rendering an script creates _files directory not cleared

[fgoerlich]

I found the same behaviour as described here when rendering an script.

The 'zip' file provides an example.

xfun::session_info('rmarkdown')
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100), RStudio 2025.5.0.496

Locale:
  LC_COLLATE=Spanish_Spain.utf8  LC_CTYPE=Spanish_Spain.utf8    LC_MONETARY=Spanish_Spain.utf8 LC_NUMERIC=C                  
  LC_TIME=Spanish_Spain.utf8    

Package version:
  base64enc_0.1.3   bslib_0.9.0       cachem_1.1.0      cli_3.6.5         digest_0.6.37     evaluate_1.0.4    fastmap_1.2.0    
  fontawesome_0.5.3 fs_1.6.6          glue_1.8.0        graphics_4.5.1    grDevices_4.5.1   highr_0.11        htmltools_0.5.8.1
  jquerylib_0.1.4   jsonlite_2.0.0    knitr_1.50        lifecycle_1.0.4   memoise_2.0.1     methods_4.5.1     mime_0.13        
  R6_2.6.1          rappdirs_0.3.3    rlang_1.1.6       rmarkdown_2.29.1  sass_0.4.10       stats_4.5.1       tinytex_0.57     
  tools_4.5.1       utils_4.5.1       xfun_0.52         yaml_2.3.10      

Pandoc version: 3.4

Checklist

When filing a bug report, please check the boxes below to confirm that you have provided us with the information we need. Have you:

• formatted your issue so it is easier for us to read?

• included a minimal, self-contained, and reproducible example?

• pasted the output from xfun::session_info('rmarkdown') in your issue?

• upgraded all your packages to their latest versions (including your versions of R, the RStudio IDE, and relevant R packages)?

• installed and tested your bug with the development version of the rmarkdown package using remotes::install_github("rstudio/rmarkdown") ?

Ejercicio_1.zip

[cderv]

Thanks for opening. I can't reproduce.

• I downloaded your zip
• Unzip and removed .html and _files folder
• Called rmarkdown::render("Ejercicio_1.R")
• The output is only .html file and the folder _files is removed

   > fs::dir_tree()
   .
   ├── Barcelona.rda
   ├── Ejercicio_1.html
   ├── Ejercicio_1.R
   └── str2num.R
  

This is with

> packageVersion("rmarkdown")
[1] ‘2.29’

[fgoerlich]

On windows?
I found the same behaviour with your version, or with the development version.

> packageVersion("rmarkdown")
[1] ‘2.29.1’

[cderv]

Yes I am on windows

Here is the reproduction

dir <- tempfile()
dir.create(dir)
owd <- setwd(dir)
xfun::download_file(
  "https://github.com/user-attachments/files/20798398/Ejercicio_1.zip",
  mode = "wb",
)
#> [1] "Ejercicio_1.zip"

