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Hemken / Statamarkdown

Functions to write Stata documentation with knitr
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Error when trying to activate package in rmarkdown #31

Closed FONDECYTACC closed 1 year ago

FONDECYTACC commented 2 years ago

Get the following error when I try to activate the library in rmarkdown

Error in if (options$noisey == TRUE) message(paste("\n", options$engine, : argument is of length zero
Hemken commented 2 years ago

Email me your document (it doesn’t look like I’ll need any data).

I’m away from the office and will be out for the next week, so expect some delay in my response.

Doug Hemken

Statistical consultant Social Science Computing Cooperative Univ. of Wisc. – Madison

@.**@.> 608-262-4327

From: FONDECYTACC @.> Sent: Friday, November 4, 2022 10:14 AM To: Hemken/Statamarkdown @.> Cc: Subscribed @.***> Subject: [Hemken/Statamarkdown] Error when trying to activate package in rmarkdown (Issue #31)

Get the following error when I try to activate the library in rmarkdown

Error in if (options$noisey == TRUE) message(paste("\n", options$engine, : argument is of length zero

— Reply to this email directly, view it on GitHubhttps://github.com/Hemken/Statamarkdown/issues/31, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACYBME46FBFVRWK7FEU6O5TWGUR3RANCNFSM6AAAAAARXI6XZM. You are receiving this because you are subscribed to this thread.Message ID: @.***>

FONDECYTACC commented 2 years ago

The document is accessible here. I did not find your email. In fact and as you say, my issue does not depend on data, but on the setup chunk.

More info on the session.

- Session info --------------------------------------------------------------------------------------------------------
 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       Windows 10 x64 (build 19042)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  Spanish_Chile.1252
 ctype    Spanish_Chile.1252
 tz       America/Santiago
 date     2022-11-04
 rstudio  2022.07.2+576 Spotted Wakerobin (desktop)
 pandoc   2.19.2 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)

