On Thu, Aug 30, 2012 at 4:37 AM, Marcus Moeller <marcus.moeller@gmx.ch>wrote:

> Hi all.
>
>      we have noticed that the following modules from the bioc archive are
>>     no longer compatible with R version 2.15.1:
>>
>>     GOstats
>>     GlobalAncova
>>     globaltest
>>     hgu133a
>>     GeneR
>>
>>     I would like to ask what is the official way to get them updated? Do
>>     I have to contact the authors directly or is there something like a
>>     Bugzilla available?
>>
>>
>> Hi, Marcus.
>>
>> You can look here for build reports:
>>
>> http://bioconductor.org/**checkResults/release/bioc-**LATEST/<http://bioconductor.org/checkResults/release/bioc-LATEST/>
>>
>> And here for software releases:
>>
>> http://www.bioconductor.org/**packages/release/BiocViews.**
>> html#___Software<http://www.bioconductor.org/packages/release/BiocViews.html#___Software>
>>
>> It looks at first glance like all the bioconductor packages except
>> GlobalAncova are building fine right now and are available.  GeneR is a
>> special case since it is not a bioconductor package.
>>
>> Could you let us know what you mean by "no longer compatible with R
>> version 2.15.1"?  What did you try to do that suggested that was the
>> case?  Be sure to include the code you are trying and the output of
>> sessionInfo().
>>
>
> I have re-checked was able to build most of the packages now, but hgu133a
> and GeneR where I got an error message like:
>
> Warning message:
> package ‘hgu133a’ is not available (for R version 2.15.1)
>

when trying to install it using:
>
> /usr/bin/R --no-save --no-restore <<<'source("http://**
> bioconductor.org/biocLite.R <http://bioconductor.org/biocLite.R>");
> biocLite("hgu133a")'
>
> Maybe hgu133a has been removed from the repository? Concerning GeneR, I am
> sure that I have installed it from the bioc repository in the past.
>
>
Hi, Marcus.

The package is now called "hgu133a.db".  The name was changed because these
packages underwent some major modifications (were restructured) a few
releases back.  GeneR was removed from Bioconductor after release 2.9.  It
is no longer available from bioconductor.  You could try contacting the
authors for an up-to-date version or download old source from previous
releases of bioconductor to build yourself.

Hope that helps.

Sean



> Greets
> Marcus
>
> Greets
> Marcus
>
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