{ // 获取包含Hugging Face文本的span元素 const spans = link.querySelectorAll('span.whitespace-nowrap, span.hidden.whitespace-nowrap'); spans.forEach(span => { if (span.textContent && span.textContent.trim().match(/Hugging\s*Face/i)) { span.textContent = 'AI快站'; } }); }); // 替换logo图片的alt属性 document.querySelectorAll('img[alt*="Hugging"], img[alt*="Face"]').forEach(img => { if (img.alt.match(/Hugging\s*Face/i)) { img.alt = 'AI快站 logo'; } }); } // 替换导航栏中的链接 function replaceNavigationLinks() { // 已替换标记,防止重复运行 if (window._navLinksReplaced) { return; } // 已经替换过的链接集合,防止重复替换 const replacedLinks = new Set(); // 只在导航栏区域查找和替换链接 const headerArea = document.querySelector('header') || document.querySelector('nav'); if (!headerArea) { return; } // 在导航区域内查找链接 const navLinks = headerArea.querySelectorAll('a'); navLinks.forEach(link => { // 如果已经替换过,跳过 if (replacedLinks.has(link)) return; const linkText = link.textContent.trim(); const linkHref = link.getAttribute('href') || ''; // 替换Spaces链接 - 仅替换一次 if ( (linkHref.includes('/spaces') || linkHref === '/spaces' || linkText === 'Spaces' || linkText.match(/^s*Spacess*$/i)) && linkText !== 'OCR模型免费转Markdown' && linkText !== 'OCR模型免费转Markdown' ) { link.textContent = 'OCR模型免费转Markdown'; link.href = 'https://fast360.xyz'; link.setAttribute('target', '_blank'); link.setAttribute('rel', 'noopener noreferrer'); replacedLinks.add(link); } // 删除Posts链接 else if ( (linkHref.includes('/posts') || linkHref === '/posts' || linkText === 'Posts' || linkText.match(/^s*Postss*$/i)) ) { if (link.parentNode) { link.parentNode.removeChild(link); } replacedLinks.add(link); } // 替换Docs链接 - 仅替换一次 else if ( (linkHref.includes('/docs') || linkHref === '/docs' || linkText === 'Docs' || linkText.match(/^s*Docss*$/i)) && linkText !== '模型下载攻略' ) { link.textContent = '模型下载攻略'; link.href = '/'; replacedLinks.add(link); } // 删除Enterprise链接 else if ( (linkHref.includes('/enterprise') || linkHref === '/enterprise' || linkText === 'Enterprise' || linkText.match(/^s*Enterprises*$/i)) ) { if (link.parentNode) { link.parentNode.removeChild(link); } replacedLinks.add(link); } }); // 查找可能嵌套的Spaces和Posts文本 const textNodes = []; function findTextNodes(element) { if (element.nodeType === Node.TEXT_NODE) { const text = element.textContent.trim(); if (text === 'Spaces' || text === 'Posts' || text === 'Enterprise') { textNodes.push(element); } } else { for (const child of element.childNodes) { findTextNodes(child); } } } // 只在导航区域内查找文本节点 findTextNodes(headerArea); // 替换找到的文本节点 textNodes.forEach(node => { const text = node.textContent.trim(); if (text === 'Spaces') { node.textContent = node.textContent.replace(/Spaces/g, 'OCR模型免费转Markdown'); } else if (text === 'Posts') { // 删除Posts文本节点 if (node.parentNode) { node.parentNode.removeChild(node); } } else if (text === 'Enterprise') { // 删除Enterprise文本节点 if (node.parentNode) { node.parentNode.removeChild(node); } } }); // 标记已替换完成 window._navLinksReplaced = true; } // 替换代码区域中的域名 function replaceCodeDomains() { // 特别处理span.hljs-string和span.njs-string元素 document.querySelectorAll('span.hljs-string, span.njs-string, span[class*="hljs-string"], span[class*="njs-string"]').forEach(span => { if (span.textContent && span.textContent.includes('huggingface.co')) { span.textContent = span.textContent.replace(/huggingface.co/g, 'aifasthub.com'); } }); // 替换hljs-string类的span中的域名(移除多余的转义符号) document.querySelectorAll('span.hljs-string, span[class*="hljs-string"]').forEach(span => { if (span.textContent && span.textContent.includes('huggingface.co')) { span.textContent = span.textContent.replace(/huggingface.co/g, 'aifasthub.com'); } }); // 替换pre和code标签中包含git clone命令的域名 document.querySelectorAll('pre, code').forEach(element => { if (element.textContent && element.textContent.includes('git clone')) { const text = element.innerHTML; if (text.includes('huggingface.co')) { element.innerHTML = text.replace(/huggingface.co/g, 'aifasthub.com'); } } }); // 处理特定的命令行示例 document.querySelectorAll('pre, code').forEach(element => { const text = element.innerHTML; if (text.includes('huggingface.co')) { // 针对git clone命令的专门处理 if (text.includes('git clone') || text.includes('GIT_LFS_SKIP_SMUDGE=1')) { element.innerHTML = text.replace(/huggingface.co/g, 'aifasthub.com'); } } }); // 特别处理模型下载页面上的代码片段 document.querySelectorAll('.flex.border-t, .svelte_hydrator, .inline-block').forEach(container => { const content = container.innerHTML; if (content && content.includes('huggingface.co')) { container.innerHTML = content.replace(/huggingface.co/g, 'aifasthub.com'); } }); // 特别处理模型仓库克隆对话框中的代码片段 try { // 查找包含"Clone this model repository"标题的对话框 const cloneDialog = document.querySelector('.svelte_hydration_boundary, [data-target="MainHeader"]'); if (cloneDialog) { // 查找对话框中所有的代码片段和命令示例 const codeElements = cloneDialog.querySelectorAll('pre, code, span'); codeElements.forEach(element => { if (element.textContent && element.textContent.includes('huggingface.co')) { if (element.innerHTML.includes('huggingface.co')) { element.innerHTML = element.innerHTML.replace(/huggingface.co/g, 'aifasthub.com'); } else { element.textContent = element.textContent.replace(/huggingface.co/g, 