The Difference Between `logr`, `logrx`, and `whirl`

The logr package for R aims to provide a straightforward logging system tailored for everyday users, such as statisticians and educators, emphasizing simplicity in recording program execution. In contrast, logrx offers an advanced logging mechanism designed specifically for clinical reporting, featuring easy traceability and reproducibility of R script executions with capabilities suited for more technical users. whirl differs in that the package provides functionalities for executing scripts in batch and simultaneously getting a log from the individual executions. In contrast the other two logging packages, the default logs are HTML reports making it easier to read, and they include the results printed in the programs being logged.

All three packages are used for keeping a record of what happens when R scripts are run, but they differ in what they offer and who they’re for. When choosing between them, you should consider what you need for your particular situation.

Execution

Each package differs notably in the approach to generating a log file. The logr package adopts a method similar to SAS, where the log is manually constructed at intermediary steps within the R script. Conversely, the logrx package allows for the creation of a log file through a single command from the R terminal, offering added compatibility for command line submission. whirl also provides a single function to create log files, and it should be noted that the execution is done through Quarto, which enables the HTML reports, but also make it more heavier on external dependencies.

# file: script.R
library(dplyr)
library(logr)

file_path <- "script.log"
log_file <- log_open(file_path)

log_print("Analyzing Fuel Efficiency Trends in Cars")

average_mpg <- mtcars %>%
  group_by(cyl) %>%
  summarise(average_mpg = mean(mpg, na.rm = TRUE))

log_print(average_mpg)

model <- lm(mpg ~ wt, data = mtcars)
summary(model)

log_print(model)

log_close() # log file path: log/script.log

=========================================================================
Log Path: ./log/script.log
Working Directory: /Users/davidblair/My Drive/Appsilon/Work Projects/examples
User Name: davidblair
R Version: 4.3.3 (2024-02-29)
Machine: Davids-Air.localdomain arm64
Operating System: Darwin 23.4.0 Darwin Kernel Version 23.4.0: Fri Mar 15 00:12:41 PDT 2024; root:xnu-10063.101.17~1/RELEASE_ARM64_T8103
Base Packages: stats graphics grDevices utils datasets methods base
Other Packages: dplyr_1.1.4 logr_1.3.6
Log Start Time: 2024-04-08 13:25:53.22436
=========================================================================

Analyzing Fuel Efficiency Trends in Cars

NOTE: Log Print Time:  2024-04-08 13:25:53.226347
NOTE: Elapsed Time: 0.00139403343200684 secs

# A tibble: 3 × 2
    cyl average_mpg
  <dbl>       <dbl>
1     4        26.7
2     6        19.7
3     8        15.1

NOTE: Data frame has 3 rows and 2 columns.

NOTE: Log Print Time:  2024-04-08 13:25:53.254377
NOTE: Elapsed Time: 0.0280299186706543 secs


Call:
lm(formula = mpg ~ wt, data = mtcars)

Coefficients:
(Intercept)           wt
     37.285       -5.344


NOTE: Log Print Time:  2024-04-08 13:25:53.267483
NOTE: Elapsed Time: 0.013106107711792 secs

=========================================================================
Log End Time: 2024-04-08 13:25:53.286294
Log Elapsed Time: 0 00:00:00
=========================================================================

From the R terminal:

logrx::axecute("script.R")

From the Command Line:

Rscript -e "logrx::axecute('script.R')"

--------------------------------------------------------------------------------
-                                logrx Metadata                                -
--------------------------------------------------------------------------------
This log was generated using logrx 0.3.0
logrx package version: 0.3.0
logrx build: CRAN (R 4.3.1)
logrx link to repository: https://github.com/pharmaverse/logrx
--------------------------------------------------------------------------------
-                          User and File Information                           -
--------------------------------------------------------------------------------
User: davidblair
File Name: script.R
File Path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging
File HashSum: 76f9dd029df25ba4f65de72631fac248fa30d7d5
--------------------------------------------------------------------------------
-                             Session Information                              -
--------------------------------------------------------------------------------
─ Session info ─────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.3 (2024-02-29)
 os       macOS Sonoma 14.4.1
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/London
 date     2024-04-08
 pandoc   NA

─ Packages ─────────────────────────────────────────────────────────────────────
 ! package     * version date (UTC) lib source
   cachem        1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
   callr         3.7.6   2024-03-25 [1] CRAN (R 4.3.1)
   cli           3.6.2   2023-12-11 [1] CRAN (R 4.3.1)
   common        1.1.2   2024-03-05 [1] CRAN (R 4.3.1)
   curl          5.2.1   2024-03-01 [1] CRAN (R 4.3.1)
   desc          1.4.3   2023-12-10 [1] CRAN (R 4.3.1)
   devtools      2.4.5   2022-10-11 [1] CRAN (R 4.3.0)
   digest        0.6.35  2024-03-11 [1] CRAN (R 4.3.1)
   dplyr       * 1.1.4   2023-11-17 [1] CRAN (R 4.3.1)
   ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.3.0)
   fansi         1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
   fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
   fs            1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
   generics      0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
   glue          1.7.0   2024-01-09 [1] CRAN (R 4.3.1)
   htmltools     0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
   htmlwidgets   1.6.4   2023-12-06 [1] CRAN (R 4.3.1)
   httpuv        1.6.15  2024-03-26 [1] CRAN (R 4.3.1)
   later         1.3.2   2023-12-06 [1] CRAN (R 4.3.1)
   lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
 V logr        * 1.3.7   2024-02-24 [1] CRAN (R 4.3.1) (on disk 1.3.6)
   logrx         0.3.0   2023-10-17 [1] CRAN (R 4.3.1)
   magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
   memoise       2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
   mime          0.12    2021-09-28 [1] CRAN (R 4.3.0)
   miniUI        0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
   pillar        1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
   pkgbuild      1.4.4   2024-03-17 [1] CRAN (R 4.3.1)
   pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
   pkgload       1.3.4   2024-01-16 [1] CRAN (R 4.3.1)
   processx      3.8.4   2024-03-16 [1] CRAN (R 4.3.1)
   profvis       0.3.8   2023-05-02 [1] CRAN (R 4.3.0)
   promises      1.2.1   2023-08-10 [1] CRAN (R 4.3.0)
   ps            1.7.6   2024-01-18 [1] CRAN (R 4.3.1)
   purrr         1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
   R6            2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
   Rcpp          1.0.12  2024-01-09 [1] CRAN (R 4.3.1)
   remotes       2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0)
   rlang         1.1.3   2024-01-10 [1] CRAN (R 4.3.1)
   rstudioapi    0.15.0  2023-07-07 [1] CRAN (R 4.3.0)
   sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
   shiny         1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1)
   stringi       1.8.3   2023-12-11 [1] CRAN (R 4.3.1)
   stringr       1.5.1   2023-11-14 [1] CRAN (R 4.3.1)
   tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
   tidyr         1.3.1   2024-01-24 [1] CRAN (R 4.3.1)
   tidyselect    1.2.1   2024-03-11 [1] CRAN (R 4.3.1)
   urlchecker    1.0.1   2021-11-30 [1] CRAN (R 4.3.0)
   usethis       2.2.3   2024-02-19 [1] CRAN (R 4.3.1)
   utf8          1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
   vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
   waiter        0.2.5   2022-01-03 [1] CRAN (R 4.3.0)
   withr         3.0.0   2024-01-16 [1] CRAN (R 4.3.1)
   xtable        1.8-4   2019-04-21 [1] CRAN (R 4.3.0)

 [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

 V ── Loaded and on-disk version mismatch.

