Bash

Last updated: 2024-03-14

Checks: 7 0

Knit directory: for-future-reference/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20190125)

The command set.seed(20190125) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: efbb8a5

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version efbb8a5. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/bash.Rmd) and HTML (docs/bash.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	44912de	John Blischak	2019-06-06	Build site.
Rmd	31da9e6	John Blischak	2019-06-06	Set a default value for an environment variable.
html	0f8b583	John Blischak	2019-03-19	Build site.
html	6414dbe	John Blischak	2019-01-29	Build site.
Rmd	79b756b	John Blischak	2019-01-29	Document Bash command hash.
html	65fb12f	John Blischak	2019-01-29	Build site.
Rmd	695323a	John Blischak	2019-01-29	wflow_publish(c("analysis/_site.yml", "analysis/bash.Rmd", "analysis/index.Rmd",

View the most recent exit code with $?

echo "a b c" | grep b
echo $?

a b c
0

echo "a b c" | grep z
echo $?

Use process substitution to save standard output to a temporary file. This is very useful for when a command only accepts files or needs to accept multiple files as input. See the very nice blog post Using Names Pipes and Process Substitution in Bioinformatics for more details.

diff <(echo -e "1\n2\n3") <(echo -e "a\nb\nc")

1,3c1,3
< 1
< 2
< 3
---
> a
> b
> c

Use hash to see a tally of the executables you have run and hash -r to reset the hash. Bash first looks in the hash prior to searching $PATH (since that is faster), so it is useful to reset the hash anytime you modify $PATH.
- What does hash -r do?
- What is the purpose of the hash command?

ls > /dev/null
ls > /dev/null
R --version > /dev/null
hash

hits    command
   1    /usr/bin/R
   2    /usr/bin/ls

Set a default value for an environment variable with ${NAME:-"default-value"} (source)

echo ${ENVAR:-"default"}

default

ENVAR="value1"
echo ${ENVAR:-"default"}

default

sessionInfo()

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       httr_1.4.7        cli_3.6.2         knitr_1.45       
 [5] rlang_1.1.3       xfun_0.42         stringi_1.8.3     processx_3.8.3   
 [9] promises_1.2.1    jsonlite_1.8.8    glue_1.7.0        rprojroot_2.0.4  
[13] git2r_0.33.0      htmltools_0.5.7   httpuv_1.6.14     ps_1.7.6         
[17] sass_0.4.8        fansi_1.0.6       rmarkdown_2.26    jquerylib_0.1.4  
[21] tibble_3.2.1      evaluate_0.23     fastmap_1.1.1     yaml_2.3.8       
[25] lifecycle_1.0.4   whisker_0.4.1     stringr_1.5.1     compiler_4.3.3   
[29] fs_1.6.3          pkgconfig_2.0.3   Rcpp_1.0.12       rstudioapi_0.15.0
[33] later_1.3.2       digest_0.6.34     R6_2.5.1          utf8_1.2.4       
[37] pillar_1.9.0      callr_3.7.5       magrittr_2.0.3    bslib_0.6.1      
[41] tools_4.3.3       cachem_1.0.8      getPass_0.2-4

Bash

John Blischak

2019-01-28