unzip("Ejercicio_1.zip")
list.files()
#> [1] "Barcelona.rda"     "Ejercicio_1.html"  "Ejercicio_1.R"    
#> [4] "Ejercicio_1.zip"   "Ejercicio_1_files" "str2num.R"
unlink("Ejercicio_1.zip")
unlink("Ejercicio_1.html")
unlink("Ejercicio_1_files/", recursive = TRUE)
before <- list.files()
before
#> [1] "Barcelona.rda" "Ejercicio_1.R" "str2num.R"
renv::init()
#> - Linking packages into the project library ... Done!
#> - Resolving missing dependencies ... 
#> # Installing packages --------------------------------------------------------
#> - Installing prettyunits ...                    OK [linked from cache]
#> - Installing progress ...                       OK [linked from cache]
#> - Installing RcppEigen ...                      OK [linked from cache]
#> The following package(s) will be updated in the lockfile:
#> 
#> # CRAN -----------------------------------------------------------------------
#> - boot             [* -> 1.3-31]
#> - cluster          [* -> 2.1.8.1]
#> - codetools        [* -> 0.2-20]
#> - digest           [* -> 0.6.37]
#> - evaluate         [* -> 1.0.4]
#> - glue             [* -> 1.8.0]
#> - highr            [* -> 0.11]
#> - jsonlite         [* -> 2.0.0]
#> - lifecycle        [* -> 1.0.4]
#> - magrittr         [* -> 2.0.3]
#> - MASS             [* -> 7.3-65]
#> - Matrix           [* -> 1.7-3]
#> - nlme             [* -> 3.1-168]
#> - nnet             [* -> 7.3-20]
#> - survival         [* -> 3.8-3]
#> - vctrs            [* -> 0.6.5]
#> - withr            [* -> 3.0.2]
#> - yaml             [* -> 2.3.10]
#> 
#> # P3M ------------------------------------------------------------------------
#> - RcppEigen        [* -> 0.3.4.0.2]
#> 
#> # RSPM -----------------------------------------------------------------------
#> - abind            [* -> 1.4-8]
#> - askpass          [* -> 1.2.1]
#> - backports        [* -> 1.5.0]
#> - base64enc        [* -> 0.1-3]
#> - bit              [* -> 4.6.0]
#> - bit64            [* -> 4.6.0-1]
#> - blob             [* -> 1.2.4]
#> - broom            [* -> 1.0.8]
#> - bslib            [* -> 0.9.0]
#> - ca               [* -> 0.71.1]
#> - cachem           [* -> 1.1.0]
#> - callr            [* -> 3.7.6]
#> - car              [* -> 3.1-3]
#> - carData          [* -> 3.0-5]
#> - cellranger       [* -> 1.1.0]
#> - cli              [* -> 3.6.5]
#> - clipr            [* -> 0.8.0]
#> - colorspace       [* -> 2.1-1]
#> - conflicted       [* -> 1.2.0]
#> - corrr            [* -> 0.4.4]
#> - cowplot          [* -> 1.1.3]
#> - cpp11            [* -> 0.5.2]
#> - crayon           [* -> 1.5.3]
#> - curl             [* -> 6.3.0]
#> - data.table       [* -> 1.17.4]
#> - DBI              [* -> 1.2.3]
#> - dbplyr           [* -> 2.5.0]
#> - Deriv            [* -> 4.1.6]
#> - doBy             [* -> 4.6.27]
#> - dplyr            [* -> 1.1.4]
#> - dtplyr           [* -> 1.3.1]
#> - fansi            [* -> 1.0.6]
#> - farver           [* -> 2.1.2]
#> - fastmap          [* -> 1.2.0]
#> - fontawesome      [* -> 0.5.3]
#> - forcats          [* -> 1.0.0]
#> - foreach          [* -> 1.5.2]
#> - Formula          [* -> 1.2-5]
#> - fs               [* -> 1.6.6]
#> - furrr            [* -> 0.3.1]
#> - future           [* -> 1.58.0]
#> - gargle           [* -> 1.5.2]
#> - gclus            [* -> 1.3.3]
#> - generics         [* -> 0.1.4]
#> - ggplot2          [* -> 3.5.2]
#> - ggrepel          [* -> 0.9.6]
#> - glmnet           [* -> 4.1-9]
#> - globals          [* -> 0.18.0]
#> - googledrive      [* -> 2.1.1]
#> - googlesheets4    [* -> 1.1.1]
#> - gtable           [* -> 0.3.6]
#> - hardhat          [* -> 1.4.1]
#> - haven            [* -> 2.5.5]
#> - hms              [* -> 1.1.3]
#> - htmltools        [* -> 0.5.8.1]
#> - httr             [* -> 1.4.7]
#> - ids              [* -> 1.0.1]
#> - igraph           [* -> 2.1.4]
#> - isoband          [* -> 0.2.7]
#> - iterators        [* -> 1.0.14]
#> - jquerylib        [* -> 0.1.4]
#> - kknn             [* -> 1.4.1]
#> - knitr            [* -> 1.50]
