Citing R-Packages via "grateful::cite_packages()" breaks in pdf-output in quarto 1.4.549, but works in 1.3.450 #8580
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DescriptionHello. I am quite a bit baffled. I recently updated to quarto v.1.4.549 - initially via SetupI have attached 4 sets of files, for the following scenarios:
Note that the file rendered is identical across all scenarios. While this means that the quarto v.1.3.450-cases contain breaking table captions, I considered equal input data more relevant in this scenario. Invalid table-captions should also not have anything to do with the issue itself. No external citations are required. Packages are installed from renv for projects, and must be installed prior to use for standalone versions if not installed already. v.1.4.549In both standalone and project setups, In HTML/DOCX, In PDF, all packages are added to the bibliography and displayed at the end of the file (again, with the exception of 1.3.450In HTML/DOCX/PDF, all citations (except for Example found in this repo I can't imagine what is causing this, but this is currently hard-breaking a project of mine; which is now retrospectively going to be downgraded to 1.3.450. Thankfully I had not yet transitioned much significant content to 1.4-features, so this at least saves me some time now. I hope these details are sufficient to reproduce this problem. Thank you. |
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Replies: 4 comments 19 replies
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Does the example have to be that big? PS: you should be consistent with the syntax inside your documents, i.e., not mixing, inline R code cell option with YAML style option and to not use Regarding, the fact that Edit: I made a simple reproducible example and don't see any issue.
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Under which version are you running quarto?
I mean; I did provide a single-file file which exhibits this issue in quarto v.1.4.549; and does not do so in v.1.3.450. However, I am tring to simplify it now.
I mentioned this merely to note that I found it odd that it didn't get cited by grateful not because I was thinking quarto to be at fault here, but didn't want to leave this outlier without comment because I am most definitely less capable of judging if there might be some interaction between I can successfully reproduce your input, which does not exhibit this issue on my system. With a bit more digging, I have also narrowed down what actually breaks on my end. See the below standalone file, converted via ---
title: "reprex_new_standalone"
bibliography: "grateful-refs.bib"
---
1.4.549 project, rendered via `quarto render` (see `_quarto.yml`)
(table [-@tbl-PackageVersions])
(table [-@tbl-PackageVersions2])
(table [-@tbl-PackageVersions3])
This is a playground for Quarto.
```{r}
library(grateful)
library(knitr)
library(yaml)
cites <- cite_packages(
output = "table",
out.dir = ".",
cite.tidyverse = TRUE,
pkgs = "All",
include.RStudio = TRUE,
dependencies = FALSE
)
print(cites)
typeof(cites)
```
```{r}
#| label: tbl-PackageVersions
knitr::kable(cites)
```
```{r}
#| label: tbl-PackageVersions2
knitr::kable(cites,caption = "a caption for the table")
```
```{r}
#| label: tbl-PackageVersions3
#| tbl-cap: a caption for the table
knitr::kable(cites)
```
```{r}
sessionInfo()
```Note that I have changed the setup a bit; in that I first generate a generic var When converted to html, all three tables render successfully on my machine. When converting to pdf, only the first table gets rendered. The remaining get scrambled as shown in . The single difference between these tables is that the first does not contain a caption. The second and third one implement a caption either via the call to
Note for clarity: The I hope this is reproducible now. P.S.: This is currently only tested to break on 1.4.549; mostly because I don't have access to the 1.3.450-installer currently and have merely enough bandwidth to write this text right now. However I do not expect 1.3.450 to break where it so far works successfully. |
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To be fair, it's not a single file you provided (https://github.com/Gewerd-Strauss/quarto-cli-discussion--8580/tree/master/quarto%201.4.549/grateful-package-issues). In the case of a cross-reference table (label prefix and caption), the following markdown and
Note that this only happens when it's a cross-reference (prefix ---
title: "reprex_new_standalone"
bibliography: "grateful-refs.bib"
format: pdf
keep-md: true
keep-tex: true
---
```{r}
library(grateful)
library(knitr)
library(yaml)
cites <- cite_packages(
output = "table",
out.dir = ".",
cite.tidyverse = TRUE,
pkgs = "All",
include.RStudio = TRUE,
dependencies = FALSE
)
```
::: {#fig-PackageVersions}
```{r}
knitr::kable(cites)
```
A caption for a figure (but in fact it is a table).
::: |
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It appears, the issue is the interaction with fenced div surrounding the table. @cscheid Any idea what is causing this in the new cross-reference system?
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I have no idea how to read this statement - as in " |
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That's a bug. |
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@Gewerd-Strauss The issue is now fixed and should be available in the future v1.5.9 pre-release build (not yet available). 