─ External software ────────────────────────────────────────────────────────────
 setting        value
 cairo
 cairoFT
 pango
 png
 jpeg
 tiff
 tcl
 curl           8.4.0
 zlib           1.2.12
 bzlib          1.0.8, 13-Jul-2019
 xz             5.4.4
 PCRE           10.42 2022-12-11
 ICU            74.1
 TRE            TRE 0.8.0 R_fixes (BSD)
 iconv          Apple or GNU libiconv 1.11
 readline       5.2

      BLAS           /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib

      lapack         /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib
 lapack_version 3.11.0

─ Python configuration ─────────────────────────────────────────────────────────
 Python is not available

────────────────────────────────────────────────────────────────────────────────
--------------------------------------------------------------------------------
-                               Masked Functions                               -
--------------------------------------------------------------------------------
function `filter` from {package:stats} by package:dplyr
function `lag` from {package:stats} by package:dplyr
function `intersect` from {package:base} by package:dplyr
function `setdiff` from {package:base} by package:dplyr
function `setequal` from {package:base} by package:dplyr
function `union` from {package:base} by package:dplyr
function `plot` from {package:base} by package:graphics
function `body<-` from {package:base} by package:methods
function `kronecker` from {package:base} by package:methods
--------------------------------------------------------------------------------
-                          Used Package and Functions                          -
--------------------------------------------------------------------------------
{package:base} library, mean, summary
{package:dplyr} %>%, group_by, summarise
{package:stats} lm
--------------------------------------------------------------------------------
-                         Program Run Time Information                         -
--------------------------------------------------------------------------------
Start time: 2024-04-08 14:15:26 BST
End time: 2024-04-08 14:15:26 BST
Run time: 0 seconds
--------------------------------------------------------------------------------
-                             Errors and Warnings                              -
--------------------------------------------------------------------------------
Errors:


Warnings:

--------------------------------------------------------------------------------
-                         Messages, Output, and Result                         -
--------------------------------------------------------------------------------
Messages:

Output:


Result:

    Call:
    lm(formula = mpg ~ wt, data = mtcars)

    Residuals:
        Min      1Q  Median      3Q     Max
    -4.5432 -2.3647 -0.1252  1.4096  6.8727

    Coefficients:
                Estimate Std. Error t value Pr(>|t|)
    (Intercept)  37.2851     1.8776  19.858  < 2e-16 ***
    wt           -5.3445     0.5591  -9.559 1.29e-10 ***
    ---
    Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

    Residual standard error: 3.046 on 30 degrees of freedom
    Multiple R-squared:  0.7528,    Adjusted R-squared:  0.7446
    F-statistic: 91.38 on 1 and 30 DF,  p-value: 1.294e-10

--------------------------------------------------------------------------------
-                               Log Output File                                -
--------------------------------------------------------------------------------
Log name: script.log
Log path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging

Use whirl::run() to execute scripts and create logs:

whirl::run("logging/script.R", summary_file = NULL)

✔ script.R: Completed succesfully

When running scripts the overall status is reported in the console. In this example we are choosing not to create a summary log, since we are only running a single script.

The HTML log is created with the name script_log.html and can be viewed below:

Information in the Log

The logrx package offers more detailed output compared to logr, as outlined in the following table. A key distinction is that logrx automatically logs code output. In logr, the user has control over what does or does not get logged. The user can specify which variables, objects, or datasets to send to the log. If the ‘autolog’ feature is activated, output from dplyr and sassy functions are logged automatically.

	logr	logrx	whirl
Log Path	✔	✔	✔
Working Directory	✔	✔
User Name	✔	✔
R Version	✔	✔	✔
Machine	✔	✔	✔
Operating System	✔	✔	✔
Base Packages	✔	✔
Other Packages	✔	✔	✔
Log Start Time	✔	✔
Log End Time.	✔	✔	✔
Elapsed Time	✔	✔
Warnings and Errors	✔	✔	✔
File Hash		✔
Package Dependencies		✔	✔
External Software		✔	(✔)*
Masked Functions		✔
Renv status			✔
Summary status			✔
Input/output files			✔

Only selected external software, such as Pandoc, Quarto, and Python versions.

Linting

The logrx tool enables the inclusion of lintR output within log messages (line 146 - 165 below). To utilize this feature, configure the log.rx.lint global option with a selection of lint rules. A comprehensive list of available rules can be accessed here.

options(log.rx.lint = list(
  lintr::line_length_linter(20)
))

library(logrx)
axecute("script.R")

--------------------------------------------------------------------------------
-                                logrx Metadata                                -
--------------------------------------------------------------------------------
This log was generated using logrx 0.3.0
logrx package version: 0.3.0
logrx build: CRAN (R 4.3.1)
logrx link to repository: https://github.com/pharmaverse/logrx
--------------------------------------------------------------------------------
-                          User and File Information                           -
--------------------------------------------------------------------------------
User: davidblair
File Name: script.R
File Path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging
File HashSum: 76f9dd029df25ba4f65de72631fac248fa30d7d5
--------------------------------------------------------------------------------
-                             Session Information                              -
--------------------------------------------------------------------------------
─ Session info ─────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.3 (2024-02-29)
 os       macOS Sonoma 14.4.1
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/London
 date     2024-04-08
 pandoc   NA

