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lgatto / RforProteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
http://lgatto.github.io/RforProteomics
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adapt to upcoming MALDIquant 1.12 #10

Closed sgibb closed 9 years ago

sgibb commented 9 years ago

Dear Laurent,

the upcoming MALDIquant release will have some changes to the Mass Spectrometry Imaging functionality. plotImsSlice is now deprecated and replaced by a complete rewritten and faster function plotMsiSlice (please note the difference IMS vs MSI; I decided to rename the new function because IMS often refers to ionmobility mass spectrometry).

This PR is a reminder. I will merge it myself when MALDIquant 1.12 is released on CRAN. It would be necessary to cherry-pick this PR into the stable/release branch on bioc as well. Also I don't really know how the vignettes are built (it seems that the Makefile could only build the RforProteomics vignette and not the RProtViz vignette). That's why this PR just replace the code in the .Rmd file. Could you explain how you generate the .html document or create the images (png + pdf) and .html file yourself?

Best wishes,

Sebastian

lgatto commented 9 years ago

Thanks for this.

It would be necessary to cherry-pick this PR into the stable/release branch on bioc as well.

The only thing that will be different in devel and release is the new ReproducibleResearch biocView in the latter. Will be trivial to back port to release.

Also I don't really know how the vignettes are built (it seems that the Makefile could only build the RforProteomics vignette and not the RProtViz vignette).

I have copied the source Rmd back to ./vignettes (instead of a stub); now it gets build automatically.

lgatto commented 9 years ago

When will you release 1.12? Do you want me to wait before pushing R4P 1.7.1 to Bioc?

sgibb commented 9 years ago

Everything is ready for releasing MALDIquant 1.12 but I have to do my real job today. I hope I can send it to CRAN tomorrow/the day after tomorrow. If you could wait these two days it would be less work for you, or?

lgatto commented 9 years ago

No hurry at all, thanks.

sgibb commented 9 years ago

I just released MALDIquant 1.12. You could merge this PR now.

lgatto commented 9 years ago

Thanks. I have applied the 5 changes manually, which seemed easier than fixing the conflicts. Closing this PR.