search

fgcz / rawDiag

Brings Orbitrap mass spectrometry data to life; multi-platform, fast and colorful R package
https://bioconductor.org/packages/rawDiag
36 stars 11 forks source link

Deprecation messages for read.XIC() and readScans() #69

Closed tobiasko closed 3 years ago

tobiasko commented 3 years ago

With the publication of rawrr we see no further need for the rawDiag functions read.XIC() and read.Scans(). Accordingly, we should display deprecation messages that announce the alternative functions in rawrr.

Some best practice info:

https://bioconductor.org/developers/how-to/deprecation/

https://r-pkgs.org/release.html#compatibility

cpanse commented 3 years ago 
> S <- rawDiag::readScans(rawfile, 1)
Warning message:
'rawDiag::readScans' is deprecated.
Use 'rawrr::readSpectrum' instead.
See help("Deprecated") 
> X <-readXICs(rawfile, masses=mZ)
Warning message:
'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated") 
> Info <- rawDiag::read.raw.info()
Error in file.exists(file) : argument "file" is missing, with no default
In addition: Warning message:
'rawDiag::read.raw.info' is deprecated.
Use 'rawrr::readFileHeader' instead.
See help("Deprecated")