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. Author manuscript; available in PMC: 2019 Nov 19.
Published in final edited form as: Nat Protoc. 2019 Feb 1;14(3):756–780. doi: 10.1038/s41596-018-0113-7

Table 6 |.

Troubleshooting table

Step Problem Probable reason Solution
2 Package installation failed R version is old or dependent package cannot be installed Update R to 3.5.0 or newer.
Try to start the R session from the root folder. The PATH variable can be set by typing into a terminal:
For Linux
$export PATH="/usr/bin:$PATH"
For MacOS
$export PATH="/usr/local/bin:$PATH"
7Avii MAGeCK crashed with an error related to the design matrix. Such as:
“Error parsing the design matrix: 0 row sums for some samples.” 		Design matrix was not in a correct format Follow the tutorial to generate a correct design matrix. https://bitbucket.org/liulab/mageck-vispr
7Bv MAGeCK-VISPR crashed with an error due to cannot find input files:
“Error in configuration file (key=library, entry=xxx): File does not exist.” 		File names or paths of the input files is incorrect. Double check the names and paths of the input files and make sure these files can be accessed.
11B FluteMLE crashed with an error due to cannot find samples:
“Error in FluteMLE(gene_summary = ‘mle.gene_summary.txt’, treatname = ‘treatment.beta’, : No sample found!” 		The index specified with the parameters “treatname” or “ctrlname” does not fit the column names of “gene_summary.txt” file. Ignore the suffix “.beta” when specifying the control names and treatment name with the parameter “treatname” and “ctrlname”