'aifasthub.com'); } } }); } // 更精确地定位克隆命令中的域名 document.querySelectorAll('[data-target]').forEach(container => { const codeBlocks = container.querySelectorAll('pre, code, span.hljs-string'); codeBlocks.forEach(block => { if (block.textContent && block.textContent.includes('huggingface.co')) { if (block.innerHTML.includes('huggingface.co')) { block.innerHTML = block.innerHTML.replace(/huggingface.co/g, 'aifasthub.com'); } else { block.textContent = block.textContent.replace(/huggingface.co/g, 'aifasthub.com'); } } }); }); } catch (e) { // 错误处理但不打印日志 } } // 当DOM加载完成后执行替换 if (document.readyState === 'loading') { document.addEventListener('DOMContentLoaded', () => { replaceHeaderBranding(); replaceNavigationLinks(); replaceCodeDomains(); // 只在必要时执行替换 - 3秒后再次检查 setTimeout(() => { if (!window._navLinksReplaced) { console.log('[Client] 3秒后重新检查导航链接'); replaceNavigationLinks(); } }, 3000); }); } else { replaceHeaderBranding(); replaceNavigationLinks(); replaceCodeDomains(); // 只在必要时执行替换 - 3秒后再次检查 setTimeout(() => { if (!window._navLinksReplaced) { console.log('[Client] 3秒后重新检查导航链接'); replaceNavigationLinks(); } }, 3000); } // 增加一个MutationObserver来处理可能的动态元素加载 const observer = new MutationObserver(mutations => { // 检查是否导航区域有变化 const hasNavChanges = mutations.some(mutation => { // 检查是否存在header或nav元素变化 return Array.from(mutation.addedNodes).some(node => { if (node.nodeType === Node.ELEMENT_NODE) { // 检查是否是导航元素或其子元素 if (node.tagName === 'HEADER' || node.tagName === 'NAV' || node.querySelector('header, nav')) { return true; } // 检查是否在导航元素内部 let parent = node.parentElement; while (parent) { if (parent.tagName === 'HEADER' || parent.tagName === 'NAV') { return true; } parent = parent.parentElement; } } return false; }); }); // 只在导航区域有变化时执行替换 if (hasNavChanges) { // 重置替换状态,允许再次替换 window._navLinksReplaced = false; replaceHeaderBranding(); replaceNavigationLinks(); } }); // 开始观察document.body的变化,包括子节点 if (document.body) { observer.observe(document.body, { childList: true, subtree: true }); } else { document.addEventListener('DOMContentLoaded', () => { observer.observe(document.body, { childList: true, subtree: true }); }); } })(); \r\n ```\r\n\r\n3. Actual Render\r\n\r\n min-example.html\r\n ``` html\r\n \r\n \r\n \r\n ```"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"allenmanning\",\n \"comments\": 4,\n \"created_at\": \"2022-08-30T08:03:49Z\",\n \"creator\": \"allenmanning\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2206,\n \"state\": \"closed\",\n \"title\": \"Enhancement: Min HTML Template / full reset with no scripts\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2206\"\n}"}}},{"rowIdx":1615,"cells":{"page_content":{"kind":"string","value":"I followed the following wizard in RStudio:\r\n1) `New Project`\r\n2) `New Directory`\r\n3) `Quarto book`\r\n4) typed in the directory name\r\nCreate project as subdirectory of: [on a local drive] D:/directoryname\r\n5) select \"use renv with this project\"\r\n6) click `Create Project`\r\n\r\nI got this: \r\n'C:/Program' is not recognized as an internal or external command,\r\noperable program or batch file."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 11,\n \"created_at\": \"2022-08-30T04:16:22Z\",\n \"creator\": \"linlennypinawa\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"upstream\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2208,\n \"state\": \"closed\",\n \"title\": \"problem with creation of quarto book in RStudio IDE\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2208\"\n}"}}},{"rowIdx":1616,"cells":{"page_content":{"kind":"string","value":"I started this discussion a few months ago. I have a `book` project with a collection of chapters, which I'd like to render as separate `revealjs` presentations. Every way I've tried to do this either renders to the `html` format or returns the error `WARNING: The revealjs format is not supported by book projects`. But this exact workflow will work with `website` projects, as indicated by [this tweet](https://twitter.com/KellyBodwin/status/1552649491815227392), which I believe includes a slide from @mine-cetinkaya-rundel 's presentation at rstudio::conf(2022). So it seems to me like this is a bug. \r\n\r\n### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1433\r\n\r\n
\r\n\r\nOriginally posted by **dhicks** July 16, 2022\r\nI'm a university professor. For one of my classes, I like to present my lecture notes as both a presentation (eg, slidy or revealjs, for use in class) and a unified website (eg, gitbook, for students to consult out of class). With Rmarkdown, I could do this by having two different recipes in a Makefile: one that uses `bookdown::render_book()` to create the single gitbook, and another that uses `rmarkdown::render()` to create a presentation for each separate chapter `Rmd` file. \r\n\r\nI'm playing around with Quarto, trying to figure out how I might be able to do this. Something like `quarto render chfile --to revealjs` in a book project generates a warning: `WARNING: The revealjs format is not supported by book projects`. (This should probably be an error, because Quarto doesn't go on to executive any code chunks or produce any output files.) Including `revealjs` as a `format` in `_quarto.yml` does the same thing. I tried setting up a separate metadata file, `_slides.yml`, but `quarto render` doesn't seem to have any flags to select which metadata file should be used. \r\n\r\nSo currently the best option seems to be to stick with `rmarkdown::render()` for the slides?