- Packages ------------------------------------------------------------------------------------------------------------
 ! package     * version  date (UTC) lib source
   assertthat    0.2.1    2019-03-21 [1] CRAN (R 4.1.2)
 P biostat3      0.1.6    2021-11-03 [?] CRAN (R 4.1.3)
   cachem        1.0.6    2021-08-19 [1] CRAN (R 4.1.2)
   callr         3.7.2    2022-08-22 [1] CRAN (R 4.1.3)
   cellranger    1.1.0    2016-07-27 [1] CRAN (R 4.1.2)
   cli           3.4.1    2022-09-23 [1] CRAN (R 4.1.3)
   colorspace    2.0-3    2022-02-21 [1] CRAN (R 4.1.2)
   crayon        1.5.2    2022-09-29 [1] CRAN (R 4.1.3)
 P curl          4.3.3    2022-10-06 [?] CRAN (R 4.1.3)
   data.table    1.14.2   2021-09-27 [1] CRAN (R 4.1.2)
 P DBI           1.1.3    2022-06-18 [?] CRAN (R 4.1.3)
 P devtools      2.4.5    2022-10-11 [?] CRAN (R 4.1.2)
 P digest        0.6.29   2021-12-01 [?] CRAN (R 4.1.2)
   dlookr        0.6.0    2022-06-07 [1] CRAN (R 4.1.3)
   dplyr         1.0.10   2022-09-01 [1] CRAN (R 4.1.3)
 P DT            0.26     2022-10-19 [?] CRAN (R 4.1.2)
   ellipsis      0.3.2    2021-04-29 [1] CRAN (R 4.1.2)
 P evaluate      0.17     2022-10-07 [?] CRAN (R 4.1.3)
   extrafont     0.18     2022-04-12 [1] CRAN (R 4.1.3)
   extrafontdb   1.0      2012-06-11 [1] CRAN (R 4.1.1)
   fansi         1.0.3    2022-03-24 [1] CRAN (R 4.1.3)
 P fastmap       1.1.0    2021-01-25 [?] CRAN (R 4.1.2)
 P forcats       0.5.2    2022-08-19 [?] CRAN (R 4.1.3)
   foreign       0.8-83   2022-09-28 [1] CRAN (R 4.1.3)
   Formula       1.2-4    2020-10-16 [1] CRAN (R 4.1.1)
 P fs            1.5.2    2021-12-08 [?] CRAN (R 4.1.2)
   gdtools       0.2.4    2022-02-14 [1] CRAN (R 4.1.2)
 P generics      0.1.3    2022-07-05 [?] CRAN (R 4.1.3)
   ggplot2       3.3.6    2022-05-03 [1] CRAN (R 4.1.3)
 P glue          1.6.2    2022-02-24 [?] CRAN (R 4.1.2)
   gridExtra     2.3      2017-09-09 [1] CRAN (R 4.1.2)
 P gtable        0.3.1    2022-09-01 [?] CRAN (R 4.1.3)
   haven         2.5.1    2022-08-22 [1] CRAN (R 4.1.3)
 P hms           1.1.2    2022-08-19 [?] CRAN (R 4.1.3)
   hrbrthemes    0.8.0    2020-03-06 [1] CRAN (R 4.1.3)
 P htmltools     0.5.3    2022-07-18 [?] CRAN (R 4.1.3)
   htmlwidgets   1.5.4    2021-09-08 [1] CRAN (R 4.1.2)
 P httpuv        1.6.6    2022-09-08 [?] CRAN (R 4.1.3)
   httr          1.4.4    2022-08-17 [1] CRAN (R 4.1.3)
   inum          1.0-4    2021-04-12 [1] CRAN (R 4.1.3)
   janitor       2.1.0    2021-01-05 [1] CRAN (R 4.1.2)
 P kableExtra    1.3.4    2021-02-20 [?] CRAN (R 4.1.3)
 P knitr         1.40     2022-08-24 [?] CRAN (R 4.1.3)
   later         1.3.0    2021-08-18 [1] CRAN (R 4.1.2)
   lattice       0.20-45  2021-09-22 [1] CRAN (R 4.1.1)
   libcoin       1.0-9    2021-09-27 [1] CRAN (R 4.1.3)
   lifecycle     1.0.3    2022-10-07 [1] CRAN (R 4.1.3)
   lubridate     1.8.0    2021-10-07 [1] CRAN (R 4.1.2)
 P magrittr      2.0.3    2022-03-30 [?] CRAN (R 4.1.3)
   MASS          7.3-58.1 2022-08-03 [1] CRAN (R 4.1.3)
   Matrix        1.5-1    2022-09-13 [1] CRAN (R 4.1.3)
   memoise       2.0.1    2021-11-26 [1] CRAN (R 4.1.2)
 P mime          0.12     2021-09-28 [?] CRAN (R 4.1.1)
 P miniUI        0.1.1.1  2018-05-18 [?] CRAN (R 4.1.2)
   muhaz         1.2.6.4  2021-04-21 [1] CRAN (R 4.1.2)
   munsell       0.5.0    2018-06-12 [1] CRAN (R 4.1.2)
   mvtnorm       1.1-3    2021-10-08 [1] CRAN (R 4.1.1)
 P openxlsx      4.2.5    2021-12-14 [?] CRAN (R 4.1.2)
 P pacman        0.5.1    2019-03-11 [?] CRAN (R 4.1.2)
   pagedown      0.19     2022-09-26 [1] CRAN (R 4.1.3)
   partykit      1.2-16   2022-06-20 [1] CRAN (R 4.1.3)
   pillar        1.8.1    2022-08-19 [1] CRAN (R 4.1.3)
   pkgbuild      1.3.1    2021-12-20 [1] CRAN (R 4.1.2)
   pkgconfig     2.0.3    2019-09-22 [1] CRAN (R 4.1.2)
   pkgload       1.3.0    2022-06-27 [1] CRAN (R 4.1.3)
 P plyr          1.8.7    2022-03-24 [?] CRAN (R 4.1.3)
   png           0.1-7    2013-12-03 [1] CRAN (R 4.1.1)
   prettyunits   1.1.1    2020-01-24 [1] CRAN (R 4.1.2)
   processx      3.7.0    2022-07-07 [1] CRAN (R 4.1.3)
   profvis       0.3.7    2020-11-02 [1] CRAN (R 4.1.3)
   promises      1.2.0.1  2021-02-11 [1] CRAN (R 4.1.2)
   ps            1.7.1    2022-06-18 [1] CRAN (R 4.1.3)
 P purrr         0.3.5    2022-10-06 [?] CRAN (R 4.1.3)
 P R6            2.5.1    2021-08-19 [?] CRAN (R 4.1.2)
 P Rcpp          1.0.9    2022-07-08 [?] CRAN (R 4.1.3)
   reactable     0.3.0    2022-05-26 [1] CRAN (R 4.1.3)
 P readr         2.1.3    2022-10-01 [?] CRAN (R 4.1.3)
   readxl        1.4.1    2022-08-17 [1] CRAN (R 4.1.3)
 P remotes       2.4.2    2021-11-30 [?] CRAN (R 4.1.2)
   renv          0.16.0   2022-09-29 [1] CRAN (R 4.1.3)
 P rio           0.5.29   2021-11-22 [?] CRAN (R 4.1.2)
 P rlang         1.0.6    2022-09-24 [?] CRAN (R 4.1.3)
 P rmarkdown     2.17     2022-10-07 [?] CRAN (R 4.1.3)
   rpart         4.1.16   2022-01-24 [1] CRAN (R 4.1.3)
   rprojroot     2.0.3    2022-04-02 [1] CRAN (R 4.1.3)
   rstudioapi    0.14     2022-08-22 [1] CRAN (R 4.1.3)
 P Rttf2pt1      1.3.11   2022-10-08 [?] CRAN (R 4.1.3)
   rvest         1.0.3    2022-08-19 [1] CRAN (R 4.1.3)
 P scales        1.2.1    2022-08-20 [?] CRAN (R 4.1.3)
   sessioninfo   1.2.2    2021-12-06 [1] CRAN (R 4.1.2)
 P shiny         1.7.2    2022-07-19 [?] CRAN (R 4.1.3)
   showtext      0.9-5    2022-02-09 [1] CRAN (R 4.1.3)
   showtextdb    3.0      2020-06-04 [1] CRAN (R 4.1.3)
   snakecase     0.11.0   2019-05-25 [1] CRAN (R 4.1.2)
 P stringi       1.7.6    2021-11-29 [?] CRAN (R 4.1.2)
 P stringr       1.4.1    2022-08-20 [?] CRAN (R 4.1.3)
   survival      3.4-0    2022-08-09 [1] CRAN (R 4.1.3)
   svglite       2.1.0    2022-02-03 [1] CRAN (R 4.1.2)
   sysfonts      0.8.8    2022-03-13 [1] CRAN (R 4.1.3)
   systemfonts   1.0.4    2022-02-11 [1] CRAN (R 4.1.2)
   tibble        3.1.8    2022-07-22 [1] CRAN (R 4.1.3)
 P tidyr         1.2.1    2022-09-08 [?] CRAN (R 4.1.3)
 P tidyselect    1.2.0    2022-10-10 [?] CRAN (R 4.1.2)
 P tzdb          0.3.0    2022-03-28 [?] CRAN (R 4.1.3)
   urlchecker    1.0.1    2021-11-30 [1] CRAN (R 4.1.3)
   usethis       2.1.6    2022-05-25 [1] CRAN (R 4.1.3)
   utf8          1.2.2    2021-07-24 [1] CRAN (R 4.1.2)
   vctrs         0.4.2    2022-09-29 [1] CRAN (R 4.1.3)
 P viridisLite   0.4.1    2022-08-22 [?] CRAN (R 4.1.3)
 P webshot       0.5.4    2022-09-26 [?] CRAN (R 4.1.3)
   withr         2.5.0    2022-03-03 [1] CRAN (R 4.1.2)
   xfun          0.33     2022-09-12 [1] CRAN (R 4.1.3)
   xml2          1.3.3    2021-11-30 [1] CRAN (R 4.1.2)
   xtable        1.8-4    2019-04-21 [1] CRAN (R 4.1.2)
   zip           2.2.1    2022-09-08 [1] CRAN (R 4.1.3)

