R - XCMS package Error - r

Question

I' ve the following problem :
Error in .C("NetCDFOpen", as.character(filename), ncid = integer(1), status = integer(1), :
C symbol name "NetCDFOpen" not in DLL for package "xcms"
How do you get this error :
nc <- xcms:::netCDFOpen(cdfFile)
ncData <- xcms:::netCDFRawData(nc)
xcms:::netCDFClose(nc)
I don't know why this don't works, although it should. For further info feel free to ask. Free .cdf files canf be found in the TargetSearchData package.
Code example :
## The directory with the NetCDF GC-MS files
cdfpath <- file.path(.find.package("TargetSearchData"), "gc-ms-data")
cdfpath

Answer 1

I don't think that it should, as you are implying. First, you are using a non-exported function through the :::. In addition, as stated by the error message, the is no NetCDFOpen symbol defined is the dll/so files.
Using the standard input functionality from xcms, works smoothly:
> library("xcms")
> cdfpath <- file.path(.find.package("TargetSearchData"), "gc-ms-data")
> cdfFile <- dir(cdfpath, full.names=TRUE)[1]
> xs <- xcmsSet(cdfFile)
7235eg04: 135:168 185:314 235:444 285:580
> xr <- xcmsRaw(cdfFile)
If you really want to input your data manually, you should use the functionality from the mzR package, which xcms depends on:
> openMSfile(cdfFile)
Mass Spectrometry file handle.
Filename: /home/lgatto/R/x86_64-unknown-linux-gnu-library/2.16/TargetSearchData/gc-ms-data/7235eg04.cdf
Number of scans: 4400
Finally, do pay attention to always provide the output of sessionInfo, to assure that you are using the latest version. In my case:
> sessionInfo()
R Under development (unstable) (2012-10-23 r61007)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.9.4 xcms_1.35.1 mzR_1.5.1
[4] Rcpp_0.9.15
loaded via a namespace (and not attached):
[1] Biobase_2.19.0 BiocGenerics_0.5.1 codetools_0.2-8 parallel_2.16.0
[5] tools_2.16.0
although if might be different for you, if you use the stable version of R and Bioconductor (currently 2.15.2/2.11).
Hope this helps.