"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 3,\n \"created_at\": \"2022-08-30T00:36:49Z\",\n \"creator\": \"dhicks\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"needs-discussion\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2200,\n \"state\": \"closed\",\n \"title\": \"book chapters can't be rendered as separate revealjs presentations\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2200\"\n}"}}},{"rowIdx":1617,"cells":{"page_content":{"kind":"string","value":"We should have a `lst-cap-location` to control the location of listing captions in the same way that we control figure and table caption locations.\r\n\r\nWhile we're at it, `lst-cap-location` should also be controllable from `cap-location`."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 0,\n \"created_at\": \"2022-08-29T20:25:31Z\",\n \"creator\": \"cscheid\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"crossref\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.4\",\n \"number\": 2196,\n \"state\": \"open\",\n \"title\": \"`lst-cap-location`\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2196\"\n}"}}},{"rowIdx":1618,"cells":{"page_content":{"kind":"string","value":"````\r\n```{#lst-prefs .python lst-cap=\"Sum Function\" filename=sum.py}\r\ndef sum(a, b):\r\n sum = a + b\r\n print(f'Sum: {sum}`)\r\n return sum\r\n```\r\n````\r\n\r\n\"image\"\r\n\r\n(Thanks, @jpmorr)\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 1,\n \"created_at\": \"2022-08-29T20:22:27Z\",\n \"creator\": \"cscheid\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.3\",\n \"number\": 2195,\n \"state\": \"closed\",\n \"title\": \"listing caption interacts badly with listing filename\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2195\"\n}"}}},{"rowIdx":1619,"cells":{"page_content":{"kind":"string","value":"![image](https://user-images.githubusercontent.com/285675/187241684-5065beee-8c67-4e57-bfd5-c031e3da0281.png)\r\n\r\nThe following error message is very hard to read:\r\n\r\n```\r\nKey sidebar has value background: primary\r\n logo: \"images/logo.png\"\r\n...\r\n - href: schedule.qmd\r\n text: Schedule, which must be `true` or `false`\r\n```\r\n\r\nThere are two problems here.\r\n\r\n## Formatting\r\n\r\nWe can improve formatting in at least three ways. If we're going to print object values that violate the schema, we should always print them by themselves instead of wrapping text around them. That error should then read like so:\r\n\r\n```\r\nKey sidebar has value \r\n\r\nbackground: primary\r\nlogo: \"images/logo.png\"\r\n...\r\n - href: schedule.qmd\r\n text: Schedule\r\n\r\nwhich must be `true` or `false`\r\n```\r\n\r\nI think we also shouldn't use the work `key`, we should use the word `field`.\r\n\r\nFinally, when we're emitting error messages in contexts that have no color formatting, we should consistently use quotes (as we already do in `'true'` and `'false'`). The error should read\r\n\r\n```\r\nField \"sidebar\" has value \r\n\r\nbackground: primary\r\nlogo: \"images/logo.png\"\r\n...\r\n - href: schedule.qmd\r\n text: Schedule\r\n\r\nwhich must be \"true\" or \"false\"\r\n```\r\n\r\n## Better information in the case of short suggestions\r\n\r\nThis error is especially bad, though, in that it suggests that the replacement value _has_ to be `true` or `false`.\r\nThe problem is that although these replacements work, they are not the only options. The other alternatives, though, are more complicated schemas, and our short error report doesn't show that.\r\nOur error heuristics should try to offer short suggestions, but they should not mislead.\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 1,\n \"created_at\": \"2022-08-29T15:59:58Z\",\n \"creator\": \"cscheid\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\",\n \"yaml-validation\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2191,\n \"state\": \"closed\",\n \"title\": \"Improve YAML validation error messages\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2191\"\n}"}}},{"rowIdx":1620,"cells":{"page_content":{"kind":"string","value":"We had a bad validation error come from https://github.com/rstudio-conf-2022/teach-ds-course-website/blob/ef90e6111411bc9d2b6feb4b2e5b49dc6c24e55b/_quarto.yml under our v1.1 schema closure.