─ Packages ─────────────────────────────────────────────────────────────────────
 ! package      * version date (UTC) lib source
   backports      1.4.1   2021-12-13 [1] CRAN (R 4.3.0)
   cachem         1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
   callr          3.7.6   2024-03-25 [1] CRAN (R 4.3.1)
   cli            3.6.2   2023-12-11 [1] CRAN (R 4.3.1)
   common         1.1.2   2024-03-05 [1] CRAN (R 4.3.1)
   crayon         1.5.2   2022-09-29 [1] CRAN (R 4.3.0)
   curl           5.2.1   2024-03-01 [1] CRAN (R 4.3.1)
   cyclocomp      1.1.1   2023-08-30 [1] CRAN (R 4.3.0)
   desc           1.4.3   2023-12-10 [1] CRAN (R 4.3.1)
   devtools       2.4.5   2022-10-11 [1] CRAN (R 4.3.0)
   digest         0.6.35  2024-03-11 [1] CRAN (R 4.3.1)
   dplyr        * 1.1.4   2023-11-17 [1] CRAN (R 4.3.1)
   ellipsis       0.3.2   2021-04-29 [1] CRAN (R 4.3.0)
   fansi          1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
   fastmap        1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
   fs             1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
   generics       0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
   glue           1.7.0   2024-01-09 [1] CRAN (R 4.3.1)
   htmltools      0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
   htmlwidgets    1.6.4   2023-12-06 [1] CRAN (R 4.3.1)
   httpuv         1.6.15  2024-03-26 [1] CRAN (R 4.3.1)
   later          1.3.2   2023-12-06 [1] CRAN (R 4.3.1)
   lazyeval       0.2.2   2019-03-15 [1] CRAN (R 4.3.0)
   lifecycle      1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
   lintr          3.1.2   2024-03-25 [1] CRAN (R 4.3.1)
 V logr         * 1.3.7   2024-02-24 [1] CRAN (R 4.3.1) (on disk 1.3.6)
   logrx        * 0.3.0   2023-10-17 [1] CRAN (R 4.3.1)
   magrittr       2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
   memoise        2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
   mime           0.12    2021-09-28 [1] CRAN (R 4.3.0)
   miniUI         0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
   pillar         1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
   pkgbuild       1.4.4   2024-03-17 [1] CRAN (R 4.3.1)
   pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
   pkgload        1.3.4   2024-01-16 [1] CRAN (R 4.3.1)
   processx       3.8.4   2024-03-16 [1] CRAN (R 4.3.1)
   profvis        0.3.8   2023-05-02 [1] CRAN (R 4.3.0)
   promises       1.2.1   2023-08-10 [1] CRAN (R 4.3.0)
   ps             1.7.6   2024-01-18 [1] CRAN (R 4.3.1)
   purrr          1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
   R6             2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
   Rcpp           1.0.12  2024-01-09 [1] CRAN (R 4.3.1)
   remotes        2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0)
   rex            1.2.1   2021-11-26 [1] CRAN (R 4.3.0)
   rlang          1.1.3   2024-01-10 [1] CRAN (R 4.3.1)
   rstudioapi     0.15.0  2023-07-07 [1] CRAN (R 4.3.0)
   sessioninfo    1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
   shiny          1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1)
   stringi        1.8.3   2023-12-11 [1] CRAN (R 4.3.1)
   stringr        1.5.1   2023-11-14 [1] CRAN (R 4.3.1)
   tibble         3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
   tidyr          1.3.1   2024-01-24 [1] CRAN (R 4.3.1)
   tidyselect     1.2.1   2024-03-11 [1] CRAN (R 4.3.1)
   urlchecker     1.0.1   2021-11-30 [1] CRAN (R 4.3.0)
   usethis        2.2.3   2024-02-19 [1] CRAN (R 4.3.1)
   utf8           1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
   vctrs          0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
   waiter         0.2.5   2022-01-03 [1] CRAN (R 4.3.0)
   withr          3.0.0   2024-01-16 [1] CRAN (R 4.3.1)
   xml2           1.3.6   2023-12-04 [1] CRAN (R 4.3.1)
   xmlparsedata   1.0.5   2021-03-06 [1] CRAN (R 4.3.0)
   xtable         1.8-4   2019-04-21 [1] CRAN (R 4.3.0)

 [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

 V ── Loaded and on-disk version mismatch.

─ External software ────────────────────────────────────────────────────────────
 setting        value
 cairo
 cairoFT
 pango
 png
 jpeg
 tiff
 tcl
 curl           8.4.0
 zlib           1.2.12
 bzlib          1.0.8, 13-Jul-2019
 xz             5.4.4
 PCRE           10.42 2022-12-11
 ICU            74.1
 TRE            TRE 0.8.0 R_fixes (BSD)
 iconv          Apple or GNU libiconv 1.11
 readline       5.2

      BLAS           /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib

      lapack         /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib
 lapack_version 3.11.0

─ Python configuration ─────────────────────────────────────────────────────────
 Python is not available

────────────────────────────────────────────────────────────────────────────────
--------------------------------------------------------------------------------
-                               Masked Functions                               -
--------------------------------------------------------------------------------
function `filter` from {package:stats} by package:dplyr
function `lag` from {package:stats} by package:dplyr
function `intersect` from {package:base} by package:dplyr
function `setdiff` from {package:base} by package:dplyr
function `setequal` from {package:base} by package:dplyr
function `union` from {package:base} by package:dplyr
function `plot` from {package:base} by package:graphics
function `body<-` from {package:base} by package:methods
function `kronecker` from {package:base} by package:methods
--------------------------------------------------------------------------------
-                          Used Package and Functions                          -
--------------------------------------------------------------------------------
{package:base} library, mean, summary
{package:dplyr} %>%, group_by, summarise
{package:stats} lm
--------------------------------------------------------------------------------
-                                Linter Results                                -
--------------------------------------------------------------------------------
Line 1 [line_length_linter] Lines should not be more than 20 characters. This
line is 22 characters.

Line 5 [line_length_linter] Lines should not be more than 20 characters. This
line is 25 characters.

Line 7 [line_length_linter] Lines should not be more than 20 characters. This
line is 25 characters.

Line 9 [line_length_linter] Lines should not be more than 20 characters. This
line is 50 characters.

Line 11 [line_length_linter] Lines should not be more than 20 characters.
This line is 36 characters.

Line 14 [line_length_linter] Lines should not be more than 20 characters.
This line is 27 characters.
--------------------------------------------------------------------------------
-                         Program Run Time Information                         -
--------------------------------------------------------------------------------
Start time: 2024-04-08 15:26:12 BST
End time: 2024-04-08 15:26:12 BST
Run time: 0 seconds
--------------------------------------------------------------------------------
-                             Errors and Warnings                              -
--------------------------------------------------------------------------------
Errors:


Warnings:

--------------------------------------------------------------------------------
-                         Messages, Output, and Result                         -
--------------------------------------------------------------------------------
Messages:

Output:


Result:

    Call:
    lm(formula = mpg ~ wt, data = mtcars)

    Residuals:
        Min      1Q  Median      3Q     Max
    -4.5432 -2.3647 -0.1252  1.4096  6.8727

    Coefficients:
                Estimate Std. Error t value Pr(>|t|)
    (Intercept)  37.2851     1.8776  19.858  < 2e-16 ***
    wt           -5.3445     0.5591  -9.559 1.29e-10 ***
    ---
    Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

    Residual standard error: 3.046 on 30 degrees of freedom
    Multiple R-squared:  0.7528,    Adjusted R-squared:  0.7446
    F-statistic: 91.38 on 1 and 30 DF,  p-value: 1.294e-10

--------------------------------------------------------------------------------
-                               Log Output File                                -
--------------------------------------------------------------------------------
Log name: script.log
Log path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging

Global Options

We’ve previously discussed the global options in the logrx package that enable the inclusion of lintr output in the log. There are several key differences between the global options in logrx and whirl, and those in logr. The options in logr primarily focus on managing script output, whereas those in logrx and whirl influence the scope of information included, regardless of the script output.

logr.autolog: Enables automatic logging for various dplyr and tidyr functions.
logr.compact: Removes any blanks spaces between log entries.
logr.traceback: Includes the full traceback for errors.
logr.warnings: Retrieves warnings encountered during log file generation, used with getOption.
logr.on: Controls whether the logr log is active.
logr.notes: Includes notes within the log.

log.rx: A blank log environment for storing log elements during execution.
log.rx.exec.env: The execution environment for program code.
log.rx.lint: Contains lintr functions/rules for script analysis.
log.rx.approved: Specifies the location of approved functions.

