[Bioc-devel] Bugfix to MassSpecWavelet

[Sergio Oller]

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
> >
> > _______________________________________________
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> >
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> --
> ---
> 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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