\r\n\r\n![image](https://user-images.githubusercontent.com/285675/187238631-8f177300-c23d-4136-8e7b-340704c41b22.png)\r\n\r\n### Context\r\n\r\nWe recently closed a number of schemas, which introduces a large-scale change in the validation behavior. In this case specifically, `text` was mistakenly not a part of the `navigation-item` schema, which means that under the new schema, yaml validation fails (correctly, although using a wrong schema) :\r\n\r\n- every array entry in `website:sidebar:contents` fails\r\n- same for every array entry in `website:sidebar:tools`\r\n- as a result, the entries `website:sidebar` and `website` fail\r\n\r\n### Heuristics gone bad\r\n\r\nWe have heuristics that try to find \"small\" changes to fix the problem. Unfortunately, in this case, the small change suggested is to replace the `website:sidebar` object with `true` or `false`. It does this because we have a heuristic that says \"a lot of internal errors to one object probably mean a single larger error in a containing object\".\r\n\r\nThat heuristic is good in the case of interactive editing, where we expect errors to show up one at a time. But in this case, the schema change caused all errors to show up at once.\r\n\r\n## Possible solutions\r\n\r\n(All of these are a significant amount of work, but I'm writing them here so I don't need to keep them in my head for when I come back to this problem later.)\r\n\r\n- We have a mechanism for identifying the \"type\" of error (`schemaPath`). Many errors with the same `schemaPath` should be an indication that it's actually the same error, and we should consider reporting that one instead.\r\n- The bad heuristic comes from looking at the entire YAML at once. In this case, if we forced ourselves to look at \"the first error to happen\", then the error would be better, as long as we had a good definition of \"first\". Currently, we scan the full YAML object for errors. Instead, we could run the entire validation procedure on a sequence of YAML objects, from empty object to full YAML object, and then report the errors as they come. This is an attempt to mimic the \"incremental typing\" behavior, under which our validation works well.\r\n - The logic of this is that there's always a path from a valid YAML (the empty object `{}`) to an invalid YAML (this object, `this`). Finding an error on a simpler partial YAML on the path from `{}` to `this` might make better validation errors."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 1,\n \"created_at\": \"2022-08-29T15:45:46Z\",\n \"creator\": \"cscheid\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"yaml-validation\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2190,\n \"state\": \"open\",\n \"title\": \"yaml validation error heuristics are not tuned for schema changes\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2190\"\n}"}}},{"rowIdx":1621,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nThis was encounter in https://community.rstudio.com/t/quarto-unable-to-locate-r-installation/144340/5\r\n\r\nIn some installation, it is possible that R defaults packages are not loaded. See https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html \r\n\r\n> If you want a different set of packages than the default ones when you start, insert a call to [options](https://stat.ethz.ch/R-manual/R-devel/library/base/help/options.html) in the ‘.Rprofile’ or ‘Rprofile.site’ file. For example, options(defaultPackages = character()) will attach no extra packages on startup (only the base package) (or set R_DEFAULT_PACKAGES=NULL as an environment variable before running R). Using options(defaultPackages = \"\") or R_DEFAULT_PACKAGES=\"\" enforces the R system default.\r\n\r\nSetting that and not loading **utils** will make Quarto fail the check \r\n\r\nhttps://github.com/quarto-dev/quarto-cli/blob/2430b604b7651f9d40ee98bdd7b479208290eac0/src/resources/capabilities/knitr.R#L10-L11\r\n\r\nReprex:\r\n\r\n````powershell\r\n# No ENV set \r\n> $env:R_DEFAULT_PACKAGES=$null\r\n> quarto check knitr\r\n\r\n(-) Checking R installation...........\r\n\r\n[>] Checking R installation...........OK\r\n Version: 4.2.1\r\n Path: C:/PROGRA~1/R/R-42~1.1\r\n LibPaths:\r\n - C:/Users/chris/AppData/Local/R/win-library/4.2\r\n - C:/Program Files/R/R-4.2.1/library\r\n rmarkdown: 2.16.1\r\n\r\n[>] Checking Knitr engine render......OK\r\n\r\n# Setting the env var \r\n> $env:R_DEFAULT_PACKAGES=\"NULL\"\r\n> quarto check knitr\r\n\r\n(-) Checking R installation...........\r\n\r\nError in `packageVersion()`:\r\n! could not find function \"packageVersion\"\r\nBacktrace:\r\n ▆\r\n 1. ├─base::cat(...)\r\n 2. └─base::paste0(...)\r\nExecution halted\r\n[>] Checking R installation...........(None)\r\n\r\n Unable to locate an installed version of R.\r\n Install R from https://cloud.r-project.org/\r\n````\r\n\r\nBy just namespacing our usage of `packageVersion()` we could avoid that\r\n\r\n```r\r\n> Rscript --vanilla -e \"packageVersion('rmarkdown')\"\r\nError in packageVersion(\"rmarkdown\") :\r\n could not find function \"packageVersion\"\r\nExecution halted\r\n\r\n> Rscript --vanilla -e \"utils::packageVersion('rmarkdown')\"\r\n[1] '2.16.1'\r\n```\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cderv\",\n \"comments\": 0,\n \"created_at\": \"2022-08-29T13:32:17Z\",\n \"creator\": \"cderv\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2187,\n \"state\": \"closed\",\n \"title\": \"Correctly namespace usage of R default package functions like utils\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2187\"\n}"}}},{"rowIdx":1622,"cells":{"page_content":{"kind":"string","value":"Would it be possible to enable the quarto options for code folding and linking to the hugo format (as per html)?