The most important options to configure whirl is listed below:

whirl.verbosity_level: Controls the level of information displayed in the console.
whirl.n_workers: How many parallel sessions can whirl use when running multiple scripts simultanously.
whirl.track_files: Should reading, writing, and deleting files be tracked? (Only possible on Linux)
whirl.check_renv: Should the R environment compliance with your renv lockfile be be checked?

Most are also available as direct arguments in whirl::run(). For the full list and more details see the whirl-options reference.

Approved Functions

logrx features the ability to designate approved functions, highlighting any functions in the script not on this list within the log file. This enhances traceability of package and function use within a validated environment.

To utilize this feature, begin by creating a list of approved functions:

approved_pkgs <- list(base = "mean",
                      dplyr = "All")

Next, build the approved_pkgs list and save its contents to a file:

library(logrx)
build_approved(approved_pkgs, file = "approved.rds")

Finally, assign the file to the global option log.rx.approved. This ensures the analysis is incorporated into the log (refer to lines 140 - 145 below):

options(log.rv.approved = "approved.rds")

axecute("script.R")

--------------------------------------------------------------------------------
-                                logrx Metadata                                -
--------------------------------------------------------------------------------
This log was generated using logrx 0.3.0
logrx package version: 0.3.0
logrx build: CRAN (R 4.3.1)
logrx link to repository: https://github.com/pharmaverse/logrx
--------------------------------------------------------------------------------
-                          User and File Information                           -
--------------------------------------------------------------------------------
User: davidblair
File Name: script.R
File Path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging
File HashSum: 76f9dd029df25ba4f65de72631fac248fa30d7d5
--------------------------------------------------------------------------------
-                             Session Information                              -
--------------------------------------------------------------------------------
─ Session info ─────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.3 (2024-02-29)
 os       macOS Sonoma 14.4.1
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/London
 date     2024-04-08
 pandoc   NA

─ Packages ─────────────────────────────────────────────────────────────────────
 ! package      * version date (UTC) lib source
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   cyclocomp      1.1.1   2023-08-30 [1] CRAN (R 4.3.0)
   desc           1.4.3   2023-12-10 [1] CRAN (R 4.3.1)
   devtools       2.4.5   2022-10-11 [1] CRAN (R 4.3.0)
   digest         0.6.35  2024-03-11 [1] CRAN (R 4.3.1)
   dplyr        * 1.1.4   2023-11-17 [1] CRAN (R 4.3.1)
   ellipsis       0.3.2   2021-04-29 [1] CRAN (R 4.3.0)
   fansi          1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
   fastmap        1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
   fs             1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
   generics       0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
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   htmlwidgets    1.6.4   2023-12-06 [1] CRAN (R 4.3.1)
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   lazyeval       0.2.2   2019-03-15 [1] CRAN (R 4.3.0)
   lifecycle      1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
   lintr          3.1.2   2024-03-25 [1] CRAN (R 4.3.1)
 V logr         * 1.3.7   2024-02-24 [1] CRAN (R 4.3.1) (on disk 1.3.6)
   logrx        * 0.3.0   2023-10-17 [1] CRAN (R 4.3.1)
   magrittr       2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
   memoise        2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
   mime           0.12    2021-09-28 [1] CRAN (R 4.3.0)
   miniUI         0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
   pillar         1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
   pkgbuild       1.4.4   2024-03-17 [1] CRAN (R 4.3.1)
   pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
   pkgload        1.3.4   2024-01-16 [1] CRAN (R 4.3.1)
   processx       3.8.4   2024-03-16 [1] CRAN (R 4.3.1)
   profvis        0.3.8   2023-05-02 [1] CRAN (R 4.3.0)
   promises       1.2.1   2023-08-10 [1] CRAN (R 4.3.0)
   ps             1.7.6   2024-01-18 [1] CRAN (R 4.3.1)
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   rex            1.2.1   2021-11-26 [1] CRAN (R 4.3.0)
   rlang          1.1.3   2024-01-10 [1] CRAN (R 4.3.1)
   rstudioapi     0.15.0  2023-07-07 [1] CRAN (R 4.3.0)
   sessioninfo    1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
   shiny          1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1)
   stringi        1.8.3   2023-12-11 [1] CRAN (R 4.3.1)
   stringr        1.5.1   2023-11-14 [1] CRAN (R 4.3.1)
   tibble         3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
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   usethis        2.2.3   2024-02-19 [1] CRAN (R 4.3.1)
   utf8           1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
   vctrs          0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
   waiter         0.2.5   2022-01-03 [1] CRAN (R 4.3.0)
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   xtable         1.8-4   2019-04-21 [1] CRAN (R 4.3.0)

 [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

 V ── Loaded and on-disk version mismatch.

─ External software ────────────────────────────────────────────────────────────
 setting        value
 cairo
 cairoFT
 pango
 png
 jpeg
 tiff
 tcl
 curl           8.4.0
 zlib           1.2.12
 bzlib          1.0.8, 13-Jul-2019
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      BLAS           /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib

      lapack         /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib
 lapack_version 3.11.0

─ Python configuration ─────────────────────────────────────────────────────────
 Python is not available

────────────────────────────────────────────────────────────────────────────────
--------------------------------------------------------------------------------
-                               Masked Functions                               -
--------------------------------------------------------------------------------
function `filter` from {package:stats} by package:dplyr
function `lag` from {package:stats} by package:dplyr
function `intersect` from {package:base} by package:dplyr
function `setdiff` from {package:base} by package:dplyr
function `setequal` from {package:base} by package:dplyr
function `union` from {package:base} by package:dplyr
function `plot` from {package:base} by package:graphics
function `body<-` from {package:base} by package:methods
function `kronecker` from {package:base} by package:methods
--------------------------------------------------------------------------------
-                          Used Package and Functions                          -
--------------------------------------------------------------------------------
{package:base} library, mean, summary
{package:dplyr} %>%, group_by, summarise
{package:stats} lm
--------------------------------------------------------------------------------
-                       Unapproved Package and Functions                       -
--------------------------------------------------------------------------------
{package:base} library, summary
{package:stats} lm
--------------------------------------------------------------------------------
-                                Linter Results                                -
--------------------------------------------------------------------------------
Line 1 [line_length_linter] Lines should not be more than 20 characters. This
line is 22 characters.

Line 5 [line_length_linter] Lines should not be more than 20 characters. This
line is 25 characters.

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line is 25 characters.

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line is 50 characters.

Line 11 [line_length_linter] Lines should not be more than 20 characters.
This line is 36 characters.

