Dear Maintainers,
since a few days I'm getting the Error Message: "Error in R_nc4_close: NetCDF: Not a valid ID" using the "xcmsSet" function from {xcms} package under R-Studio Version 3.5.3 in Windows10 (64bit).
Our code for generating the chromatogramm list from raw cdf-data out of GC-MS-Analysis and getting the xcmxSet out of that list:
### List Chromatograms
lchrom <- list.files(path = "./cdf/", recursive = F, full.names = T, pattern =".CDF")
### adjust order of chromatograms to 1, 2, 3, ...
temp <- unlist(strsplit(lchrom, c("G")))[c(FALSE, TRUE)]
temp <- unlist(strsplit(temp, c("."), fixed = TRUE))[c(TRUE, FALSE)]
temp <- as.numeric(temp)
lchrom <- lchrom[order(temp)]
### Start xcms analysis
system.time(
xsgc <- xcmsSet(lchrom[1], method="matchedFilter", step = 0.5, fwhm = 2, snthresh = 3, max = 10000, BPPARAM = SnowParam(workers = 3) )
)
After the xcmsSet function we received the following error message:
"Error in R_nc4_close: NetCDF: Not a valid ID"
With R-Studio Version 3.4.3 and xcms 3.0.2 everything worked as always..
Our loaded packages are:
Biobase2.42.0
BiocGenerics 0.28.0
BiocParallel 1.16.6
CAMERA 1.38.1
data.table 1.12.2
MSnbase 2.8.3
mzR 2.16.2
parallel 3.5.2
ProtGenerics 1.14.0
Rcpp 1.0.1
S4 Vectors 0.20.1
stats4 3.5.2
xcms 3.4.4
Hi Dominic,
The issue you are having was recently noted on the xcms github page: NetCDF: Not a valid ID error when using CentOS with NetCDF library 4.6.2 (https://github.com/sneumann/xcms/issues/363)
It looks like Johannes has already fixed the issue. You can install the patched version using the command:
devtools::install_github("sneumann/xcms", ref = "RELEASE_3_8")
Hopefully that fixes the issue for you!
Problem solved,
thank you!!!