Fixes #229, #186, #228

[kodesiba]

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The spirit of logrx

While many packages to facilitate the logging of code already exist in the R ecosystem, it is hard to find a solution that works well for clinical programming applications. Many logging implementations are more implicit and rely on user input to create the log for the execution of a script. While this is useful for logging specific events of an application, in clinical programming a log has a set purpose.

logrx is built around the concept of creating a log for the execution of an R script that provides an overview of what happened as well as the environment that it happened in. We set out to create a flexible logging utility that could provide the necessary information to anyone reviewing the code execution so they can recreate the execution environment and run the code for themselves. Please make sure your Pull Request meets this spirit of logrx.

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• Updated relevant unit tests or have written new unit tests. Remember to remove any configured log objects at the end of every test using log_remove().
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• Run devtools::document() so all .Rd files in the man folder and the NAMESPACE file in the project root are updated appropriately
• Run pkgdown::build_site() and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.
• Update NEWS.md if the changes pertain to a user-facing function (i.e. it has an @export tag) or documentation aimed at users (rather than developers)
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[github-actions]

Package	Line Rate	Health
logrx	89%	✔
Summary	89% (710 / 795)	✔

[kodesiba]

@bms63 @nicholas-masel @parmsam-pfizer this should be it for random documentation updates. I don't know how much more we want to say in these but I'm happy to update things if anyone sees any part that is still lacking.

I can't run off logs on my current setup so I wanted to see if someone else could rerun the logs we have in the data-raw folder and then copy them in to \vignettes\articles once this is through. Once these are built I can do a final release PR to main and build for CRAN!

[bms63]

I can't get the pkgdown site to build. Are others able to build it?

[bms63]

it is interesting. the vignette builds by itself. but if i run line by line it crashes

[bms63]

@parmsam-pfizer any ideas - is it working on your end?

[parmsam-pfizer]

That's odd. Same here. I'll look into this further to see what's going on. It knits to HTML without issues but has an error reading the log when I run it manually chunk by chunk.

[bms63]

@kodesiba I rerun all the .R files to produce the .log files

[bms63]

let me know if you need any other help

[parmsam-pfizer]

Related to the sessioninfo update. It seems to have messed up a convention I was using to nest/subnest the log. Looking into a fix now.

[parmsam-pfizer]

@bms63, should work now. Just tested it on my machine.

[bms63]

I get this warning now

Still can't build the website locally. If you are able to build it then we can merge in and I can review stuff from the dev site

[bms63]

I think the script should be exposed in the vignette - i set echo = TRUE

[parmsam-pfizer]

Yeah, that's normal. It comes from readr::read_table() function I used. It tries it best to parse some sections on first pass.

logrx/R/read_log_file.R

Lines 194 to 200 in cc2b597

	parsed_log$`Session Information`$`Packages` <-
	nested_log$`Session Information`$`Packages` %>%
	# remove indicator whether the package is attached to the search path
	stringr::str_replace_all("\\*", " ") %>%
	# account for loaded packages due to load_all()
	stringr::str_replace_all(" P ", " ") %>%
	readr::read_table(skip = 1, col_names = FALSE)

[bms63]

I set error = TRUE and the site builds with this now

[bms63]

Could we merge to main and see if it publishes. if it doesn't then we should fix this. my build is not building the RMD file unless I set error = TRUE

session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.3 (2023-03-15)
os Ubuntu 20.04.6 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate C.UTF-8
ctype C.UTF-8
tz UTC
date 2025-04-30
rstudio 2024.04.2+764.pro1 Chocolate Cosmos (server)
pandoc 3.1.11 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/x86_64/ (via rmarkdown)
quarto 1.7.29 @ /usr/bin/quarto