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This line is 27 characters.
--------------------------------------------------------------------------------
-                         Program Run Time Information                         -
--------------------------------------------------------------------------------
Start time: 2024-04-08 16:03:28 BST
End time: 2024-04-08 16:03:28 BST
Run time: 0 seconds
--------------------------------------------------------------------------------
-                             Errors and Warnings                              -
--------------------------------------------------------------------------------
Errors:


Warnings:

--------------------------------------------------------------------------------
-                         Messages, Output, and Result                         -
--------------------------------------------------------------------------------
Messages:

Output:


Result:

    Call:
    lm(formula = mpg ~ wt, data = mtcars)

    Residuals:
        Min      1Q  Median      3Q     Max
    -4.5432 -2.3647 -0.1252  1.4096  6.8727

    Coefficients:
                Estimate Std. Error t value Pr(>|t|)
    (Intercept)  37.2851     1.8776  19.858  < 2e-16 ***
    wt           -5.3445     0.5591  -9.559 1.29e-10 ***
    ---
    Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

    Residual standard error: 3.046 on 30 degrees of freedom
    Multiple R-squared:  0.7528,    Adjusted R-squared:  0.7446
    F-statistic: 91.38 on 1 and 30 DF,  p-value: 1.294e-10

--------------------------------------------------------------------------------
-                               Log Output File                                -
--------------------------------------------------------------------------------
Log name: script.log
Log path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging

Run multiple scripts

A key functionality whirl is to support the execution of entire analysis projects. It is possible to define batches of scripts to run simultanously, and the order in which the different steps should be executed.

It is all controlled by a yaml configuration file (use whirl::use_whirl() to get started) such as the one below:

_whirl.yml:

steps:
  - name: "Initial step"
    paths:
      - "setup.R"
  - name: "First batch of programs"
    paths:
      - "prgA.R"
      - "prgB.R"
  - name: "Run all programs with 2 prefix"
    paths:
      - "2_*.R"

Here three steps are defined, where the first step is to run setup.R. After this we want to run prgA.R and prgB.R simultanously, and after these two have finished we run all R scripts starting with 2_ (imagine they depend on previous output from e.g. prgA.R).

To run all steps you just call run() with the configuration file as input:

whirl::run("_whirl.yml")

In this scenario it becomes relevant to check the summary log as well (defaults to summary.html), which have the execution status of each script, and a link to the individual logs.

Summary

The decision between using logr, logrx, or whirl hinges on specific needs. logr offers greater control over the output, at the expense of detailed environmental context. Conversely, logrx provides more comprehensive details and quicker log generation, along with better support for command line execution, but offers less control over the output. whirl creates detailed logs with similar information as logrx, but by also including the script and it’s printed outputs it allows the user to include any additional information in the log, or to use run() to create analysis reports directly that also includes relevant information on the execution environment. whirl also offers a framework for execution of a project consisting of multiple scripts.

