[Bioc-devel] Bugfix to MassSpecWavelet

[Hervé Pagès]

Hi Sergio,

Have you tried to reach to the co-authors of the package, which are also 
co-authors of the associated paper?

   https://pubmed.ncbi.nlm.nih.gov/16820428/

One of them has a profile page at Duke University, with email address 
and links to Linkedln profile and Twitter feed.

We'll need to make sure that the maintainer address in MassSpecWavelet 
is current.

Let us know how it goes.

Thanks,

H.

On 26/03/2022 11:07, Sergio Oller wrote:
> Thank you for your reply, Steffen.
>
> I just saw that the R 4.2 devel NEWS tells us that passing a matrix as the
> wavelet argument on the MassSpecWavelet::cwt() function will raise an error
> instead of print a warning.
>
> My small patch fixes that issue (as a reminder, it's at the fix-cwt-seq
> branch of my fork below, the diff is shown in this link:
>
> https://github.com/zeehio/MassSpecWavelet/pull/1/files
>
> Quoting the relevant R devel news entry:
>
> Calling ‘if()’ or ‘while()’ with a condition of length greater than one
> gives an error rather than a warning. Consequently, environment variable
> ‘_R_CHECK_LENGTH_1_CONDITION_’ no longer has any effect.
>
> Hopefully with your reply my original email will reach the maintainer's
> inbox.
>
> Best
>
> Sergio
>
>
> El dc., 23 de març 2022, 11:46, Neumann, Steffen <sneumann using ipb-halle.de> va
> escriure:
>
>> Hi Sergio,
>>
>> thanks for putting this together. I am not maintaining MSW, but we're
>> using it as dependency in xcms. I am optimistic it will be taken up at
>> some stage.
>>
>> Yours,
>> Steffen
>>
>>
>>
>>
>>
>> On Mon, 2022-03-21 at 12:11 +0100, Sergio Oller wrote:
>>> Dear Bioc-devel,
>>>
>>> I would like to submit two fixes to the MassSpecWavelet package. I
>>> tried contacting the maintainer but he/she was not replying after
>>> some
>>> weeks. I am not sure if I may have fallen into a spam folder.
>>>
>>> I hope that either some Bioconductor maintainer may pull the fixes
>>> and
>>> apply them or the original package maintainer may see this and commit
>>> them.
>>>
>>> The fixes consist of (1) fixing a warning triggered when the argument
>>> "wavelet" of cwt() is given as a matrix (and it is compared to a
>>> scalar string inside an if() ) and (2) using length.out=  in the
>>> seq()
>>> call instead of length= to avoid partial matching.
>>>
>>> They could both be applied to the current release and the development
>>> one.
>>>
>>> The diff of the changes is available here for your convenience:
>>>
>> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fzeehio%2FMassSpecWavelet%2Fpull%2F1%2Ffiles&data=04%7C01%7C%7Ce21b95a347cc4d8f962908da0ca9580a%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C637836219271127401%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=XoAyQ2n8GEIFsZFXBHSQeMAhLHerGjfoBO%2FYS357sds%3D&reserved=0
>>> And it is available for you to pull in the fix-cwt-seq branch from
>>> the
>>> git repository:
>>>
>> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fzeehio%2FMassSpecWavelet.git&data=04%7C01%7C%7Ce21b95a347cc4d8f962908da0ca9580a%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C637836219271127401%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=p8jeWDfWybqsk80v69TuFy4g%2Bwmh8J%2Ba4otSVy8dAQ4%3D&reserved=0
>>> If there is any other (better) procedure for me to follow to get this
>>> merged, my apologies. I will be happy to adapt and proceed as
>>> indicated. The documentation regarding git in bioconductor I read
>>> assumed I was committing to my own repository, and not trying to
>>> contribute to someone else's.
>>>
>>> Thanks in advance,
>>> Sergio
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>>
>> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=04%7C01%7C%7Ce21b95a347cc4d8f962908da0ca9580a%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C637836219271127401%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=jF7xJWTzXI55ZV2pPiUpBG7A1WPRH9pnnGn1AXrWOYE%3D&reserved=0
>> --
>> ---
>> IPB Halle                    Bioinformatics and Scientific Data
>> Dr. Steffen Neumann          http://www.IPB-Halle.DE
>> Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
>> 06120 Halle                       +49 (0) 345 5582 - 0
>> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
>>
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com