I'm working on data processing of LC/MS/MS experiments using XCMS R package. An error occured when collecting fragments, showing “unable to find an inherited method for function ‘collect’ for signature ‘"xcmsRaw"’”. So, a sample data which could successfully go through the process  was tested, but still got the same error. The details are listed below:

> sessionInfo()

R version 3.2.3 (2015-12-10)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:

[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:

[1] parallel stats graphics grDevices utils datasets methods base

other attached packages:

[1] xcms_1.46.0 Biobase_2.30.0 ProtGenerics_1.2.1 BiocGenerics_0.16.1

[5] mzR_2.4.0 Rcpp_0.12.3

loaded via a namespace (and not attached):

[1] RColorBrewer_1.1-2 codetools_0.2-14 grid_3.2.3 lattice_0.20-33

> xs xs

An "xcmsRaw" object with 100 mass spectra

Time range: 1190-1309.2 seconds (19.8-21.8 minutes)

Mass range: 500-849.9333 m/z

Intensity range: 100008-828487000

MSn data on 22 mass(es)

with 44 MSn spectra

Profile method: bin

Profile step: 1 m/z (351 grid points from 500 to 850 m/z)

Memory usage: 2.71 MB

> coll

The data and the commands seem to have no problems,  neither is the R environment. So it puzzles me how this error happens. Any suggestion is highly appreciated.