[Bioc-devel] Dependency to PEER

[Martin Morgan]

On 09/25/2018 07:07 PM, Christian Mertes wrote:
> Hi,
> 
> thanks for the answers.
> 
> Since we only use 5 functions from the package within one function in our package, I hoped to get around it by masking this function in a special way.

not sure what that means; better not to be devious if that is what 
'special' means.

I think an appropriate thing to do would be to illustrate installation / 
evaluation functionality in a non-evaluated code chunk in the vignette. 
Your reviewer will be understanding.

Martin

> 
> The package is not dependent on PEER and works without it perfectly. Its just to make it easier for the user if he wants to use a different normalisation method.
> 
> Best,
> Christian
> 
>> On 25. Sep 2018, at 13:39, Robert Castelo <robert.castelo using upf.edu> wrote:
>>
>> hi,
>>
>> it seems that the PEER repository hasn't been updated in the last 7 years and that the package is distributed under a GPL-2 license. if i'm interpreting this correctly, you could copy&paste that code into your package redistributing it under the GPL-2 license and asking the users of PEER to cite the PEER paper when using it.
>>
>> cheers,
>>
>> robert.
>>
>> On 25/09/2018 18:55, Kasper Daniel Hansen wrote:
>>> It is a major weakness of PEER that it has not been submitted to a standard
>>> repository. Of course, that is up to the PEER developers, but the community
>>> should put pressure on them.
>>>
>>> On Tue, Sep 25, 2018 at 12:40 PM Christian Mertes <mertes using in.tum.de> wrote:
>>>
>>>> Hi all,
>>>>
>>>> Im the developer of OUTRIDER. Our package normalises RNA-seq count data
>>>> and finds expression outliers within the population.
>>>> During the development we compared our approach against PCA and PEER. The
>>>> later one is a well established method to normalise RNA-seq data.
>>>>
>>>> https://github.com/gagneurlab/OUTRIDER <
>>>> https://github.com/gagneurlab/OUTRIDER>
>>>> https://github.com/PMBio/peer <https://github.com/PMBio/peer>
>>>>
>>>> For PEER, an R package exists on GitHub, but it is not in CRAN nor
>>>> Bioconductor, even it would fit really well with Bioconductor.
>>>>
>>>> We would like to leave the user the option to switch between the different
>>>> normalisation methods within our package (auto encoder, peer, pca, sea, …).
>>>> But since the Bioconductor requirements are that all loaded libraries need
>>>> to be within CRAN or BioC, my question is how we should implement this.
>>>>
>>>> Is there a best practice for this? Does we have to ask the developer of
>>>> PEER to push it on CRAN or do we get around this? Or can we flag one
>>>> function to be not checked by Bioconductor for dependencies and use
>>>> require(peer) within the function?
>>>>
>>>> Thanks for any advices in advance!
>>>>
>>>> Best,
>>>> Christian
>>>>
>>>>
>>>>
>>>>
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>>>>
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>>
> 
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