at 11:52 PM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:
> 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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>>>>
>>
>>
>
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>



-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265