--- title: "The Difference Between `logr`, `logrx`, and `whirl`" format: html: code-overflow: wrap --- ```{css, echo=FALSE} .output-block { max-height: 400px; overflow-y: scroll; } ``` The [`logr`](https://github.com/dbosak01/logr/) package for R aims to provide a straightforward logging system tailored for everyday users, such as statisticians and educators, emphasizing simplicity in recording program execution. In contrast, [`logrx`](https://github.com/pharmaverse/logrx/) offers an advanced logging mechanism designed specifically for clinical reporting, featuring easy traceability and reproducibility of R script executions with capabilities suited for more technical users. [`whirl`](https://github.com/NovoNordisk-OpenSource/whirl) differs in that the package provides functionalities for executing scripts in batch and simultaneously getting a log from the individual executions. In contrast the other two logging packages, the default logs are HTML reports making it easier to read, and they include the results printed in the programs being logged. All three packages are used for keeping a record of what happens when R scripts are run, but they differ in what they offer and who they're for. When choosing between them, you should consider what you need for your particular situation. ### Execution Each package differs notably in the approach to generating a log file. The `logr` package adopts a method similar to SAS, where the log is manually constructed at intermediary steps within the R script. Conversely, the `logrx` package allows for the creation of a log file through a single command from the R terminal, offering added compatibility for command line submission. `whirl` also provides a single function to create log files, and it should be noted that the execution is done through [Quarto](https://quarto.org), which enables the HTML reports, but also make it more heavier on external dependencies. ::: {.panel-tabset} ## `logr` ```{r, eval=FALSE} #| class: output-block # file: script.R library(dplyr) library(logr) file_path <- "script.log" log_file <- log_open(file_path) log_print("Analyzing Fuel Efficiency Trends in Cars") average_mpg <- mtcars %>% group_by(cyl) %>% summarise(average_mpg = mean(mpg, na.rm = TRUE)) log_print(average_mpg) model <- lm(mpg ~ wt, data = mtcars) summary(model) log_print(model) log_close() # log file path: log/script.log ``` <br> ```{t} #| class: output-block ========================================================================= Log Path: ./log/script.log Working Directory: /Users/davidblair/My Drive/Appsilon/Work Projects/examples User Name: davidblair R Version: 4.3.3 (2024-02-29) Machine: Davids-Air.localdomain arm64 Operating System: Darwin 23.4.0 Darwin Kernel Version 23.4.0: Fri Mar 15 00:12:41 PDT 2024; root:xnu-10063.101.17~1/RELEASE_ARM64_T8103 Base Packages: stats graphics grDevices utils datasets methods base Other Packages: dplyr_1.1.4 logr_1.3.6 Log Start Time: 2024-04-08 13:25:53.22436 ========================================================================= Analyzing Fuel Efficiency Trends in Cars NOTE: Log Print Time: 2024-04-08 13:25:53.226347 NOTE: Elapsed Time: 0.00139403343200684 secs # A tibble: 3 × 2 cyl average_mpg <dbl> <dbl> 1 4 26.7 2 6 19.7 3 8 15.1 NOTE: Data frame has 3 rows and 2 columns. NOTE: Log Print Time: 2024-04-08 13:25:53.254377 NOTE: Elapsed Time: 0.0280299186706543 secs Call: lm(formula = mpg ~ wt, data = mtcars) Coefficients: (Intercept) wt 37.285 -5.344 NOTE: Log Print Time: 2024-04-08 13:25:53.267483 NOTE: Elapsed Time: 0.013106107711792 secs ========================================================================= Log End Time: 2024-04-08 13:25:53.286294 Log Elapsed Time: 0 00:00:00 ========================================================================= ``` ## `logrx` From the R terminal: ```{r, eval=FALSE} logrx::axecute("script.R") ``` From the Command Line: ```{bash, eval=FALSE} Rscript -e "logrx::axecute('script.R')" ``` ```{t} #| class: output-block -------------------------------------------------------------------------------- - logrx Metadata - -------------------------------------------------------------------------------- This log was generated using logrx 0.3.0 logrx package version: 0.3.0 logrx build: CRAN (R 4.3.1) logrx link to repository: https://github.com/pharmaverse/logrx -------------------------------------------------------------------------------- - User and File Information - -------------------------------------------------------------------------------- User: davidblair File Name: script.R File Path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging File HashSum: 76f9dd029df25ba4f65de72631fac248fa30d7d5 -------------------------------------------------------------------------------- - Session Information - -------------------------------------------------------------------------------- ─ Session info ───────────────────────────────────────────────────────────────── setting value version R version 4.3.3 (2024-02-29) os macOS Sonoma 14.4.1 system aarch64, darwin20 ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/London date 2024-04-08 pandoc NA ─ Packages ───────────────────────────────────────────────────────────────────── ! package * version date (UTC) lib source cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0) callr 3.7.6 2024-03-25 [1] CRAN (R 4.3.1) cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) common 1.1.2 2024-03-05 [1] CRAN (R 4.3.1) curl 5.2.1 2024-03-01 [1] CRAN (R 4.3.1) desc 1.4.3 2023-12-10 [1] CRAN (R 4.3.1) devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0) digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.1) dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.1) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.1) httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.3.1) later 1.3.2 2023-12-06 [1] CRAN (R 4.3.1) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) V logr * 1.3.7 2024-02-24 [1] CRAN (R 4.3.1) (on disk 1.3.6) logrx 0.3.0 2023-10-17 [1] CRAN (R 4.3.1) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0) mime 0.12 2021-09-28 [1] CRAN (R 4.3.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.1) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.1) processx 3.8.4 2024-03-16 [1] CRAN (R 4.3.1) profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0) promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0) ps 1.7.6 2024-01-18 [1] CRAN (R 4.3.1) purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1) remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0) rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1) stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.1) stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.1) tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.3.1) tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.1) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0) usethis 2.2.3 2024-02-19 [1] CRAN (R 4.3.1) utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1) waiter 0.2.5 2022-01-03 [1] CRAN (R 4.3.0) withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0) [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library V ── Loaded and on-disk version mismatch. ─ External software ──────────────────────────────────────────────────────────── setting value cairo cairoFT pango png jpeg tiff tcl curl 8.4.0 zlib 1.2.12 bzlib 1.0.8, 13-Jul-2019 xz 5.4.4 PCRE 10.42 2022-12-11 ICU 74.1 TRE TRE 0.8.0 R_fixes (BSD) iconv Apple or GNU libiconv 1.11 readline 5.2 BLAS /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib lapack /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib lapack_version 3.11.0 ─ Python configuration ───────────────────────────────────────────────────────── Python is not available ──────────────────────────────────────────────────────────────────────────────── -------------------------------------------------------------------------------- - Masked Functions - -------------------------------------------------------------------------------- function `filter` from {package:stats} by package:dplyr function `lag` from {package:stats} by package:dplyr function `intersect` from {package:base} by package:dplyr function `setdiff` from {package:base} by package:dplyr function `setequal` from {package:base} by package:dplyr function `union` from {package:base} by package:dplyr function `plot` from {package:base} by package:graphics function `body<-` from {package:base} by package:methods function `kronecker` from {package:base} by package:methods -------------------------------------------------------------------------------- - Used Package and Functions - -------------------------------------------------------------------------------- {package:base} library, mean, summary {package:dplyr} %>%, group_by, summarise {package:stats} lm -------------------------------------------------------------------------------- - Program Run Time Information - -------------------------------------------------------------------------------- Start time: 2024-04-08 14:15:26 BST End time: 2024-04-08 14:15:26 BST Run time: 0 seconds -------------------------------------------------------------------------------- - Errors and Warnings - -------------------------------------------------------------------------------- Errors: Warnings: -------------------------------------------------------------------------------- - Messages, Output, and Result - -------------------------------------------------------------------------------- Messages: Output: Result: Call: lm(formula = mpg ~ wt, data = mtcars) Residuals: Min 1Q Median 3Q Max -4.5432 -2.3647 -0.1252 1.4096 6.8727 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 37.2851 1.8776 19.858 < 2e-16 *** wt -5.3445 0.5591 -9.559 1.29e-10 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 3.046 on 30 degrees of freedom Multiple R-squared: 0.7528, Adjusted R-squared: 0.7446 F-statistic: 91.38 on 1 and 30 DF, p-value: 1.294e-10 -------------------------------------------------------------------------------- - Log Output File - -------------------------------------------------------------------------------- Log name: script.log Log path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging ``` ## `whirl` Use `whirl::run()` to execute scripts and create logs: ```{r} #| label: whirl setup #| include: false options(whirl.verbosity_level = "minimal") ``` ```{r} #| label: whirl run whirl::run("logging/script.R", summary_file = NULL) ``` When running scripts the overall status is reported in the console. In this example we are choosing not to create a summary log, since we are only running a single script. The HTML log is created with the name `script_log.html` and