error when reading .mzML with xcms::xcmsSet
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Entering edit mode
buescher • 0
@buescher-11996
Last seen 3.1 years ago

Hi,

I' currently trying to run an R-stript that heavily relies on xcms on a machine running centOS. The script runs just fine locally (OSX Sierra). On the centOS machine I have R installed as well as xcms with all dependencies. And I made sure that the user under which I'm running R has full access to the directory 'data' and all files therein.

The code basically looks like this:

library(xcms)
library(RMySQL)
library(openxlsx)

mydir <- 'data'

xs   <- xcmsSet(files=mydir, method="centWave", ppm=100,
                peakwidth=c(3,25), snthresh=3, prefilter=c(2,1000) )

 

When running the script get this error message:

locale::facet::_S_create_c_locale name not valid
Error: BiocParallel errors
  element index: 1, 2, 3, 4
  first error: invalid class "rampSource" object: Could not open mzML/mzXML/mzData file: /data/tmp/20161207193911/data/00000017.mzML

 

Any help is greatly appreciated!

Thanks

 

P.S. here is the output of sessionInfo():

R version 3.3.1 (2016-06-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=C                 LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] openxlsx_3.0.0       RMySQL_0.10.9        DBI_0.5-1           
 [4] xcms_1.50.0          Biobase_2.34.0       ProtGenerics_1.6.0  
 [7] BiocGenerics_0.20.0  mzR_2.8.0            Rcpp_0.12.8         
[10] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
 [1] RANN_2.5               lattice_0.20-34        codetools_0.2-15      
 [4] MASS_7.3-45            MassSpecWavelet_1.40.0 grid_3.3.1            
 [7] plyr_1.8.4             stats4_3.3.1           S4Vectors_0.12.1      
[10] Matrix_1.2-7.1         splines_3.3.1          BiocParallel_1.8.1    
[13] RColorBrewer_1.1-2     tools_3.3.1            survival_2.40-1       
[16] multtest_2.30.0 

software error R mzR xcms • 651 views
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Entering edit mode

This is indeed strange - what happens if you call

xr <- xcmsRaw("/data/tmp/20161207193911/data/00000017.mzML")

?

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