Refusal to scan all scripts either with scan_project_files() & create_checkpoint() #308
Description
Hello,
Trying to implement a checkpoint for my project resulted in the functions scan_project_files() & create_checkpoint() refusing to scan any of my script (either R or RMarkdown).
I put copies of the R & Rstudio session infos, the script setting up the checkpoint with the results on the console below.
I'm a bit confused the package & functions failed this way. After tweaking and reseraching the issues of this Github page (both opened and closed), I'm still unable to pinpoint what exactly failed.
This are relevant (I think) information I collected while trying to debug the issue :
- changing the namming format of the script files, even to bare minimum (one word with no special characters) doesn't solve the issue
- copying the script to the main directory instead of putting them in their own folder doesn't solve the issue
- using a brand new Rproject with no version control (in my case Git/Github) and running the code with a test script containing a copy of the library() calls does solve the issue
- I branched my project in order to introduce the chekpoint package
I search the Issues page for both the main console result ('Following files could not be scanned') adn 'git" to check if this issue was solved. In the first cas, I see no previous issue published, for the second there is one on git integration but is closed (I supposed it is solved) but do not contain info pointing me to a way to solve the issue in my original R project.
I strongly suspect that the problem originates in the fact I use version control for this project.
Do you confirm there is an incompatibility between usig Git/GitHub and the package ?
I fell the need to post this issue despite the results exposed above because version control is most of the time part of a reproductible research/data analysis R project and find odd the package failed in this circumstances.
If not, is there a piece of documentation (not found yet after seaching) indicating special parmaters or procedures for using the package with Git/GitHub ?
Best regards,
R & R Studio session info
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] checkpoint_1.0.0
loaded via a namespace (and not attached):
[1] zip_2.1.1 compiler_4.0.5 pillar_1.6.1 prettyunits_1.1.1 tools_4.0.5 uuid_0.1-4 digest_0.6.27 pkgbuild_1.2.0 jsonlite_1.7.2 tibble_3.1.1 lifecycle_1.0.0
[12] pkgconfig_2.0.3 rlang_0.4.11 cli_2.5.0 rstudioapi_0.13 filelock_1.0.2 curl_4.3.1 xfun_0.22 withr_2.4.2 stringr_1.4.0 knitr_1.33 rappdirs_0.3.3
[23] desc_1.3.0 vctrs_0.3.8 rprojroot_2.0.2 glue_1.4.2 R6_2.5.0 processx_3.5.2 fansi_0.4.2 callr_3.7.0 magrittr_2.0.1 rematch2_2.1.2 pkgdepends_0.1.2
[34] ps_1.6.0 ellipsis_0.3.2 assertthat_0.2.1 lpSolve_5.6.15 pkgcache_1.2.2 tinytex_0.31 utf8_1.2.1 stringi_1.5.3 crayon_1.4.1
> rstudioapi::versionInfo()
$citation
To cite RStudio in publications use:
RStudio Team (2021). RStudio: Integrated Development Environment for R. RStudio, PBC, Boston, MA URL http://www.rstudio.com/.
A BibTeX entry for LaTeX users is
@Manual{,
title = {RStudio: Integrated Development Environment for R},
author = {{RStudio Team}},
organization = {RStudio, PBC},
address = {Boston, MA},
year = {2021},
url = {http://www.rstudio.com/},
}
$mode
[1] "desktop"
$version
[1] ‘1.4.1106’
$release_name
[1] "Tiger Daylily"
Script and Consol results
> #ETAPE 00 - Checkpoint de reproductivité
>
> #1 - Chargement des packages ----
>
> library(checkpoint)
checkpoint: Part of the Reproducible R Toolkit from Microsoft
https://mran.microsoft.com/documents/rro/reproducibility/
>
> #2 - Options générales ----
>
> scan_project_files()
$pkgs
[1] "rmarkdown"
$errors
[1] "./editeurs/02-Analyse_de_structure_brute.R" "./editeurs/02-Analyse_de_structure_brute.Rmd" "./editeurs/03-Production_des_tableaux_de_travail.R"
[4] "./editeurs/03-Production_des_tableaux_de_travail.Rmd"
Warning message:
Following files could not be scanned:
./editeurs/02-Analyse_de_structure_brute.R
./editeurs/02-Analyse_de_structure_brute.Rmd
./editeurs/03-Production_des_tableaux_de_travail.R
./editeurs/03-Production_des_tableaux_de_travail.Rmd
>
> create_checkpoint(snapshot_date = "2021-08-02",
+ r_version = "4.0.5",
+ checkpoint_location = ".")
Creating checkpoint directory D:/[R] PSCE2009_these/PSCE2009_these/.checkpoint/2021-08-02/lib/x86_64-w64-mingw32/4.0.5
v Loading metadata database ... done
i No downloads are needed
Warning messages:
1: Following files could not be scanned:
./editeurs/02-Analyse_de_structure_brute.R
./editeurs/02-Analyse_de_structure_brute.Rmd
./editeurs/03-Production_des_tableaux_de_travail.R
./editeurs/03-Production_des_tableaux_de_travail.Rmd
2: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Using compatibility `.name_repair`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.