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MassBank / RMassBank

Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html
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mzR dropped `mzData` format, drop or replace? #304

Closed meowcat closed 2 years ago

meowcat commented 2 years ago

https://github.com/sneumann/mzR/blob/master/NEWS o Removed RAMP backend, dropping ability to read mzData Leading to failure on bioc build, since we still have mzData files in the RMassBankXCMS vignette:

https://github.com/MassBank/RMassBank/blob/1ea06508d1736b11070dec945631a08cee57d079/vignettes/RMassBankXCMS.Rmd#L90-L92

https://master.bioconductor.org/checkResults/3.15/bioc-LATEST/RMassBank/nebbiolo1-buildsrc.html

@sneumann, do you have these files in mzML? Or should we just drop this example?

sneumann commented 2 years ago

Hi, I converted the files in https://github.com/MassBank/RMassBankData/commit/0547193c48172c5006548f1ed425f9b2f0ca8719, but I have the feeling I can't push to BioC upstream for permission reasons.

I also switched filenames in the vignette in https://github.com/MassBank/RMassBank/commit/e51aa6faa8b091c53272ee62dc53a3315133b25c But I am not going to merge anything because I am confused about branches (master, main, dev, ...) and which version is where. A PR is tried to create had far more commits that what I actually did. Can @tsufz help ? Yours, Steffen

meowcat commented 2 years ago

Hi, I had a strange error on pushing to Bioc upstream ("test-merge" hook even though it was only one commit without any strange features) but now it seems to have gone through regardless. Let's see in the build

meowcat commented 2 years ago

Builds fine on Bioc, some Win builds have a problem but that's on Bioc's side and will resolve (checked with Lori)