How to save all console output to file in R

Question

I want to redirect all console text to a file  Here is what I tried    gt  sink  test log   type c  output    message     gt  a  lt -  a   gt  a  gt  How come I do not see this in log Error  unexpected symbol in  How come    Here is what I got in test log    1   a    Here is what I want in test log    gt  a  lt -  a   gt  a  1   a   gt  How come I do not see this in log Error  unexpected symbol in  How come    What am I doing wrong  Thanks

User · Answer

Run R in emacs with ESS  Emacs Speaks Statistics  r-mode  I have one window open with my script and R code  Another has R running  Code is sent from the syntax window and evaluated  Commands  output  errors  and warnings all appear in the running R window session  At the end of some work period  I save all the output to a file  My own naming system is   R for scripts and   Rout for save output files  Here s a screenshot with an example

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Set your Rgui preferences for a large number of lines  then timestamp and save as file at suitable intervals

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To save text from the console  run the analysis and then choose  Windows   File Save to File

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You have to sink  output  and  message  separately  the sink function only looks at the first element of type   Now if you want the input to be logged too  then put it in a script   script R  1 5   1 3     prints and gives a warning stop  foo     an error   And at the prompt    con  lt - file  test log   sink con  append TRUE  sink con  append TRUE  type  message      This will echo all input and not truncate 150  character lines    source  script R   echo TRUE  max deparse length 10000     Restore output to console sink    sink type  message      And look at the log    cat readLines  test log    sep   n

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If you want to get error messages saved in a file zz  lt - file  quot Errors txt quot   open  quot wt quot   sink zz  type  quot message quot    the output will be  Error in print errr    object  errr  not found Execution halted  This output will be saved in a file named Errors txt  In case  you want printed values of console to a file you can use  split  argument  zz  lt - file  quot console txt quot   open  quot wt quot   sink zz   split TRUE  print  quot cool quot   print errr   output will be   1   quot cool quot   in console txt file  So all your console output will be printed in a file named console txt

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You can print to file and at the same time see progress having  or not  screen  while running a R script  When not using screen  use R CMD BATCH yourscript R  amp  and step 4   When using screen  in a terminal  start screen  screen   run your R script  R CMD BATCH yourscript R   Go to another screen pressing CtrlA  then c  look at your output with  real-time    tail -f yourscript Rout   Switch among screens with  CtrlA then n

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You can t  At most you can save output with sink and input with savehistory separately  Or    use external tool like script  screen or tmux

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If you have access to a command line  you might prefer running your script from the command line with R CMD BATCH      begin contents of script R     a  lt -  a  a How come I do not see this in log      end contents of script R      At the command prompt      in many un x variants   C    in windows   run    R CMD BATCH script R  amp    The trailing   amp   is optional and runs the command in the background  The default name of the log file has  out  appended to the extension  i e   script Rout          begin contents of script Rout     R version 3 1 0  2014-04-10  --  Spring Dance  Copyright  C  2014 The R Foundation for Statistical Computing Platform  i686-pc-linux-gnu  32-bit   R is free software and comes with ABSOLUTELY NO WARRANTY  You are welcome to redistribute it under certain conditions  Type  license    or  licence    for distribution details     Natural language support but running in an English locale  R is a collaborative project with many contributors  Type  contributors    for more information and  citation    on how to cite R or R packages in publications   Type  demo    for some demos   help    for on-line help  or  help start    for an HTML browser interface to help  Type  q    to quit R    Previously saved workspace restored    gt  a  lt -  a   gt  a  1   a   gt  How come I do not see this in log Error  unexpected symbol in  How come  Execution halted      end contents of script Rout

User · Answer

If you are able to use the bash shell  you can consider simply running the R code from within a bash script and piping the stdout and stderr streams to a file  Here is an example using a heredoc   File  test sh     bin bash   this is a bash script echo  Hello World  this is bash   test1   echo  This is a test    echo  Here is some R code    Rscript --slave --no-save --no-restore -   test1   lt  lt EOF      R code   cat   nHello World  this is R n     args  lt - commandArgs TRUE    bash message lt -args 1    cat   nThis is a message from bash  n     cat   n  paste0 bash message    n   EOF    end of script    Then when you run the script with both stderr and stdout piped to a log file     chmod  x test sh     test sh     test sh  amp  gt test log   cat test log Hello World  this is bash Here is some R code   Hello World  this is R  This is a message from bash    This is a test   Other things to look at for this would be to try simply pipping the stdout and stderr right from the R heredoc into a log file  I haven t tried this yet but it will probably work too

[file] How to save all console output to file in R?

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