object 'mzf' not found

[kozo2]

I am converting the Rmd files in this repo to md to translate this repo to multiple languages using GitHub + Crowdin.

library(rmarkdown)
render("10-raw.Rmd", md_document())

• https://github.com/bioconductor-translations/rformassspectrometry-translation
• https://bioconductor.crowdin.com/rformassspectrometry

And I the following error:

> render("10-raw.Rmd", md_document())

processing file: 10-raw.Rmd
  |..                                                                                                      |   2%
  ordinary text without R code

  |....                                                                                                    |   4%
label: rwpkgs (with options) 
List of 3
 $ echo   : logi FALSE
 $ message: logi FALSE
 $ warning: logi FALSE

  |......                                                                                                  |   6%
  ordinary text without R code

  |........                                                                                                |   7%
label: unnamed-chunk-1 (with options) 
List of 6
 $ results  : chr "markup"
 $ fig.cap  : chr "Schematic representation of what is referred to by *raw data*: a collection of mass spectra and a table contain"| __truncated__
 $ echo     : logi FALSE
 $ purl     : logi FALSE
 $ out.width: chr "100%"
 $ fig.align: chr "center"

  |..........                                                                                              |   9%
  ordinary text without R code

  |............                                                                                            |  11%
label: unnamed-chunk-2 (with options) 
List of 1
 $ message: logi FALSE

  |.............                                                                                           |  13%
  ordinary text without R code

  |...............                                                                                         |  15%
label: spectradata1
  |.................                                                                                       |  17%
  ordinary text without R code

  |...................                                                                                     |  19%
label: spectra1
  |.....................                                                                                   |  20%
  ordinary text without R code

  |.......................                                                                                 |  22%
label: spectra2
Quitting from lines 89-92 (10-raw.Rmd) 
Error in eval(expr, envir, enclos) : object 'mzf' not found

Can I ask you to assign a mzML path to the mzf for this solution?

[lgatto]

As per issue #7, the mzf holding the filename is created in the previous chapter.

[kozo2]

I close this issue for the same reason as

• https://github.com/rformassspectrometry/docs/issues/7#issuecomment-1165932225
• https://github.com/rformassspectrometry/docs/issues/7#issuecomment-1165933946

[kozo2]

I had the same misunderstanding as https://github.com/rformassspectrometry/docs/issues/7#issuecomment-1165968934 , sorry... Now I am able to resolve this issue.