 [1] C:/Users/CISS Fondecyt/Mi unidad/Alvacast/SISTRAT 2022 (github)/renv/library/R-4.1/x86_64-w64-mingw32
 [2] C:/Users/CISS Fondecyt/AppData/Local/Temp/Rtmp8EIqAu/renv-system-library

 P -- Loaded and on-disk path mismatch.
Hemken commented 2 years ago

Got it. It’ll probably be a week before I can look in detail.

Doug Hemken

Statistical consultant Social Science Computing Cooperative Univ. of Wisc. – Madison

@.**@.> 608-262-4327

From: FONDECYTACC @.> Sent: Friday, November 4, 2022 10:41 AM To: Hemken/Statamarkdown @.> Cc: Doug Hemken @.>; Comment @.> Subject: Re: [Hemken/Statamarkdown] Error when trying to activate package in rmarkdown (Issue #31)

The document is accessible herehttps://raw.githubusercontent.com/FONDECYTACC/nDP/main/Fiscalia_merge4.Rmd. I did not find your email. In fact and as you say, my issue does not depend on data, but on the setup chunk.

More info on the session.

— Reply to this email directly, view it on GitHubhttps://github.com/Hemken/Statamarkdown/issues/31#issuecomment-1303779482, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACYBME422FAFFXPNRFJI563WGUVA7ANCNFSM6AAAAAARXI6XZM. You are receiving this because you commented.Message ID: @.***>

remlapmot commented 2 years ago

This is one of the most complicated Rmd files that I've ever seen.

Given that there's only 1 stata chunk right at the end of the file, could I ask, do you obtain this error in much simpler Rmd files?

Hemken commented 1 year ago

I cannot reproduce this problem.

Other problems: I cannot reproduce the error.

The YAML header is malformed, it has toc-float twice.

You load numerous packages that I have not installed (and shouldn't need to). Please give us a simpler RMD file that produces the same error.

There is a code chunk that begins at line 73 and continues through the end of the document.

knitr checks that the beginning and ending code chunk fences (typically, backticks) must match in the number of backticks and the amount of indentation. In this RMD file, the indendation does not match after line 73.

You should see a warning on the RStudio render tab similar to: In addition: Warning messages: 1: The closing backticks on line 13 (" ") in stata-do.RMD do not match the opening backticks "" on line 8. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). 2: The closing backticks on line 20 (" ") in stata-do.RMD do not match the opening backticks "" on line 15. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote).

Hemken commented 1 year ago

If you would like to reopen this issue, please give us a much simpler example to reproduce the error message.