dataMaid
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Problems rendering PDF data report from within markdown chunk
This little bit of code will produce an error if output="html"
is removed or changed to output="pdf"
when calling makeDataReport()
.
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
```{r lalssldl}
library(dataMaid)
data(trees)
makeDataReport(trees, output = "html", replace=TRUE)
```
Have you identified the issue behind this bug? If so, is it a big hairy bug not for the faint of heart? I still get it with: dataMaid v1.2.0 [Pkg: 2018-10-03 from CRAN (R 3.5.3)] R version 3.5.3 (2019-03-11). Platform: x86_64-w64-mingw32/x64 (64-bit)(Windows >= 8 x64 (build 9200)).
Looking at the tex file, I see unbalanced \begin{minipage} \end{minipage} <<<< missing at the bottom, although the Rmd file has both \bmini and \emini \bminitwo \emini <<<<<< present
My use-case is actually more complex: generating the Rmd with render = FALSE, openResult = FALSE, then promoting headings 1 # level, then inserting that Rmd file back into my main document as an appendix via chunk options child = tmp.Rmd, which works beautifully for html but fails for pdf. I'm trying to decide whether to look in your code in case it's a relatively easy bug I might be competent to fix, or just add some form of post-processing the Rmd to my heading promotion filter.
To be honest I haven't looked at this bug in quite some time. Will try to figure out exactly what is causing it
Hmm. I just did a check with the most recent version on GitHub and I'm not receiving an error anymore. At least not for the MWE I listed above.
If I run
makeDataReport(trees, replace=TRUE, render = FALSE, openResult = FALSE)
then it appears to work (at least in the sense that an error isn't thrown).
Could you provide a simple example matching your situation which faults? Oh ... and try with the GitHub version
I just checked with R 3.6.0, dataMaid_1.2.0, pandoc 2.7.2, MiKTeX 2.9 on MSwin . Even running from the R console, omitting Rmd & R Studio, I get an Rmd intermediate file but not the pdf file, as R throws the following error after the warning to make sure the pdf file isn't open:
! LaTeX Error: \begin{minipage} on input line 545 ended by \end{document}.
Error: Failed to compile codebook_airquality.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See codebook_airquality.log for more info.
If I open that Rmd file and knit to html it works, but If I knit to pdf again it throws an error and fails. The codebook_airquality.log file has lots of Overfull \hbox messages in the log file (attached) and then an unmatched \begin{minipage}
! LaTeX Error: \begin{minipage} on input line 545 ended by \end{document}.
My simple example:
library(datasets) library(dataMaid) str(airquality) makeCodebook(airquality, output = 'pdf', replace = TRUE) sessionInfo() rmarkdown::pandoc_version()
Do you have a different LaTeX engine or version of pandoc in your toolchain? Or are you running on a different (better) OS?
Just tried to run your example and got a nice pdf-file out of this. Did you use the most recent version of dataMaid
from github or the CRAN version. I think the error you encounter here might be similar to #45 and that should be fixed in the newest version. I pushed a copy to CRAN yesterday (v 1.3.0) so please try that and see if it fixes something.
My session_info()
output can be seen below.
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils
[5] datasets methods base
other attached packages:
[1] pander_0.6.3 ggplot2_3.1.1
[3] dataMaid_1.2.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 pillar_1.4.0
[3] compiler_3.6.0 DEoptimR_1.0-8
[5] plyr_1.8.4 forcats_0.4.0
[7] tools_3.6.0 digest_0.6.18
[9] evaluate_0.13 jsonlite_1.6
[11] tibble_2.1.1 gtable_0.3.0
[13] pkgconfig_2.0.2 rlang_0.3.4
[15] whoami_1.3.0 rstudioapi_0.10
[17] yaml_2.2.0 xfun_0.7
[19] haven_2.1.0 gridExtra_2.3
[21] withr_2.1.2 stringr_1.4.0
[23] knitr_1.22.8 httr_1.4.0
[25] dplyr_0.8.1.9000 hms_0.4.2
[27] grid_3.6.0 tidyselect_0.2.5
[29] reshape_0.8.8 glue_1.3.1
[31] robustbase_0.93-5 R6_2.4.0
[33] rmarkdown_1.12 purrr_0.3.2
[35] magrittr_1.5 scales_1.0.0
[37] htmltools_0.3.6 rsconnect_0.8.13
[39] assertthat_0.2.1 colorspace_1.4-1
[41] labeling_0.3 tinytex_0.13
[43] stringi_1.4.3 lazyeval_0.2.2
[45] munsell_0.5.0 crayon_1.3.4
> rmarkdown::pandoc_version()
[1] ‘2.7.1’