#> - labeling         [* -> 0.4.3]
#> - lattice          [* -> 0.22-7]
#> - listenv          [* -> 0.9.1]
#> - lme4             [* -> 1.1-37]
#> - lubridate        [* -> 1.9.4]
#> - MatrixModels     [* -> 0.5-4]
#> - memoise          [* -> 2.0.1]
#> - mgcv             [* -> 1.9-3]
#> - microbenchmark   [* -> 1.5.0]
#> - mime             [* -> 0.13]
#> - minqa            [* -> 1.2.8]
#> - modelr           [* -> 0.1.11]
#> - nloptr           [* -> 2.2.1]
#> - numDeriv         [* -> 2016.8-1.1]
#> - openssl          [* -> 2.3.3]
#> - parallelly       [* -> 1.45.0]
#> - pbkrtest         [* -> 0.5.4]
#> - permute          [* -> 0.9-7]
#> - pillar           [* -> 1.10.2]
#> - pkgconfig        [* -> 2.0.3]
#> - prettyunits      [* -> 1.2.0]
#> - processx         [* -> 3.8.6]
#> - progress         [* -> 1.2.3]
#> - ps               [* -> 1.9.1]
#> - purrr            [* -> 1.0.4]
#> - qap              [* -> 0.1-2]
#> - quantreg         [* -> 6.1]
#> - R6               [* -> 2.6.1]
#> - ragg             [* -> 1.4.0]
#> - rappdirs         [* -> 0.3.3]
#> - rbibutils        [* -> 2.3]
#> - RColorBrewer     [* -> 1.1-3]
#> - Rcpp             [* -> 1.0.14]
#> - Rdpack           [* -> 2.6.4]
#> - readr            [* -> 2.1.5]
#> - readxl           [* -> 1.4.5]
#> - reformulas       [* -> 0.4.1]
#> - registry         [* -> 0.5-1]
#> - rematch          [* -> 2.0.0]
#> - rematch2         [* -> 2.1.2]
#> - renv             [* -> 1.1.4]
#> - reprex           [* -> 2.1.1]
#> - rlang            [* -> 1.1.6]
#> - rmarkdown        [* -> 2.29]
#> - rsample          [* -> 1.3.0]
#> - rstudioapi       [* -> 0.17.1]
#> - rvest            [* -> 1.0.4]
#> - sass             [* -> 0.4.10]
#> - scales           [* -> 1.4.0]
#> - selectr          [* -> 0.4-2]
#> - seriation        [* -> 1.5.7]
#> - shape            [* -> 1.4.6.1]
#> - slider           [* -> 0.3.2]
#> - SparseM          [* -> 1.84-2]
#> - sparsevctrs      [* -> 0.3.4]
#> - stringi          [* -> 1.8.7]
#> - stringr          [* -> 1.5.1]
#> - sys              [* -> 3.4.3]
#> - systemfonts      [* -> 1.2.3]
#> - textshaping      [* -> 1.0.1]
#> - tibble           [* -> 3.2.1]
#> - tidyr            [* -> 1.3.1]
#> - tidyselect       [* -> 1.2.1]
#> - tidyverse        [* -> 2.0.0]
#> - timechange       [* -> 0.3.0]
#> - tinytex          [* -> 0.57]
#> - TSP              [* -> 1.2-5]
#> - tzdb             [* -> 0.5.0]
#> - utf8             [* -> 1.2.5]
#> - uuid             [* -> 1.2-1]
#> - vegan            [* -> 2.6-10]
#> - viridisLite      [* -> 0.4.2]
#> - vroom            [* -> 1.6.5]
#> - warp             [* -> 0.2.1]
#> - xfun             [* -> 0.52]
#> - xml2             [* -> 1.3.8]
#> - yardstick        [* -> 1.3.2]
#> 
#> The version of R recorded in the lockfile will be updated:
#> - R                [* -> 4.5.0]
#> 
#> - Lockfile written to "C:/Users/chris/AppData/Local/Temp/Rtmp4M7cho/file36386f2b7d3b/renv.lock".
rmarkdown::render("Ejercicio_1.R")
#> processing file: Ejercicio_1.spin.Rmd
#> output file: Ejercicio_1.knit.md
#> "C:/Users/chris/scoop/shims/pandoc" +RTS -K512m -RTS Ejercicio_1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Ejercicio_1.html --lua-filter "C:\Users\chris\AppData\Local\R\win-library\4.5\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\chris\AppData\Local\R\win-library\4.5\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "C:\Users\chris\AppData\Local\R\win-library\4.5\rmarkdown\rmarkdown\lua\table-classes.lua" --embed-resources --standalone --variable bs3=TRUE --section-divs --template "C:\Users\chris\AppData\Local\R\win-library\4.5\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "C:\Users\chris\AppData\Local\Temp\Rtmp4M7cho\rmarkdown-str3638357473e4.html"
#> 
#> Output created: Ejercicio_1.html
# don't consider the renv files
after <- setdiff(list.files(), c("renv", "renv.lock"))
after
#> [1] "Barcelona.rda"    "Ejercicio_1.html" "Ejercicio_1.R"   
#> [4] "str2num.R"  
# new files or folder ?
setdiff(after, before) 
#> [1] "Ejercicio_1.html"

