Problems when trying to render references (.bib file) in html format #10997
-
DescriptionBug descriptionI'm facing problems trying to render references (.bib file) in html format using Quarto. When I try to render the document I get an error message indicating some problem in the the reference file of chapter 5: Error position:
The complete content of my reference file is here. I checked for formatting and spelling mistakes such as missing code delimiters { , = or even empty spaces, but I couldn't find any. All smalls adjustments I tried (deleting or inserting { , or spaces) did not solve the problem. When I make small adjustments in the file content, the error message, most of the time, keep indicating a problem always in the last line and in the last character position or the file content, even when the indicated position has no characters inserted (as shown in the image above). Checking in Stackoverflow I realized that my problem is a bit similar to the one addressed in the following question "Quarto Render having diff of engine output timed out issue", except for the fact that he is running Python while I am running my analyzes in R. Despite that, I still haven't been able to see a way to solve my problem. I coudn´t figure out yet how to elaborate a small self-contained "working" (reproducible) example of my situation. My environment:Windows 10 Home Version 22H2 Intel(R) Core(TM) i3-6100T RStudio 2024.04.0+735 "Chocolate Cosmos" Release (a00d0e775dbc93e0d79a1bf474e3e8e8de677383, 2024-04-24) for windows Quarto 1.4.551 Quarto check output:Quarto 1.4.551
[>] Checking versions of quarto binary dependencies...
Pandoc version 3.1.11: OK
Dart Sass version 1.69.5: OK
Deno version 1.37.2: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
Version: 1.4.551
Path: C:\Users\Arlindo_Casa\AppData\Local\Programs\Quarto\bin
CodePage: unknown
[>] Checking tools....................OK
TinyTeX: (external install)
Chromium: (not installed)
[>] Checking LaTeX....................OK
Using: TinyTex
Path: C:\Users\Arlindo_Casa\AppData\Roaming\TinyTeX\bin\windows\
Version: 2024
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.8.2
Path: C:/Users/Arlindo_Casa/AppData/Local/Programs/Python/Python38-32/python.exe
Jupyter: 4.6.3
Kernels: python3
(|) Checking Jupyter engine render....Traceback (most recent call last):
File "C:\Users\Arlindo_Casa\AppData\Local\Programs\Quarto\share\jupyter\jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "C:\Users\Arlindo_Casa\AppData\Local\Programs\Quarto\share\jupyter\notebook.py", line 14, in <module>
from yaml import safe_load
ModuleNotFoundError: No module named 'yaml'
[>] Checking Jupyter engine render....OK
This is the structure of my _quarto.yml file: |
Beta Was this translation helpful? Give feedback.
Replies: 1 comment 4 replies
-
|
My guess is that there's a missing brace or quote or a special character somewhere (most likely not in that particular reference) which is causing the trouble. First thing I'd do is to remove that reference and render your book to see if that works. If the book does render properly without that reference, try adding the reference again and remplace each line with dummy texts manually. Re-render after every line changed to identify which one is causing the issue. Otherwise, you'll have to remove references bit by bit to identify the one making the rendering fail and fix it. Only render the part of book using that particular |
Beta Was this translation helpful? Give feedback.
-
|
I applied all the suggested procedures and after some time of testing I ended up discovering that the problem was in the italic encoding used in some references in the .bib format {\textit{ }. See an example below (highlighted in bold): @book{Pereira_2013, After removing this code from all references that contained it, the rendering process was successful. Then I was wondering how I could generate italicized words in references, but for now I will leave it without this type of marking. The tip of temporarily deleting the other chapters and trying to render only the chapter with the supposed problem was especially useful, as it greatly speeded up the process, which even so, still took a long time. Thank you very much Arnoud @arnaudgallou |
Beta Was this translation helpful? Give feedback.
-
That process works to help debug everything and is not limited to Quarto. |
Beta Was this translation helpful? Give feedback.
-
What you have in that example works, although you don't need to enclose I had a quick look at your references that use There's an opening |
Beta Was this translation helpful? Give feedback.
-
|
So the problem was not the use of the code itself, as I believed, but rather its misuse in one of my cited references. Thanks again @arnaudgallou for alerting me to this. I will be more attentive about this kind of problem from now on. |
Beta Was this translation helpful? Give feedback.
My guess is that there's a missing brace or quote or a special character somewhere (most likely not in that particular reference) which is causing the trouble.
First thing I'd do is to remove that reference and render your book to see if that works. If the book does render properly without that reference, try adding the reference again and remplace each line with dummy texts manually. Re-render after every line changed to identify which one is causing the issue.
Otherwise, you'll have to remove references bit by bit to identify the one making the rendering fail and fix it.
Only render the part of book using that particular
.bibfile to save time.