rmarkdown
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rstudio
rendering an script creates _files directory not cleared
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:
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[X] formatted your issue so it is easier for us to read?
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[X] included a minimal, self-contained, and reproducible example?
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[X] pasted the output from
xfun::session_info('rmarkdown')in your issue? -
[X] upgraded all your packages to their latest versions (including your versions of R, the RStudio IDE, and relevant R packages)?
-
[X] installed and tested your bug with the development version of the rmarkdown package using
remotes::install_github("rstudio/rmarkdown")?
Thanks for opening. I can't reproduce.
- I downloaded your zip
- Unzip and removed
.htmland_filesfolder - 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’
On windows? I found the same behaviour with your version, or with the development version.
> packageVersion("rmarkdown")
[1] ‘2.29.1’
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.
───────────────────────────────────────────────────────────────────────