setwd(owd)
unlink(dir, recursive = TRUE)

As you can, renders works and only diff is the HTML file.

Session info

> sessioninfo::session_info()
─ Session info ────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.0 (2025-04-11 ucrt)
 os       Windows 11 x64 (build 26100)
 system   x86_64, mingw32
 ui       Rgui
 language (EN)
 collate  French_France.utf8
 ctype    French_France.utf8
 tz       Europe/Paris
 date     2025-06-19
 pandoc   3.7.0.2 @ C:/Users/chris/scoop/shims/ (via rmarkdown)
 quarto   NA @ C:\\Users\\chris\\scoop\\apps\\quarto\\current\\bin\\quarto.exe

─ Packages ────────────────────────────────────────────────────────────
 package      * version    date (UTC) lib source
 abind          1.4-8      2024-09-12 [1] RSPM
 askpass        1.2.1      2024-10-04 [1] RSPM
 backports      1.5.0      2024-05-23 [1] CRAN (R 4.5.0)
 broom          1.0.8      2025-03-28 [1] RSPM
 bslib          0.9.0      2025-01-30 [1] RSPM
 ca             0.71.1     2020-01-24 [1] RSPM
 cachem         1.1.0      2024-05-16 [1] RSPM
 callr          3.7.6      2024-03-25 [1] CRAN (R 4.5.0)
 car            3.1-3      2024-09-27 [1] RSPM
 carData        3.0-5      2022-01-06 [1] RSPM
 cli            3.6.5      2025-04-23 [1] CRAN (R 4.5.0)
 clipr          0.8.0      2022-02-22 [1] RSPM
 codetools      0.2-20     2024-03-31 [2] CRAN (R 4.5.0)
 corrr          0.4.4      2022-08-16 [1] RSPM
 crayon         1.5.3      2024-06-20 [1] RSPM
 credentials    2.0.2      2024-10-04 [1] RSPM
 curl           6.3.0      2025-06-06 [1] RSPM
 digest         0.6.37     2024-08-19 [1] CRAN (R 4.5.0)
 dplyr        * 1.1.4      2023-11-17 [1] RSPM
 evaluate       1.0.4      2025-06-18 [1] CRAN (R 4.5.0)
 farver         2.1.2      2024-05-13 [1] RSPM
 fastmap        1.2.0      2024-05-15 [1] RSPM
 forcats      * 1.0.0      2023-01-29 [1] RSPM
 foreach        1.5.2      2022-02-02 [1] RSPM
 Formula        1.2-5      2023-02-24 [1] RSPM
 fs             1.6.6      2025-04-12 [1] CRAN (R 4.5.0)
 furrr          0.3.1      2022-08-15 [1] RSPM
 future         1.58.0     2025-06-05 [1] RSPM
 generics       0.1.4      2025-05-09 [1] RSPM
 ggplot2      * 3.5.2      2025-04-09 [1] RSPM
 glmnet       * 4.1-9      2025-06-02 [1] RSPM
 globals        0.18.0     2025-05-08 [1] RSPM
 glue           1.8.0      2024-09-30 [1] CRAN (R 4.5.0)
 gtable         0.3.6      2024-10-25 [1] RSPM
 hms            1.1.3      2023-03-21 [1] RSPM
 htmltools      0.5.8.1    2024-04-04 [1] RSPM
 igraph         2.1.4      2025-01-23 [1] RSPM
 iterators      1.0.14     2022-02-05 [1] RSPM
 jquerylib      0.1.4      2021-04-26 [1] RSPM
 jsonlite       2.0.0      2025-03-27 [1] CRAN (R 4.5.0)
 kknn         * 1.4.1      2025-05-19 [1] RSPM