─ Packages ───────────────────────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
brio 1.1.5 2024-04-24 [1] RSPM (R 4.2.0)
cachem 1.1.0 2024-05-16 [1] RSPM (R 4.2.0)
callr 3.7.6 2024-03-25 [1] RSPM (R 4.2.0)
cli 3.6.4 2025-02-13 [1] RSPM (R 4.2.0)
desc 1.4.3 2023-12-10 [1] RSPM (R 4.2.0)
devtools 2.4.5 2022-10-11 [1] RSPM (R 4.2.0)
digest 0.6.37 2024-08-19 [1] RSPM (R 4.2.0)
dplyr * 1.1.4 2023-11-17 [1] RSPM (R 4.2.0)
ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.2.0)
evaluate 1.0.3 2025-01-10 [1] RSPM (R 4.2.0)
fastmap 1.2.0 2024-05-15 [1] RSPM (R 4.2.0)
fs 1.6.5 2024-10-30 [1] RSPM (R 4.2.0)
generics 0.1.3 2022-07-05 [1] RSPM (R 4.2.0)
glue 1.8.0 2024-09-30 [1] RSPM (R 4.2.0)
hms 1.1.3 2023-03-21 [1] RSPM (R 4.2.0)
htmltools 0.5.8.1 2024-04-04 [1] RSPM (R 4.2.0)
htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.2.0)
httpuv 1.6.15 2024-03-26 [1] RSPM (R 4.2.0)
knitr 1.49 2024-11-08 [1] RSPM (R 4.2.0)
later 1.4.1 2024-11-27 [1] RSPM (R 4.2.0)
lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.2.0)
P logrx * 0.3.2.9000 2025-04-30 [?] load_all()
magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.2.0)
memoise 2.0.1 2021-11-26 [1] RSPM (R 4.2.0)
mime 0.12 2021-09-28 [1] RSPM (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.2.0)
pillar 1.10.1 2025-01-07 [1] RSPM (R 4.2.0)
pkgbuild 1.4.6 2025-01-16 [1] RSPM (R 4.2.0)
pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.2.0)
pkgdown 2.1.1 2024-09-17 [1] RSPM (R 4.2.0)
pkgload 1.4.0 2024-06-28 [1] RSPM (R 4.2.0)
processx 3.8.6 2025-02-21 [1] RSPM (R 4.2.0)
profvis 0.4.0 2024-09-20 [1] RSPM (R 4.2.0)
promises 1.3.2 2024-11-28 [1] RSPM (R 4.2.0)
ps 1.9.0 2025-02-18 [1] RSPM (R 4.2.0)
purrr 1.0.4 2025-02-05 [1] RSPM (R 4.2.0)
R6 2.6.1 2025-02-15 [1] RSPM (R 4.2.0)
Rcpp 1.0.14 2025-01-12 [1] RSPM (R 4.2.0)
readr 2.1.5 2024-01-10 [1] RSPM (R 4.2.0)
remotes 2.5.0 2024-03-17 [1] RSPM (R 4.2.0)
renv * 1.1.4 2025-03-20 [1] RSPM (R 4.2.0)
rlang 1.1.5 2025-01-17 [1] RSPM (R 4.2.0)
rmarkdown 2.29 2024-11-04 [1] RSPM (R 4.2.0)
rprojroot 2.0.4 2023-11-05 [1] RSPM (R 4.2.0)
rstudioapi 0.17.1 2024-10-22 [1] RSPM (R 4.2.0)
sessioninfo 1.2.3 2025-02-05 [1] RSPM (R 4.2.0)
shiny 1.10.0 2024-12-14 [1] RSPM (R 4.2.0)
stringi 1.8.4 2024-05-06 [1] RSPM (R 4.2.0)
stringr * 1.5.1 2023-11-14 [1] RSPM (R 4.2.0)
testthat * 3.2.3 2025-01-13 [1] RSPM (R 4.2.0)
tibble 3.2.1 2023-03-20 [1] RSPM (R 4.2.0)
tidyr * 1.3.1 2024-01-24 [1] RSPM (R 4.2.0)
tidyselect 1.2.1 2024-03-11 [1] RSPM (R 4.2.0)
tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.2.0)
urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.2.0)
usethis 3.1.0 2024-11-26 [1] RSPM (R 4.2.0)
vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.2.0)
withr 3.0.2 2024-10-28 [1] RSPM (R 4.2.0)
xfun 0.51 2025-02-19 [1] RSPM (R 4.2.0)
xtable 1.8-4 2019-04-21 [1] RSPM (R 4.2.0)
yaml 2.3.10 2024-07-26 [1] RSPM (R 4.2.0)

[1] /cloud/lib/x86_64-pc-linux-gnu-library/4.2
[2] /opt/R/4.2.3/lib/R/library

• ── Packages attached to the search path.
  P ── Loaded and on-disk path mismatch.

[kodesiba]

@bms63 happy to merge this to main if we want to see what happens

[kodesiba]

@bms63 since you know what section needs to be updated in the vignette can you add the error = true part, the run looks to have failed