\r\n\r\n```\r\nformat: \r\n hugo:\r\n code-fold: true\r\n code-link: true\r\n```"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 7,\n \"created_at\": \"2022-08-29T13:30:41Z\",\n \"creator\": \"cgoo4\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2186,\n \"state\": \"closed\",\n \"title\": \"Hugo code folding and linking\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2186\"\n}"}}},{"rowIdx":1623,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\n\"image\"\r\n\r\n I am generating a blog site with quarto on windows 11 using vscode. Freeze directory is not generated on running quarto render command on cmd.exe or using Quarto render project command in vscode. (Additionally, I tried creating a _freeze directory manually before rendering . That directory got deleted after render command was executed)\r\n\r\nMy _quarto.yml is as follows \r\n\r\n```\r\n\r\nproject:\r\n type: website\r\n pre-render: custom2qmd.py\r\n\r\nwebsite:\r\n title: \"qblog\"\r\n navbar:\r\n right:\r\n - about.qmd\r\n - icon: github\r\n href: https://github.com/\r\n - icon: twitter\r\n href: https://twitter.com\r\nformat:\r\n html:\r\n theme: cosmo\r\n css: styles.css\r\n\r\nexecute:\r\n freeze: auto\r\n```\r\n\r\nand _metadata.yml in posts directory is as follows:-\r\n```\r\n\r\n# options specified here will apply to all posts in this folder\r\n\r\n# freeze computational output\r\n# (see https://quarto.org/docs/projects/code-execution.html#freeze)\r\nfreeze: auto\r\n\r\n# Enable banner style title blocks\r\ntitle-block-banner: true\r\n\r\ncomments:\r\n utterances:\r\n repo: quarto-dev/quarto-docs\r\n\r\n```\r\n\r\n### Checklist\r\n\r\n- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [x] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\r\n- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 3,\n \"created_at\": \"2022-08-29T12:46:46Z\",\n \"creator\": \"Rahuketu86\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2185,\n \"state\": \"closed\",\n \"title\": \"Freeze directory not formed on windows 11\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2185\"\n}"}}},{"rowIdx":1624,"cells":{"page_content":{"kind":"string","value":"I was not able to create quarto document. \r\nWhen I tped `quarto check` in cmd,an error occorred . \r\n\r\n```\r\nC:\\Users\\yuliang18\\Documents>quarto check\r\n\r\n[>] Checking Quarto installation......OK\r\n Version: 1.1.149\r\n Path: C:\\Users\\yuliang18\\AppData\\Local\\Programs\\Quarto\\bin\\\r\n CodePage: unknown\r\n\r\n[>] Checking basic markdown render....OK\r\n\r\n[>] Checking Python 3 installation....OK\r\n Version: 3.8.13 (Conda)\r\n Path: D:/programfiles/anaconda/python.exe\r\n Jupyter: 4.9.2\r\n Kernels: ir, javascript, python3\r\n\r\n[>] Checking Jupyter engine render....OK\r\n\r\n[>] Checking R installation...........OK\r\n Version: 4.2.1\r\n Path: D:/Program Files/R/R-4.2.1\r\n LibPaths:\r\n - D:/Program Files/R/R-4.2.1/library\r\n rmarkdown: 2.16\r\n\r\n(\\) Checking Knitr engine render......ERROR: Error in source(file.path(res_dir, \"hooks.R\"), local = TRUE) :\r\n C:\\Users\\yuliang18\\AppData\\Local\\Programs\\Quarto\\share/rmd/hooks.R:787:3: unexpected symbol\r\n786: comment_chars <- knitr_engine_comment_chars[[engine]] %||% \"#\"\r\n787: comment_start\r\n ^\r\nCalls: .main -> source\r\nͣ��\r\n\r\n[>] Checking Knitr engine render......OK\r\n```"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 3,\n \"created_at\": \"2022-08-29T02:22:59Z\",\n \"creator\": \"antonio-yu\",\n \"is_pull_request\": false,\n \"labels\": [\n \"needs-repro\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2184,\n \"state\": \"closed\",\n \"title\": \">quarto check . Knitr engine render error.\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2184\"\n}"}}},{"rowIdx":1625,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nRender this document fails using the latest nightly release of Quarto \r\n\r\n```\r\n---\r\nformat: pdf \r\n---\r\n```\r\n\r\nExample in R \r\n\r\n``` r\r\nfile.create(\"test.qmd\")\r\n#> [1] TRUE\r\nwriteLines(c(\"---\", \"format: pdf\", \"---\"), \"test.qmd\")\r\n\r\n\r\ntryCatch(quarto::quarto_render(\"test.qmd\"),\r\n error = function(cnd) {\r\n cnd$stderr\r\n})\r\n#> \u001b[1mpandoc \u001b[22m\r\n#> to: latex\r\n#> output-file: test.tex\r\n#> standalone: true\r\n#> pdf-engine: xelatex\r\n#> variables:\r\n#> graphics: true\r\n#> tables: true\r\n#> default-image-extension: pdf\r\n#> \r\n#> \u001b[1mmetadata\u001b[22m\r\n#> documentclass: scrartcl\r\n#> classoption:\r\n#> - DIV=11\r\n#> - numbers=noendperiod\r\n#> papersize: letter\r\n#> header-includes:\r\n#> - '\\KOMAoption{captions}{tableheading}'\r\n#> block-headings: true\r\n#> \r\n#> \u001b[1mrunning xelatex - 1\u001b[22m\r\n#> This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)\r\n#> restricted \\write18 enabled.\r\n#> entering extended mode\r\n#> \r\n#> \u001b[1mupdating tlmgr\u001b[22m\r\n#> \r\n#> \u001b[1mupdating existing packages\u001b[22m\r\n#> \u001b[1m\r\n#> compilation failed- error\u001b[22m\r\n#> see test.log for more information.