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
This is indeed strange - what happens if you call
?