can be viewed below: ```{=html} <iframe src="script_log.html" width=100% height=600></iframe> ``` ::: ### Information in the Log The `logrx` package offers more detailed output compared to `logr`, as outlined in the following table. A key distinction is that `logrx` automatically logs code output. In `logr`, the user has control over what does or does not get logged. The user can specify which variables, objects, or datasets to send to the log. If the 'autolog' feature is activated, output from dplyr and sassy functions are logged automatically. | | logr | logrx | whirl | |----------------------|------|-------|-------| | Log Path | ✔ | ✔ | ✔ | | Working Directory | ✔ | ✔ | | | User Name | ✔ | ✔ | | | R Version | ✔ | ✔ | ✔ | | Machine | ✔ | ✔ | ✔ | | Operating System | ✔ | ✔ | ✔ | | Base Packages | ✔ | ✔ | | | Other Packages | ✔ | ✔ | ✔ | | Log Start Time | ✔ | ✔ | | | Log End Time. | ✔ | ✔ | ✔ | | Elapsed Time | ✔ | ✔ | | | Warnings and Errors | ✔ | ✔ | ✔ | | File Hash | | ✔ | | | Package Dependencies | | ✔ | ✔ | | External Software | | ✔ | (✔)* | | Masked Functions | | ✔ | | | Renv status | | | ✔ | | Summary status | | | ✔ | | Input/output files | | | ✔ | * Only selected external software, such as Pandoc, Quarto, and Python versions. ### Linting The `logrx` tool enables the inclusion of `lintR` output within log messages (line 146 - 165 below). To utilize this feature, configure the `log.rx.lint` global option with a selection of lint rules. A comprehensive list of available rules can be accessed [here](https://lintr.r-lib.org/reference/linters.html). ```{r, eval=FALSE} options(log.rx.lint = list( lintr::line_length_linter(20) )) library(logrx) axecute("script.R") ``` ```{t} #| class: output-block -------------------------------------------------------------------------------- - logrx Metadata - -------------------------------------------------------------------------------- This log was generated using logrx 0.3.0 logrx package version: 0.3.0 logrx build: CRAN (R 4.3.1) logrx link to repository: https://github.com/pharmaverse/logrx -------------------------------------------------------------------------------- - User and File Information - -------------------------------------------------------------------------------- User: davidblair File Name: script.R File Path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging File HashSum: 76f9dd029df25ba4f65de72631fac248fa30d7d5 -------------------------------------------------------------------------------- - Session Information - -------------------------------------------------------------------------------- ─ Session info ───────────────────────────────────────────────────────────────── setting value version R version 4.3.3 (2024-02-29) os macOS Sonoma 14.4.1 system aarch64, darwin20 ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/London date 2024-04-08 pandoc NA ─ Packages ───────────────────────────────────────────────────────────────────── ! package * version date (UTC) lib source backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0) cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0) callr 3.7.6 2024-03-25 [1] CRAN (R 4.3.1) cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) common 1.1.2 2024-03-05 [1] CRAN (R 4.3.1) crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0) curl 5.2.1 2024-03-01 [1] CRAN (R 4.3.1) cyclocomp 1.1.1 2023-08-30 [1] CRAN (R 4.3.0) desc 1.4.3 2023-12-10 [1] CRAN (R 4.3.1) devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0) digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.1) dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.1) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.1) httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.3.1) later 1.3.2 2023-12-06 [1] CRAN (R 4.3.1) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) lintr 3.1.2 2024-03-25 [1] CRAN (R 4.3.1) V logr * 1.3.7 2024-02-24 [1] CRAN (R 4.3.1) (on disk 1.3.6) logrx * 0.3.0 2023-10-17 [1] CRAN (R 4.3.1) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0) mime 0.12 2021-09-28 [1] CRAN (R 4.3.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.1) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.1) processx 3.8.4 2024-03-16 [1] CRAN (R 4.3.1) profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0) promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0) ps 1.7.6 2024-01-18 [1] CRAN (R 4.3.1) purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1) remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0) rex 1.2.1 2021-11-26 [1] CRAN (R 4.3.0) rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1) stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.1) stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.1) tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.3.1) tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.1) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0) usethis 2.2.3 2024-02-19 [1] CRAN (R 4.3.1) utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1) waiter 0.2.5 2022-01-03 [1] CRAN (R 4.3.0) withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.1) xmlparsedata 1.0.5 2021-03-06 [1] CRAN (R 4.3.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0) [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library V ── Loaded and on-disk version mismatch. ─ External software ──────────────────────────────────────────────────────────── setting value cairo cairoFT pango png jpeg tiff tcl curl 8.4.0 zlib 1.2.12 bzlib 1.0.8, 13-Jul-2019 xz 5.4.4 PCRE 10.42 2022-12-11 ICU 74.1 TRE TRE 0.8.0 R_fixes (BSD) iconv Apple or GNU libiconv 1.11 readline 5.2 BLAS /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib lapack /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib lapack_version 3.11.0 ─ Python configuration ───────────────────────────────────────────────────────── Python is not available ──────────────────────────────────────────────────────────────────────────────── -------------------------------------------------------------------------------- - Masked Functions - -------------------------------------------------------------------------------- function `filter` from {package:stats} by package:dplyr function `lag` from {package:stats} by package:dplyr function `intersect` from {package:base} by package:dplyr function `setdiff` from {package:base} by package:dplyr function `setequal` from {package:base} by package:dplyr function `union` from {package:base} by package:dplyr function `plot` from {package:base} by package:graphics function `body<-` from {package:base} by package:methods function `kronecker` from {package:base} by package:methods -------------------------------------------------------------------------------- - Used Package and Functions - -------------------------------------------------------------------------------- {package:base} library, mean, summary {package:dplyr} %>%, group_by, summarise {package:stats} lm -------------------------------------------------------------------------------- - Linter Results - -------------------------------------------------------------------------------- Line 1 [line_length_linter] Lines should not be more than 20 characters. This line is 22 characters. Line 5 [line_length_linter] Lines should not be more than 20 characters. This line is 25 characters. Line 7 [line_length_linter] Lines should not be more than 20 characters. This line is 25 characters. Line 9 [line_length_linter] Lines should not be more than 20 characters. This line is 50 characters. Line 11 [line_length_linter] Lines should not be more than 20 characters. This line is 36 characters. Line 14 [line_length_linter] Lines should not be more than 20 characters. This line is 27 characters. -------------------------------------------------------------------------------- - Program Run Time Information - -------------------------------------------------------------------------------- Start time: 2024-04-08 15:26:12 BST End time: 2024-04-08 15:26:12 BST Run time: 0 seconds -------------------------------------------------------------------------------- - Errors and Warnings - -------------------------------------------------------------------------------- Errors: Warnings: -------------------------------------------------------------------------------- - Messages, Output, and Result - -------------------------------------------------------------------------------- Messages: Output: Result: Call: lm(formula = mpg ~ wt, data = mtcars) Residuals: Min 1Q Median 3Q Max -4.5432 -2.3647 -0.1252 1.4096 6.8727 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 37.2851 1.8776 19.858 < 2e-16 *** wt -5.3445 0.5591 -9.559 1.29e-10 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 3.046 on 30 degrees of freedom Multiple R-squared: 0.7528, Adjusted R-squared: 0.7446 F-statistic: 91.38 on 1 and 30 DF, p-value: 1.294e-10 -------------------------------------------------------------------------------- - Log Output File - -------------------------------------------------------------------------------- Log name: script.log Log path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging ``` ### Global Options We've previously discussed the global options in the `logrx` package that enable the inclusion of `lintr` output in the log. There are several key differences between the global options in `logrx` and `whirl`, and those in `logr`. The options in `logr` primarily focus on managing script output, whereas those in `logrx` and `whirl` influence the scope of information included, regardless of the script output. ::: {.panel-tabset} ## `logr` 1. `logr.autolog`: Enables automatic logging for various `dplyr` and `tidyr` functions. 2. `logr.compact`: Removes any blanks spaces between log entries. 3. `logr.traceback`: Includes the full traceback for errors. 4. `logr.warnings`: Retrieves warnings encountered during log file generation, used with `getOption`. 5. `logr.on`: Controls whether the `logr` log is active. 6. `logr.notes`: Includes notes within the log. ## `logrx` 1. `log.rx`: A blank log environment for storing log elements during execution. 2. `log.rx.exec.env`: The execution environment for program code. 3. `log.rx.lint`: Contains `lintr` functions/rules for script analysis. 4. `log.rx.approved`: Specifies the location of approved functions. ## `whirl` The most important options to configure `whirl` is listed below: 1. `whirl.verbosity_level`: Controls the level of information displayed in the console. 1. `whirl.n_workers`: How many parallel sessions can `whirl` use when running multiple scripts simultanously. 