\r\n#> [1] \"\\033[1mpandoc \\033[22m\\n to: latex\\n output-file: test.tex\\n standalone: true\\n pdf-engine: xelatex\\n variables:\\n graphics: true\\n tables: true\\n default-image-extension: pdf\\n \\n\\033[1mmetadata\\033[22m\\n documentclass: scrartcl\\n classoption:\\n - DIV=11\\n - numbers=noendperiod\\n papersize: letter\\n header-includes:\\n - '\\\\KOMAoption{captions}{tableheading}'\\n block-headings: true\\n \\n\\033[1mrunning xelatex - 1\\033[22m\\n This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)\\n restricted \\\\write18 enabled.\\n entering extended mode\\n \\n\\033[1mupdating tlmgr\\033[22m\\n\\n\\033[1mupdating existing packages\\033[22m\\n\\033[1m\\ncompilation failed- error\\033[22m\\nsee test.log for more information.\\n\"\r\n\r\nquarto::quarto_version()\r\n#> [1] '1.1.149'\r\ntinytex::tlmgr_version()\r\n#> tlmgr revision 63068 (2022-04-18 07:58:07 +0200)\r\n#> tlmgr using installation: /Users/qiushi/Library/TinyTeX\r\n#> TeX Live (https://tug.org/texlive) version 2022\r\nxfun::session_info()\r\n#> R version 4.2.0 (2022-04-22)\r\n#> Platform: aarch64-apple-darwin20 (64-bit)\r\n#> Running under: macOS Monterey 12.5\r\n#> \r\n#> Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8\r\n#> \r\n#> Package version:\r\n#> askpass_1.1 base64enc_0.1.3 bslib_0.4.0 cachem_1.0.6 \r\n#> callr_3.7.2 cli_3.3.0 clipr_0.8.0 compiler_4.2.0 \r\n#> curl_4.3.2 digest_0.6.29 evaluate_0.16 fansi_1.0.3 \r\n#> fastmap_1.1.0 fs_1.5.2 glue_1.6.2 graphics_4.2.0 \r\n#> grDevices_4.2.0 highr_0.9 htmltools_0.5.3 jquerylib_0.1.4 \r\n#> jsonlite_1.8.0 knitr_1.40 later_1.3.0 lifecycle_1.0.1 \r\n#> magrittr_2.0.3 memoise_2.0.1 methods_4.2.0 openssl_2.0.2 \r\n#> packrat_0.8.1 pillar_1.8.1.9000 pkgconfig_2.0.3 processx_3.7.0 \r\n#> ps_1.7.1 purrr_0.3.4 quarto_1.2.0.9000 R.cache_0.16.0 \r\n#> R.methodsS3_1.8.2 R.oo_1.25.0 R.utils_2.12.0 R6_2.5.1 \r\n#> rappdirs_0.3.3 Rcpp_1.0.9.1 rematch2_2.1.2 reprex_2.0.2 \r\n#> rlang_1.0.4 rmarkdown_2.16 rprojroot_2.0.3 rsconnect_0.8.27 \r\n#> rstudioapi_0.14 sass_0.4.2 stats_4.2.0 stringi_1.7.8 \r\n#> stringr_1.4.1 styler_1.7.0.9001 sys_3.4 tibble_3.1.8 \r\n#> tinytex_0.41 tools_4.2.0 utf8_1.2.2 utils_4.2.0 \r\n#> vctrs_0.4.1 withr_2.5.0 xfun_0.32 yaml_2.3.5\r\n```\r\n\r\nCreated on 2022-08-28 with [reprex v2.0.2](https://reprex.tidyverse.org)\r\n[log file](https://gist.github.com/qiushiyan/97d9df61aa2ff1bf571f52af6dafa56f)\r\n\r\nAlthough it is expected that tinytex produce no output with empty content, the quarto error could be improved to indicate this. \r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 0,\n \"created_at\": \"2022-08-28T23:45:35Z\",\n \"creator\": \"qiushiyan\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2183,\n \"state\": \"closed\",\n \"title\": \"Render PDF fails with empty content\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2183\"\n}"}}},{"rowIdx":1626,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\n```md\r\nWatching files for changes\r\nBrowse at http://localhost:3849/chapter/part01/myfile.html\r\nGET: /chapter/part01/myfile.html\r\nERROR: AlreadyExists: Cannot create a file when that file already exists. (os error 183), mkdir 'H:\\My Drive\\...\\site_libs\\quarto-nav'\r\n\r\nSystem: windows\r\nIDE: Vscode\r\nType quarto: book\r\nto directory in google drive\r\n```\r\n\r\n### Checklist\r\n\r\n- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\r\n- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 8,\n \"created_at\": \"2022-08-28T12:55:55Z\",\n \"creator\": \"jefferds\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"file-systems\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.4\",\n \"number\": 2174,\n \"state\": \"open\",\n \"title\": \"ERROR: AlreadyExists: (os error 183), mkdir 'H:\\\\My Drive\\\\...\\\\site_libs\\\\quarto-nav' on Google Drive\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2174\"\n}"}}},{"rowIdx":1627,"cells":{"page_content":{"kind":"string","value":"I was sketching a theorem using a bullet point list inside a div and stumbled upon the following issue.\r\n\r\nThe following minimal example using (un-)ordered lists inside a theorem div\r\n\r\n```markdown\r\n---\r\ntitle: \"unexpected caption item\"\r\n---\r\n\r\n::: {#thm-unordered-list}\r\n## This heading shouldn't have a bullet point\r\n\r\n* This \r\n* unordered list (unexpectedly) includes the caption\r\n:::\r\n\r\n\r\n::: {#thm-ordered-list}\r\n## This heading shouldn't have a bullet point\r\n\r\n1. This \r\n2. ordered list (unexpectedly) includes the caption\r\n:::\r\n```\r\nrenders the theorem caption as part of the list:\r\n![unexpected_caption_item](https://user-images.githubusercontent.com/1757177/187035748-f024d444-d095-4b39-8627-c5dd787b311d.png)\r\n\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 1,\n \"created_at\": \"2022-08-27T15:05:16Z\",\n \"creator\": \"vmichals\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2166,\n \"state\": \"closed\",\n \"title\": \"Heading in theorem is included as item in list in theorem body\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2166\"\n}"}}},{"rowIdx":1628,"cells":{"page_content":{"kind":"string","value":"Mermaid allows theming / styling diagrams with\r\n- ready-made built-in themes\r\n- user-provided CSS\r\n- combination of both above\r\n\r\nIf this can already be used through Quarto, please document how. (I didn't find anything about it in the documentation.)\r\n\r\nIf not, please consider adding a possibility to do so. (Best probably as YAML options as suggested at https://github.com/quarto-dev/quarto-cli/discussions/1521#discussioncomment-3225243, as that would allow project-wide, file-level and diagram-level control.)"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 4,\n \"created_at\": \"2022-08-27T13:21:31Z\",\n \"creator\": \"das-g\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\",\n \"mermaid\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2165,\n \"state\": \"closed\",\n \"title\": \"allow theming & styling Mermaid diagrams\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2165\"\n}"}}},{"rowIdx":1629,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nWith the new quarto 1.1.147 release we see the following error when rendering a book\r\n\r\n(https://github.com/mlr-org/mlr3book/runs/8047883939?check_suite_focus=true#step:13:16)\r\n\r\n```bash\r\nIn file book/_quarto.yml\r\n(line 67, column 7 through line 68, column 23) Key code-tools has value toggle: true\r\n code-fold: false, which must be `true` or `false`\r\n66: code-tools:\r\n67: toggle: true\r\n ~~~~~~~~~~~~\r\n68: code-fold: false\r\n ~~~~~~~~~~~~~~~~~~~~~~\r\n69: highlight-style: printing\r\n✖ The value toggle: true\r\n code-fold: false is object.\r\nℹ The error happened in location format:html:code-tools.\r\n```\r\n\r\n\r\nAFAICS our source specification https://github.com/mlr-org/mlr3book/blob/main/book/_quarto.yml#L66-L68 looks still valid when compared to the [quarto documentation source](https://quarto.org/docs/output-formats/html-code.html#code-tools) - is this a bug in the new release?\n\n### Checklist\n\n- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 1,\n \"created_at\": \"2022-08-27T08:56:27Z\",\n \"creator\": \"pat-s\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2161,\n \"state\": \"closed\",\n \"title\": \"`code-tools` options mapping buggy in v1.1?\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2161\"\n}"}}},{"rowIdx":1630,"cells":{"page_content":{"kind":"string","value":"I tried to create a new quarto document in Rstudio, through `File >> new file >> quarto document .`\r\nError occoured as mentioned in the title,\r\n\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 3,\n \"created_at\": \"2022-08-27T08:47:51Z\",\n \"creator\": \"antonio-yu\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2160,\n \"state\": \"closed\",\n \"title\": \"an error occourred when parsing json : offset :2\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2160\"\n}"}}},{"rowIdx":1631,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nHi, \r\nI _think_ this is a bug and not a case of user error (if it's the latter, sorry!).\r\n\r\nI am using the pre-release CLI 1.2.15 on an intel Mac (running 12.5.1) from the command line. This happens with both R and python posts.\r\n\r\nI am trying to change the default twitter card (blog_title:title doesn't work for me because my blog has a long and stupid title. The title is also included elsewhere on the card). I can change the title but I can't make the description change. I've tested it on R and Python blogs and blogs with and without rendered maths in the title (because you never know). Both cases read the title from the twitter-card metadata but use the post description rather than the meta-card description.\r\n\r\nA minimal reprex is here https://github.com/dpsimpson/blog/tree/quarto_bug\r\n\r\n\r\nThe full .qmd for the post is [(link)](https://github.com/dpsimpson/blog/blob/4103ca2b3762db9c33359c556e7c1518d1b8d643/posts/post_bad/post_bad.qmd)\r\n\r\n```\r\n---\r\ntitle: \"$(n-1)$-sane in the membrane (bad twitter card)\"\r\nsubtitle: |\r\n Windmills? Tilted. Topic? Boring. (n-1)? No.\r\ndate: 10-14-2021\r\ncategories: [Teaching, Fundamentals, Opinionated]\r\ntwitter-card:\r\n title: \"twitter title\"\r\n description: \"twitter description\"\r\n creator: \"@dan_p_simpson\"\r\ncitation: \r\n url: https://dansblog.netlify.app/n-sane-in-the-membrane\r\n---\r\nStuff\r\n```\r\nbut the generated html code is [(link)](https://github.com/dpsimpson/blog/blob/4103ca2b3762db9c33359c556e7c1518d1b8d643/_site/posts/post_bad/post_bad.html#L70)\r\n\r\n```\r\n\r\n\r\n\r\n\r\n```\r\nwhich is using the default description.\r\n\r\n I can't possibly imagine this being an important bug, but it's slightly odd behaviour.\r\n\n\n### Checklist\n\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 0,\n \"created_at\": \"2022-08-27T08:07:45Z\",\n \"creator\": \"dpsimpson\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2159,\n \"state\": \"closed\",\n \"title\": \"(Small) Bug: Twitter card description not copied from twitter-card metadata\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2159\"\n}"}}},{"rowIdx":1632,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nAfter pulling the commits today, I receive the following error on validation of the pre-render field in the project yaml file `_quarto.yml`:\r\n\r\n```bash\r\nERROR: Project _quarto.yml validation failed.