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

[Wolfgang Huber]

Hi Vince,

my two cents...: a long term commitment to maintaining sma might end up 
creating more work than the short term pain of moving the useful bits to 
MLInterfaces, Biobase or limma?

	Best wishes
	Wolfgang

nt Carey wrote:
> 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)
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
> 
> 

-- 

Best wishes
      Wolfgang

-------------------------------------------------------
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber