I am using ChAMP do run a methylation analysis on the 450k dataset. I am not running every step individually but using the champ.process function to run the entire pipeline just by providing location to my IDAT directory which has my the sample_sheet.csv file. The program does run for a while, it produces the CHAMP_RESULTS directory and few other files but dies at or during normalization. Below is the a snippet of my error log file. Could you please tell me what happening here and is there a way to fix this?
[>>>>> ChAMP.NORM START <<<<<<]
champ.norm Results will be saved in ./CHAMP_RESULT//CHAMP_Normalization/
[ SWAN method call for BOTH rgSet and mset input, FunctionNormalization call for rgset only , while PBC and BMIQ only needs beta value. Please set parameter correctly. ]
<< Normalizing data with BMIQ Method >>
Note that,BMIQ function may fail for bad quality samples (Samples did not even show beta distribution).
3 cores will be used to do parallel BMIQ computing.
Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, :
internet routines cannot be loaded
Calls: champ.process ... makePSOCKcluster -> newPSOCKnode -> socketConnection