1. `whirl.track_files`: Should reading, writing, and deleting files be tracked? (Only possible on Linux) 1. `whirl.check_renv`: Should the R environment compliance with your `renv` lockfile be be checked? Most are also available as direct arguments in `whirl::run()`. For the full list and more details see the [whirl-options](https://novonordisk-opensource.github.io/whirl/reference/whirl-options.html) reference. ::: ### Approved Functions `logrx` features the ability to designate approved functions, highlighting any functions in the script not on this list within the log file. This enhances traceability of package and function use within a validated environment. To utilize this feature, begin by creating a list of approved functions: ```{r} approved_pkgs <- list(base = "mean", dplyr = "All") ``` Next, build the `approved_pkgs` list and save its contents to a file: ```{r} library(logrx) build_approved(approved_pkgs, file = "approved.rds") ``` Finally, assign the file to the global option `log.rx.approved`. This ensures the analysis is incorporated into the log (refer to lines 140 - 145 below): ```{r} options(log.rv.approved = "approved.rds") ``` ```{r, eval=FALSE} axecute("script.R") ``` ```{t} #| class: output-block -------------------------------------------------------------------------------- - logrx Metadata - -------------------------------------------------------------------------------- This log was generated using logrx 0.3.0 logrx package version: 0.3.0 logrx build: CRAN (R 4.3.1) logrx link to repository: https://github.com/pharmaverse/logrx -------------------------------------------------------------------------------- - User and File Information - -------------------------------------------------------------------------------- User: davidblair File Name: script.R File Path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging File HashSum: 76f9dd029df25ba4f65de72631fac248fa30d7d5 -------------------------------------------------------------------------------- - Session Information - -------------------------------------------------------------------------------- ─ Session info ───────────────────────────────────────────────────────────────── setting value version R version 4.3.3 (2024-02-29) os macOS Sonoma 14.4.1 system aarch64, darwin20 ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/London date 2024-04-08 pandoc NA ─ Packages ───────────────────────────────────────────────────────────────────── ! package * version date (UTC) lib source backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0) cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0) callr 3.7.6 2024-03-25 [1] CRAN (R 4.3.1) cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) common 1.1.2 2024-03-05 [1] CRAN (R 4.3.1) crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0) curl 5.2.1 2024-03-01 [1] CRAN (R 4.3.1) cyclocomp 1.1.1 2023-08-30 [1] CRAN (R 4.3.0) desc 1.4.3 2023-12-10 [1] CRAN (R 4.3.1) devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0) digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.1) dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.1) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.1) httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.3.1) later 1.3.2 2023-12-06 [1] CRAN (R 4.3.1) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) lintr 3.1.2 2024-03-25 [1] CRAN (R 4.3.1) V logr * 1.3.7 2024-02-24 [1] CRAN (R 4.3.1) (on disk 1.3.6) logrx * 0.3.0 2023-10-17 [1] CRAN (R 4.3.1) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0) mime 0.12 2021-09-28 [1] CRAN (R 4.3.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.1) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.1) processx 3.8.4 2024-03-16 [1] CRAN (R 4.3.1) profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0) promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0) ps 1.7.6 2024-01-18 [1] CRAN (R 4.3.1) purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1) remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0) rex 1.2.1 2021-11-26 [1] CRAN (R 4.3.0) rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1) stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.1) stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.1) tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.3.1) tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.1) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0) usethis 2.2.3 2024-02-19 [1] CRAN (R 4.3.1) utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1) waiter 0.2.5 2022-01-03 [1] CRAN (R 4.3.0) withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.1) xmlparsedata 1.0.5 2021-03-06 [1] CRAN (R 4.3.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0) [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library V ── Loaded and on-disk version mismatch. ─ External software ──────────────────────────────────────────────────────────── setting value cairo cairoFT pango png jpeg tiff tcl curl 8.4.0 zlib 1.2.12 bzlib 1.0.8, 13-Jul-2019 xz 5.4.4 PCRE 10.42 2022-12-11 ICU 74.1 TRE TRE 0.8.0 R_fixes (BSD) iconv Apple or GNU libiconv 1.11 readline 5.2 BLAS /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib lapack /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib lapack_version 3.11.0 ─ Python configuration ───────────────────────────────────────────────────────── Python is not available ──────────────────────────────────────────────────────────────────────────────── -------------------------------------------------------------------------------- - Masked Functions - -------------------------------------------------------------------------------- function `filter` from {package:stats} by package:dplyr function `lag` from {package:stats} by package:dplyr function `intersect` from {package:base} by package:dplyr function `setdiff` from {package:base} by package:dplyr function `setequal` from {package:base} by package:dplyr function `union` from {package:base} by package:dplyr function `plot` from {package:base} by package:graphics function `body<-` from {package:base} by package:methods function `kronecker` from {package:base} by package:methods -------------------------------------------------------------------------------- - Used Package and Functions - -------------------------------------------------------------------------------- {package:base} library, mean, summary {package:dplyr} %>%, group_by, summarise {package:stats} lm -------------------------------------------------------------------------------- - Unapproved Package and Functions - -------------------------------------------------------------------------------- {package:base} library, summary {package:stats} lm -------------------------------------------------------------------------------- - Linter Results - -------------------------------------------------------------------------------- Line 1 [line_length_linter] Lines should not be more than 20 characters. This line is 22 characters. Line 5 [line_length_linter] Lines should not be more than 20 characters. This line is 25 characters. Line 7 [line_length_linter] Lines should not be more than 20 characters. This line is 25 characters. Line 9 [line_length_linter] Lines should not be more than 20 characters. This line is 50 characters. Line 11 [line_length_linter] Lines should not be more than 20 characters. This line is 36 characters. Line 14 [line_length_linter] Lines should not be more than 20 characters. This line is 27 characters. -------------------------------------------------------------------------------- - Program Run Time Information - -------------------------------------------------------------------------------- Start time: 2024-04-08 16:03:28 BST End time: 2024-04-08 16:03:28 BST Run time: 0 seconds -------------------------------------------------------------------------------- - Errors and Warnings - -------------------------------------------------------------------------------- Errors: Warnings: -------------------------------------------------------------------------------- - Messages, Output, and Result - -------------------------------------------------------------------------------- Messages: Output: Result: Call: lm(formula = mpg ~ wt, data = mtcars) Residuals: Min 1Q Median 3Q Max -4.5432 -2.3647 -0.1252 1.4096 6.8727 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 37.2851 1.8776 19.858 < 2e-16 *** wt -5.3445 0.5591 -9.559 1.29e-10 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 3.046 on 30 degrees of freedom Multiple R-squared: 0.7528, Adjusted R-squared: 0.7446 F-statistic: 91.38 on 1 and 30 DF, p-value: 1.294e-10 -------------------------------------------------------------------------------- - Log Output File - -------------------------------------------------------------------------------- Log name: script.log Log path: /Users/davidblair/My Drive/Appsilon/Work Projects/examples/logging ``` ### Run multiple scripts A key functionality `whirl` is to support the execution of entire analysis projects. It is possible to define batches of scripts to run simultanously, and the order in which the different steps should be executed. It is all controlled by a yaml configuration file (use [`whirl::use_whirl()`](https://novonordisk-opensource.github.io/whirl/reference/use_whirl.html) to get started) such as the one below: `_whirl.yml`: ```yaml steps: - name: "Initial step" paths: - "setup.R" - name: "First batch of programs" paths: - "prgA.R" - "prgB.R" - name: "Run all programs with 2 prefix" paths: - "2_*.R" ``` Here three steps are defined, where the first step is to run `setup.R`. After this we want to run `prgA.R` and `prgB.R` simultanously, and after these two have finished we run all R scripts starting with `2_` (imagine they depend on previous output from e.g. `prgA.R`). To run all steps you just call `run()` with the configuration file as input: ```{r} #| eval: false whirl::run("_whirl.yml") ``` In this scenario it becomes relevant to check the summary log as well (defaults to `summary.html`), which have the execution status of each script, and a link to the individual logs. ### Summary The decision between using `logr`, `logrx`, or `whirl` hinges on specific needs. `logr` offers greater control over the output, at the expense of detailed environmental context. Conversely, `logrx` provides more comprehensive details and quicker log generation, along with better support for command line execution, but offers less control over the output. `whirl` creates detailed logs with similar information as `logrx`, but by also including the script and it's printed outputs it allows the user to include any additional information in the log, or to use `run()` to create analysis reports directly that also includes relevant information on the execution environment. `whirl` also offers a framework for execution of a project consisting of multiple scripts.