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Common Errors/Warnings in the NP³ MS Workflow

Installation and setup

Make sure that all system requirements are installed:

System requirements: Packages tzdata, zip, wget and which must be installed.

Otherwise, an error with the related missing package may be raised.

In the Pre-process Step 2

The following error without interruption:

error self$finalize()?

Just ignore this message, this is a bug in the R XCMS 1 from the current version used.

The following warning during the input file (.mzXML) reading followed by the error below. Or just the error:

Warning: Setting LC_MEASUREMENT failed, using "C" Error in pwizModule$open(filename): locale::facet::_S_create_c_locale name not valid

Your system is trying to pass a locale that isn't generated or recognized. You can force R to use a universal fallback configuration.

Solution:

For quick fix, in the terminal run: 

export LC_ALL=C.UTF-8
or

export LC_ALL="en_US.UTF-8"

For permanent fix, add this environment variable to your default configurations, in the terminal run: 

echo 'export LC_ALL=C.UTF-8' >> ~/.bashrc
source ~/.bashrc

The following error before starting pre-processing:

Error: package or namespace load failed for ‘utils’: .onLoad failed in loadNamespace() for 'utils', details: call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE) error: error in running command

Error: package or namespace load failed for ‘stats’: .onLoad failed in loadNamespace() for 'utils', details: call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE) error: error in running command

During startup - Warning messages: 1: package ‘utils’ in options("defaultPackages") was not found
2: package ‘stats’ in options("defaultPackages") was not found
Error: package or namespace load failed for ‘dplyr’: .onLoad failed in loadNamespace() for 'utils', details: call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE) error: error in running command Execution halted

Your unix system is missing the package which.

Solution:

Install package which in the terminal and try again. Google for installation instructions in your specific unix system.