Skip to content

Latest commit

 

History

History
143 lines (87 loc) · 4.04 KB

04-02-creating_log_files_automatically.md

File metadata and controls

143 lines (87 loc) · 4.04 KB

(creating-log-files-automatically)=

Creating log files automatically

An alternative (or complement) to creating log files explicitly is to use native functionality of the software to create them. This usually is triggered when using the command line to run the software, and thus may be considered an advanced topic. The examples below are for Linux/macOS, but similar functionality exists for Windows.

:::::{tab-set}

::::{tab-item} Stata

To automatically create a log file, run Stata from the command line with the -b option:

stata -b do main.do

which will create a file main.log in the same directory as main.do.

:::{warning} For this to work, the filename cannot include spaces. :::

On Windows, follow instructions here.

::::

::::{tab-item} R

To automatically create a log file, run R from the command line using the BATCH functionality, as follows:

R CMD BATCH options infile outfile

where

  • options are optional options from the command R

  • infile is the required input file with the code to be executed

  • outfile is the name of an optional output file. If no output file is provided, the name of infile is taken as default, appending the extension .Rout to it.

:::{warning} On Windows, you may need to include the full path of R: C:\Program Files\R\R-4.1.0\bin\R.exe CMD BATCH main.R :::

This will create a file main.Rout in the same directory as main.R. If you prefer a different name for the output file, you can specify it.

R CMD BATCH main.R main.$(date +%F-%H:%M:%S).Rout

which will create a second-precise date-time stamped log file. Finally, if you want to prevent R from saving or restoring its environment (by default, R CMD BATCH does both), you can specify the --no-save and --no-restore options.

R CMD BATCH --no-save --no-restore main.R main.$(date +%F-%H:%M:%S).Rout

The most output, and the least "inherited" information, is obtained by running the following command:

R CMD BATCH --debugger --verbose --vanilla main.R main.$(date +%F-%H:%M:%S).Rout

:::{warning} If there are other commands, such as sink(), active in the R code, the main.Rout file will not contain some output. :::

To see more information, check the manual documentation by typing ?BATCH (or help(BATCH)) from within an R interactive session. Or by typing R CMD BATCH --help from the command line.

::::

::::{tab-item} MATLAB

To automatically create a log file, run MATLAB from the command line as follows:

matlab -nodisplay -r "addpath(genpath('.')); main" -logfile matlab.log

A similar command on Windows would be:

start matlab -nosplash  -minimize -r  "addpath(genpath('.'));main"  -logfile matlab.log

::::

::::{tab-item} Julia, Python

In order to capture screen output in Julia and Python, on Unix-like system (Linux, macOS), the following can be run:

julia main.jl | tee main-$(date +%F-%H_%M)-${USER}.log

or

python main.py | tee main-$(date +%F-%H_%M)-${USER}.log

which will create a log file with everything that would normally appear on the console using the tee command.

::::

:::::

Takeaways

What this does

This ensures

  • that your code runs without problem, after all the debugging.
  • that your code runs without manual intervention.
  • that your code generates a log file that you can inspect, and that you could share with others.

What this does not do

This does not ensure

  • that it will run on somebody else's computer
    • because it does not guarantee that all the software is there
    • because it does not guarantee that all the directories for input or output are there
    • because many intermediate files might be present that are not in the replication package
    • because it does not guarantee that all the directory names are correctly adjusted everywhere in your code
  • that it actually produces all the outputs
    • because some outputs might be present from test runs

What to do next

To solve some of these problems, let's go to the next step.