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fgcz / rawDiag

Brings Orbitrap mass spectrometry data to life; multi-platform, fast and colorful R package
https://bioconductor.org/packages/rawDiag
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R 4.0.2 - Error: `x` must be a vector, not a `data.frame/rawDiag` object. #59

Open cpanse opened 4 years ago

cpanse commented 4 years ago 
cp@fgcz-148:~ > R

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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[Previously saved workspace restored]

R> library(rawDiag)
Package 'rawDiag' version 0.0.34
R> ?read.raw
R> ?read.raw
R>  (rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))
[1] "/home/cp/R/x86_64-pc-linux-gnu-library/4.0/rawDiag/extdata/sample.raw"
     system.time(RAW <- read.raw(file = rawfile))
R>      system.time(RAW <- read.raw(file = rawfile))
executing mono /home/cp/R/x86_64-pc-linux-gnu-library/4.0/rawDiag/exec/fgcz_raw.exe /home/cp/R/x86_64-pc-linux-gnu-library/4.0/rawDiag/extdata/sample.raw qc ...
MasterScanNumber calculated
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
   user  system elapsed 
  0.411   0.043   0.442 
Warning messages:
1: In is.rawDiag(object) :
  missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
2: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
R> PlotScanFrequency(RAW)
Error: `x` must be a vector, not a `data.frame/rawDiag` object.
Run `rlang::last_error()` to see where the error occurred.
R>
cpanse commented 4 years ago

solution 

class(RAW) <- 'data.frame'
PlotScanFrequency(RAW)
Stortebecker commented 3 years ago

Same problem here, using rawDiag 0.0.34 and R 3.6.2. Thanks for the workaround!

cpanse commented 3 years ago

@Stortebecker please see also our latest release https://github.com/fgcz/rawDiag/releases/tag/0.0.38 and our new package: https://github.com/fgcz/rawR C