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POWhy my bash can't execute R script?
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copied!<p>My script use an access to mysql to get command arguments to launch Rscript. Its use is as follows : Rscript $RFILE $ARGUMENTS (RFILE corresponding to path to Rscript, and ARGUMENTS corresponding to path file used and agr).</p> <p>I try, different way, but I still have errors, here a copy of my bash script :</p> <pre><code>#!/usr/bin/env bash # Execute R process # ----------------- ### Mysql Setup ### USER=... PASS=... HOST=... DB=... # Get Job ID process # Use to retrieve args in my DB ID=$1 # Get script name RFILE=$(mysql -u$USER -p$PASS -e "SELECT script_name FROM JobProcess WHERE script_run_id=$ID;" $DB) SUBSTRING="script_name" RFILE="${RFILE//$SUBSTRING}" # Get script_args ARGUMENTS=$(mysql -u$USER -p$PASS -e "SELECT script_args FROM JobProcess WHERE script_run_id=$ID;" $DB) SUBSTRING2="script_args" ARGUMENTS="${ARGUMENTS//$SUBSTRING2}" RUN="Rscript $RFILE $ARGUMENTS" # Try Different execute process Rscript $RFILE $ARGUMENTS #eval "$RUN" #`Rscript $RFILE $ARGUMENTS` #$RUN </code></pre> <p>I verified my command line (via echo), and if I made a copy-paste to my shell I can run my R script. But from my bash, I can't execute my script (but command line is good).</p> <p>By using : Rscript $RFILE $ARGUMENTS, <code>Rscript $RFILE $ARGUMENTS</code> and $RUN, I have this error : </p> <pre><code>Error in parse(text = args[[i]]) : unexpected end of input in ""path_in='/Users/GR/web-app/Rproject/Inputs/Rscript/Gene-level" Calls: eval -> parse Execution halted </code></pre> <p>By using : eval "$RUN", I have this error :</p> <pre><code>/Users/GR/web-app/Rproject/Scripts/Rscript.sh: line 38: /Users/GR/web-app/Rproject/Scripts/arg_file_test.R: Permission denied /Users/GR/web-app/Rproject/Scripts/Rscript.sh: line 44: path_in<-"/Users/GR/web-app/Rproject/Inputs/Rscript/Gene-level Description for Modules.csv": No such file or directory </code></pre> <p>If I try this in my shell script, all works fine :</p> <pre><code>SCRIPT="/Users/GR/web-app/Rproject/Scripts/arg_file_test.R" FILE1="path_in='/Users/GR/web-app/Rproject/Inputs/Rscript/Gene-level Description for Modules.csv'" FILE2="path_in2='/Users/GR/web-app/Rproject/Inputs/Rscript/Template_Auto.csv'" FILES="\"$FILE1\" \"$FILE2\"" ARG="l=32 w=33" RUN="Rscript $SCRIPT $FILES $ARG" </code></pre> <p>Someone has an idea ?</p> <p>Thanks</p>

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