pdf - How to suppress pdfcrop printing when using R rmarkdown render function? -

I tried to print stdout and stderr generated by RDMRDead, but when calling R Rmarkdown render function, But it does not know how to do

I have already used the cool option to touch the pandok command line execution, but it will override the printing of pdfcrop does not do.

Do anyone have some tips to fix this? / P>

I have run the script here:

  Rscript RNASeq_QC_run.R -v 1 --count ~ / devel / r / projects / rnaseq_qc / data / dataTest_Count_expression_generic2.txt - format generic - Design - / Devell / R / Project / RNCAction / Data / DataType Dispatch TTT - Outdoor Test / Out 5 & amp; & Gt; Test / Out 5.log  

This call is to present the function:

  generic_report_path & lt; - system.file ("Report", "QC_RNASeq_Count_generic.Rmd", package = "qc4rnaseq") generic_report_file & lt; - Paste (unlisted (strsplit (basename (Generic_report_path), ".rmd")), ".pdf", sep = "") render (input = Samany_report_path, Autput_form = "pdf_docum ENT", output_file = generic_report_file, output_dir = outdir_abs_path , Intermediates_dir = outdir_abs_path, cool = TRUE)  

Here is the content of the exam / out5.log: (between both stdout (regular) and stderr bold: **) Production

  ** crop /private/tmp/qc4rnaseq_run/test/out5/QC_RNASeq_Count_generic_files/figure-latex/unnamed-chunk-2-1.pdf** PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Arbedic == & gt; 1 page written on `/private/tmp/qc4rnaseq_run/test/out5/QC_RNASeq_Count_generic_files/figure-latex/unnamed-chunk-2-1.pdf ' ** /private/tmp/qc4rnaseq_run/test/out5/QC_RNASeq_Count_generic_files/figure-latex/unnamed-chunk-3-1.pdf** PDFCROP 1.38, 2012/11/02 crop - Copyright (c) 2002-2012 by Haikou Oberdiak . ==> 1 page written on `/private/tmp/qc4rnaseq_run/test/out5/QC_RNASeq_Count_generic_files/figure-latex/unnamed-chunk-3-1.pdf ' ** /private/tmp/qc4rnaseq_run/test/out5/QC_RNASeq_Count_generic_files/figure-latex/unnamed-chunk-4-1.pdf** PDFCROP 1.38, 2012/11/02 crop - Copyright (c) 2002-2012 by Haikou Oberdiak . ==> `/private/tmp/qc4rnaseq_run/test/out5/QC_RNASeq_Count_generic_files/figure-latex/unnamed-chunk-4-1.pdf 'written on one page execution time: 7.12010 9 seconds   
 < div class = "post-text" itemprop = "text"> 
 I found a solution to suppress messages using suppressMessages function even though it does not suppress all messages are only sent to stderr.  
 Here are my amendments:  
  suppressMessages (Render (input = generic_report_path, output_format = "pdf_document" are now buried all messages sent to stderr, but my script Not all messages sent to stdout, but output I.  
 This is still hidden print related to pdfcrop:  
  PDFCROP 1.38, 2012/11 / 02 - Copyright (c) == & gt; `/private/tmp/qc4rnaseq_run/test/out7/QC_RNASeq_Count_generic_files/figure-latex/unnamed-chunk-2-1.pdf 'typed one page by 2002-2012 Heiko Orbedik PDFCROP 1.38, 2012/11/02 - Copyright Female) were 1 page written == & gt; `/private/tmp/qc4rnaseq_run/test/out7/QC_RNASeq_Count_generic_files/figure-latex/unnamed-chunk-3-1.pdf 'by 2002-2012 Heiko Orbedik. PDFCROP 1.38, 11/02/2012 - Copyright (c) == by 2002-2012 Heiko Orbedik & gt; on `/private/tmp/qc4rnaseq_run/test/out7/QC_RNASeq_Count_generic_files/figure-latex/unnamed-chunk-4-1.pdf ' 1 page written