 knitr          1.50       2025-03-16 [1] RSPM
 labeling       0.4.3      2023-08-29 [1] RSPM
 lattice        0.22-7     2025-04-02 [1] RSPM
 lifecycle      1.0.4      2023-11-07 [1] CRAN (R 4.5.0)
 listenv        0.9.1      2024-01-29 [1] RSPM
 lubridate    * 1.9.4      2024-12-08 [1] RSPM
 magrittr       2.0.3      2022-03-30 [1] CRAN (R 4.5.0)
 Matrix       * 1.7-3      2025-03-11 [2] CRAN (R 4.5.0)
 openssl        2.3.3      2025-05-26 [1] RSPM
 pak            0.8.0.2    2025-04-24 [1] local
 parallelly     1.45.0     2025-06-02 [1] RSPM
 pillar         1.10.2     2025-04-05 [1] RSPM
 pkgconfig      2.0.3      2019-09-22 [1] RSPM
 pkgload        1.4.0      2024-06-28 [1] CRAN (R 4.5.0)
 processx       3.8.6      2025-02-21 [1] CRAN (R 4.5.0)
 ps             1.9.1      2025-04-12 [1] CRAN (R 4.5.0)
 purrr        * 1.0.4      2025-02-05 [1] CRAN (R 4.5.0)
 R6             2.6.1      2025-02-15 [1] CRAN (R 4.5.0)
 RColorBrewer   1.1-3      2022-04-03 [1] RSPM
 Rcpp           1.0.14     2025-01-12 [1] RSPM
 readr        * 2.1.5      2024-01-10 [1] RSPM
 registry       0.5-1      2019-03-05 [1] RSPM
 renv           1.1.4      2025-03-20 [1] RSPM
 reprex         2.1.1      2024-07-06 [1] RSPM
 rlang          1.1.6      2025-04-11 [1] CRAN (R 4.5.0)
 rmarkdown      2.29       2024-11-04 [1] RSPM
 rsample        1.3.0      2025-04-02 [1] RSPM
 rstudioapi     0.17.1     2024-10-22 [1] RSPM
 sass           0.4.10     2025-04-11 [1] RSPM
 scales         1.4.0      2025-04-24 [1] RSPM
 seriation      1.5.7      2024-12-05 [1] RSPM
 sessioninfo    1.2.3.9000 2025-06-02 [1] Github (r-lib/sessioninfo@5d07442)
 shape          1.4.6.1    2024-02-23 [1] RSPM
 stringi        1.8.7      2025-03-27 [1] CRAN (R 4.5.0)
 stringr      * 1.5.1      2023-11-14 [1] CRAN (R 4.5.0)
 survival       3.8-3      2024-12-17 [2] CRAN (R 4.5.0)
 sys            3.4.3      2024-10-04 [1] RSPM
 tibble       * 3.2.1      2023-03-20 [1] RSPM
 tidyr        * 1.3.1      2024-01-24 [1] RSPM
 tidyselect     1.2.1      2024-03-11 [1] RSPM
 tidyverse    * 2.0.0      2023-02-22 [1] RSPM
 timechange     0.3.0      2024-01-18 [1] RSPM
 TSP            1.2-5      2025-05-27 [1] RSPM
 tzdb           0.5.0      2025-03-15 [1] RSPM
 utf8           1.2.5      2025-05-01 [1] RSPM
 vctrs          0.6.5      2023-12-01 [1] CRAN (R 4.5.0)
 withr          3.0.2      2024-10-28 [1] CRAN (R 4.5.0)
 xfun           0.52       2025-04-02 [1] CRAN (R 4.5.0)
 yaml           2.3.10     2024-07-26 [1] CRAN (R 4.5.0)
 yardstick      1.3.2      2025-01-22 [1] RSPM

 [1] C:/Users/chris/AppData/Local/R/win-library/4.5
 [2] C:/Program Files/R/R-4.5.0/library
 * ── Packages attached to the search path.

───────────────────────────────────────────────────────────────────────