gtsave breaks when in the loop

[rjazwiec]

Prework

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Description

Table is saved to .docx properly when in separate chunk. When I try to generate many files from a loop it gives

Unknown output format doc
Pandoc can convert to DOCX, but not to DOC.
Error: pandoc document conversion failed with error 22

When generating .RTF files from the same loop it works properly

Reproducible example

Sample of data:

baza <- structure(list(data_file = c("032_01_012", "032_01_013", "032_01_026", 
"032_01_077", "032_01_088", "032_02_012", "032_02_040", "032_02_075", 
"032_02_086", "032_02_093", "032_03_013", "032_03_070"), chrom_number = c(12, 
13, 26, 77, 88, 12, 40, 75, 86, 93, 13, 70), seq_number = c(1, 
1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3), sample_id = c("BLK", "ZS", 
"1001A_Day_88_0.25h", "2002B_Day_88_2h", "2501B_Day_88_8h", "BLK", 
"1002A_Day_176_PD", "2001B_Day_176_8h", "2002B_Day_176_12h", 
"2501B_Day_176_4h", "ZS", "2001B_Day_267_12h"), sample_name = c("BLK", 
"ZS", "1001A_Day_88_0.25h", "2002B_Day_88_2h", "2501B_Day_88_8h", 
"BLK", "1002A_Day_176_PD", "2001B_Day_176_8h", "2002B_Day_176_12h", 
"2501B_Day_176_4h", "ZS", "2001B_Day_267_12h"), type = c("DoubleBlank", 
"Blank", "Sample", "Sample", "Sample", "DoubleBlank", "Sample", 
"Sample", "Sample", "Sample", "Blank", "Sample"), compound = c("HNK", 
"HNK", "HNK", "HNK", "HNK", "DHNK", "KET", "HNK", "HNK", "HNK", 
"KET", "HNK"), is_reint = c(0.622, 0.853, 0.873, 0.862, 0.873, 
2.495, 2.307, 0.886, 0.905, 0.875, 2.512, 0.916)), row.names = c(NA, 
-12L), class = c("tbl_df", "tbl", "data.frame"))

Code:

seq <- 2

sub <- paste("Run 032_", str_pad(seq, 2, pad = "0"), sep = "")
  
  seq_list <- baza %>%
    filter(seq_number == seq) %>%
    rowid_to_column("No") %>%
    select(No, chromatogram_no = data_file,
           sample_name, compound) %>%
    gt() %>%
    tab_header(title = "Reintegrated chromatogram list",
                       subtitle = sub)
  
  gtsave(
    seq_list,
    filename = paste("reintegrated_list_", sub, ".docx", sep = ""),
    path = "Reintegrated/"
  )

Works properly for single seq. Works for any of seq from dataframe.

When put in a loop like this:

seq <- 1:3

for (sequence in seq) {
  sub <- paste("Run 032_", str_pad(sequence, 2, pad = "0"), sep = "")
  
  seq_list <- baza %>%
    filter(seq_number == sequence) %>%
    rowid_to_column("No") %>%
    select(No, chromatogram_no = data_file,
           sample_name, compound) %>%
    gt() %>%
    tab_header(title = "Reintegrated chromatogram list",
               subtitle = sub)
  
  gtsave(
    seq_list,
    filename = paste("reintegrated_list_", sub, ".docx", sep = ""),
    path = "Reintegrated/"
  )
  
}

Gives error message quoted previously.

When one line is changed to:

filename = paste("reintegrated_list_", sub, ".rtf", sep = "")

It properly generates 3 files.

Expected result

It should generate .docx files.

Session info

R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=Polish_Poland.utf8 LC_CTYPE=Polish_Poland.utf8 LC_MONETARY=Polish_Poland.utf8 LC_NUMERIC=C
[5] LC_TIME=Polish_Poland.utf8

time zone: Europe/Warsaw
tzcode source: internal

attached base packages:
[1] stats graphics grDevices datasets utils methods base

other attached packages:
[1] gtsummary_1.7.2 gt_0.10.1 janitor_2.2.0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[8] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.0 tidyverse_2.0.0 renv_1.0.7

loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3 xml2_1.3.6 stringi_1.8.3 hms_1.1.3 digest_0.6.35
[7] magrittr_2.0.3 evaluate_0.23 grid_4.3.2 timechange_0.3.0 fastmap_1.1.1 broom.helpers_1.15.0
[13] fansi_1.0.6 scales_1.3.0 cli_3.6.2 crayon_1.5.2 rlang_1.1.3 bit64_4.0.5
[19] munsell_0.5.1 withr_3.0.0 yaml_2.3.8 parallel_4.3.2 tools_4.3.2 tzdb_0.4.0
[25] colorspace_2.1-0 vctrs_0.6.5 R6_2.5.1 lifecycle_1.0.4 snakecase_0.11.1 fs_1.6.3
[31] bit_4.0.5 vroom_1.6.5 pkgconfig_2.0.3 pillar_1.9.0 gtable_0.3.4 glue_1.7.0
[37] xfun_0.43 tidyselect_1.2.1 rstudioapi_0.16.0 knitr_1.46 htmltools_0.5.8.1 rmarkdown_2.26
[43] compiler_4.3.2

[rjazwiec]

Ok. I accidently found solution.
The problem is not in the loop.
I saw that error was not in the first time I ran the loop. But when I was writing this issue i missed it.

The problem is that gtsave have problem with overwriting .docx documents (that's not the case with .rtf)

Simple but slow fix:

if (file.exists("file_to_save.docx")) {
  file.remove("file_to_save.docx")
} 

 gtsave(
    seq_list,
    filename = "file_to_save.docx",
    path = "Reintegrated/"
  )