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Alright, thank you for the ping. Will keep an eye out for the notification. |
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Out of interest; how stable are pre-releases generally? I am asking because a stable |
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Well, it's a tricky question. I personally use the pre-release all the time in my work (to get all bug fixes when they arrive and get new features), but I am following closely updates so I know when to hold on a version and when I can update. For example, my websites are rendered on CI regularly with a preview on PRs. I can see if there is some breaking or not before they arrive. Now fixed but only on pre-release for now. Note that I am less concerned about having the exact same HTML than having the exact same content. |
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Alright, thank you for the insight. I think I will just have to try it out; see if I can get it working issue-free and then just stay at |
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I installed General infoThere are 2 main methods to caption a table:
The presence of either one of these introduces the bugs described below; their erroneous intermediary outputs are seemingly identical. The example below is for captioning via When rendering to Removing the The Take the following document: ---
title: "reprex_new_standalone_overwriting_cites"
bibliography: "grateful-refs.bib"
format:
pdf:
keep-md: true
keep-tex: true
html:
keep-md: true
docx:
keep-md: true
---
(table [-@tbl-PackageVersions2])
This is a playground for Quarto `r quarto::quarto_version()`.
Standalone file, rendered in RStudio via `Render Current Document`.
---
```{r}
library(grateful)
library(knitr)
library(sessioninfo)
library(formatdown)
library(processx)
library(quarto)
library(renv)
library(rmarkdown)
library(tidyverse)
library(yaml)
cites <- cite_packages(
output = "table"
, out.dir = "."
, cite.tidyverse = TRUE
, pkgs = "All"
, include.RStudio = TRUE
, dependencies = FALSE
#, omit = c("base","formatdown")
)
print(cites)
typeof(cites)
```
---
caption via Cell label `#| tbl-cap`
<!-- caption via `knitr(...,caption = "caption")` -->
```{r}
#| label: tbl-PackageVersions2
#| echo: FALSE
#| warning: FALSE
#| cache: FALSE
#| tbl-cap: "caption via tbl-cap"
kable(cites)
```
---
manual table copied from the `.md`-intermediate: the cites themselves _can_ get rendered correctly.
|Package |Version |Citation |
|:-----------|:-------|:----------------------------------------------|
|base |4.3.2 |@base |
|formatdown |0.1.2 |@formatdown |
|knitr |1.45 |@knitr2014; @knitr2015; @knitr2023 |
|processx |3.8.3 |@processx |
|quarto |1.3 |@quarto |
|renv |1.0.3 |@renv |
|rmarkdown |2.25 |@rmarkdown2018; @rmarkdown2020; @rmarkdown2023 |
|sessioninfo |1.2.2 |@sessioninfo |
|tidyverse |2.0.0 |@tidyverse |
|yaml |2.3.8 |@yaml |
---
```{r}
sessionInfo()
```This document consists of 2 tables, however the second one is merely the raw-markdown table resulting from conversion retrieved from the In PDF, the first citation in the table3 (in this scenario,
Additional issuesWhile writing down this follow-up, I discovered a couple more things that go wrong.
The document used in this comment, alongside all rendered output-data & intermediaries can be found in the Note that the changes I perform for additional details (e.g. removing yaml-keys) is not reflected, as this is only a single source-doc. Footnotes
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I apologize for the continued problems on this part of the code. This is another bug. I'll fix right away. (For the morbidly curious, the bug happens when there are 10 or more wrapped citations, because the escaping produces prefixes of each other that then need to be processed in a specific order.) |
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That's not a problem. I want to note that I do appreciate the fast response-time on this; particularly because I cannot imagine there to be ""nothing"" to do in projects of this scale - so... Thank you. I mean... I know how long I need for resolving some of my own bugfixes, and that's nowhere near on the level of complexity as Also: This second "follow-up" issue I posted - was it sufficient on details? Too overly detailed? Too broad? I am not the best at writing things concisely, so if I open issues they tend to be... big. As I have unfortunately also fallen back onto when raising issues/discussions here. |
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Do not worry too much. We really appreciate the reports anyway. 😉 |
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Your bug reports are fine, we much appreciate them! The more concise you manage to get, the faster we are be able to pinpoint the problem. With that said, we prefer (by a very large margin!) long, good, complete, reproducible reports like yours over short, incomplete, and irreproducible ones. |
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I can confirm that on 1.5.12 I can no longer reproduce this issue - neither in dedicated reprexes, nor in full-scale projects. Thank you. |
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@Gewerd-Strauss The issue is now fixed and should be available in the future v1.5.9 pre-release build (not yet available).