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1 ##============ Sink warnings and errors to a file ==============
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2 ## use the sink() function to wrap all code within it.
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3 ##==============================================================
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4 zz = file(Sys.getenv('TOOL_LOG'))
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5 sink(zz)
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6 sink(zz, type = 'message')
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7
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8 #------------import libraries--------------------
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9 options(stringsAsFactors = FALSE)
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10
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11 library(getopt)
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12 library(rmarkdown)
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13 #------------------------------------------------
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14
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15 #------------------------------------------------
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16 options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'),
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17 sep = '|', header = TRUE)
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18
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19
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20 #-----------------render Rmd--------------
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21 render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/dynamic_tool.Rmd'),
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22 output_file = Sys.getenv('REPORT'))
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23 #------------------------------------------
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24
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25
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26 ##--------end of code rendering .Rmd templates----------------
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27 sink()
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28 ##=========== End of sinking output============================= |
