Hi, I am using bioconductor packages in R. I keep getting this error: 

Error: could not find function "xcmsSet" 

This is what I ran. 

# load required libraries
library(xcms)
library(CAMERA)

# set nslaves for the number of available cores of your machine
# Follow xcms vignette to understand data structure
# http://www.bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.pdf

nslaves <- 4

xset <- xcmsSet(
         "C:/", method='centWave', ppm=2, peakwidth=c(10,50),
        snthresh=3, prefilter=c(3,100), integrate=1, mzdiff=-0.00005,
           verbose.columns=TRUE,fitgauss=FALSE, nSlaves=nslaves
        )

# negative mode
xset2 <- xcmsSet(
         "C:/", method='centWave', ppm=2, peakwidth=c(10,50),
          snthresh=3, prefilter=c(3,100), integrate=1, mzdiff=-0.00005,
          verbose.columns=TRUE,fitgauss=FALSE, nSlaves=nslaves
         )

xcms is there in my win-library and all other bioconductor package neccesary. I also checked for xcmsSet in the unitTest folder of the xcms package. it is there as runit.xcmsSet.R.

I tried to load the library (xcms) alone. I get this error on mzR package:

> library(xcms)
Loading required package: mzR
Loading required package: Rcpp
Error : .onLoad failed in loadNamespace() for 'mzR', details:
  call: value[[3L]](cond)
  error: failed to load module Ramp from package mzR
invalid assignment for reference class field ‘class_pointer’, should be from class “externalptr” or a subclass (was class “character”)
In addition: Warning messages:
1: package ‘Rcpp’ was built under R version 3.0.3 
2: In fun(libname, pkgname) :
   mzR has been built against a different Rcpp version
 than is installed on your system. This might lead to errors
 when loading mzR. If you encounter such issues, please send
 a report, including the output of sessionInfo() to the Bioc
 mailing list -- http://www.bioconductor.org/help/mailing-list.
Error: package ‘mzR’ could not be loaded 

I also see the packages Rcpp and mzR in my library. I have downloaded the latest zip ofr this package. No result.Pls Help

Could you please provide some more information on the R you are using? the output of sessionInfo() would e.g. be useful. There is definitely a problem with the mzR package...
 

Thanks Johannes. I run R 3.0.1 now, when I started getting the error, I installed latest R 3.2.5 and I got same errors. so I simply removed the new version, believing versions were not the problem. When I shifted version, I copied every file within win-library to ensure my packages were still there. Anyway, sessionInfo()

Error: could not find function "xcmsSet"
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252   
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] Biobase_2.30.0      BiocGenerics_0.16.1

 I also tried the latest mzR and latest Rcpp al to no avail. I have also used earlier versions of Rcpp, then it will say Rcpp; could not be found by mzR': 

> library(xcms)
Loading required package: mzR
Error: package ‘Rcpp’ required by ‘mzR’ could not be found
In addition: Warning message:
package ‘mzR’ was built under R version 3.2.3 .