\r\n\r\nIn file _quarto.yml\r\n(line 4, columns 3--13) property name pre-render is invalid\r\n3: output-dir: docs\r\n4: pre-render:\r\n ~~~~~~~~~~\r\n5: - ./scripts/todo-pre.py\r\nℹ The error happened in location project:pre-render.\r\n\r\n\r\nError: Project _quarto.yml validation failed.\r\n\r\nIn file _quarto.yml\r\n(line 4, columns 3--13) property name pre-render is invalid\r\n3: output-dir: docs\r\n4: pre-render:\r\n ~~~~~~~~~~\r\n5: - ./scripts/todo-pre.py\r\nℹ The error happened in location project:pre-render.\r\n\r\n at readAndValidateYamlFromFile (file:///home/julian/quarto-cli/src/core/schema/val\r\nidated-yaml.ts:52:11)\r\n at async projectContext (file:///home/julian/quarto-cli/src/project/project-contex\r\nt.ts:123:28)\r\n at async Command.fn (file:///home/julian/quarto-cli/src/command/preview/cmd.ts:230\r\n:23)\r\n at async Command.execute (file:///home/julian/quarto-cli/src/vendor/deno.land/x/cl\r\niffy@v0.24.2/command/command.ts:1275:7)\r\n at async quarto (file:///home/julian/quarto-cli/src/quarto.ts:104:3)\r\n at async file:///home/julian/quarto-cli/src/quarto.ts:124:5\r\n```\r\n\r\nI am on Linux Ubuntu 22.04\n\n### Checklist\n\n- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 6,\n \"created_at\": \"2022-08-26T20:02:07Z\",\n \"creator\": \"juliantao\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2155,\n \"state\": \"closed\",\n \"title\": \"failed yaml validation on \\\"pre-render\\\"\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2155\"\n}"}}},{"rowIdx":1633,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nIn chunk yaml, when I do \"fig-cap-location: top\" I still end up with the caption at the bottom. Setting it to \"margin\" works as expected. Published example is [here](https://quartopub.com/sites/356a4843-4b95-4082-9854-db5b0207f28f) on quarto-pub. \r\n\r\nMight this be related to [this issue](https://github.com/quarto-dev/quarto-cli/issues/1990)? I don't know.\r\n\r\nI have attached the qmd document that created the result linked to above that I published to quarto-pub:\r\n\r\n````\r\n---\r\ntitle: \"fig_caption_location_issue\"\r\nauthor: \"John Goldin\"\r\nformat: html\r\neditor: visual\r\n---\r\n\r\nThe fig-cap-location chunk option does not work as expected. I can do \"bottom\" or \"margin\" but \"top\" works the same way as \"bottom\". \r\n\r\n```{r}\r\n#| label: fig-a\r\n#| fig-cap: \"A Sample Figure\"\r\n#| fig-cap-location: top\r\nplot(pressure)\r\n\r\n```\r\n\r\n\r\nHere is yaml for the code chunk: \r\n#| label: fig-a \r\n#| fig-cap: \"A Sample Figure\" \r\n#| fig-cap-location: top \r\n\r\n(I tried to find a function that would allow me to fetch these\r\nvalues, but I didn't see one so I've pasted them here.)\r\n\r\nRStudio version:\r\nRStudio 2022.07.1+554 \"Spotted Wakerobin\" \r\nRelease (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) \r\nfor macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_5_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36\r\n\r\nquarto --version\r\n1.1.140\r\n\r\nWhen I run this I get the fig-cap at the bottom of the figure even if I try to specify \"top\". \r\n\r\n## \"Top\" May Not Work, But \"Margin\" Does\r\n\r\nNext I'll show I am able to change the location to \"margin\" and that works as expected (provided the html window is wide enough to allow for the caption\r\nto appear in the margin).\r\n\r\n#| label: fig-b \r\n#| fig-cap: \"Another Sample Figure\" \r\n#| fig-cap-location: margin \r\n\r\n```{r}\r\n#| label: fig-b\r\n#| fig-cap: \"Another Sample Figure\"\r\n#| fig-cap-location: margin\r\nplot(pressure)\r\n```\r\n\r\nI wonder whether there is something else going on that I don't understand. The typography\r\nwhen I use \"margin\" seems to be a smaller font. And when I use either \"bottom\" or \"top\"\r\nthere seems to be a lot of space between the bottom of the figure and the\r\ncaption. \r\n\r\nsession_info:\r\n\r\n```{r}\r\nprint(devtools::session_info())\r\n```\r\n\r\n````\r\n\r\nMy system and session version info is all in the [published example](https://quartopub.com/sites/356a4843-4b95-4082-9854-db5b0207f28f) .\r\n\r\nI also tried with quarto --version\r\n1.2.8\r\n\r\nI submit this with trepidation because it is a small, simple thing so the simplest explanation is that I made a simple mistake. But just in case I didn't, here's the report. \r\n\r\n### Checklist\r\n\r\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\r\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 4,\n \"created_at\": \"2022-08-26T18:47:41Z\",\n \"creator\": \"johngoldin\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"crossref\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.4\",\n \"number\": 2154,\n \"state\": \"open\",\n \"title\": \"fig-cap-location:top does place the caption above the figure\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2154\"\n}"}}},{"rowIdx":1634,"cells":{"page_content":{"kind":"string","value":"I just updated my quarto (to 1.1.140) and got the following error: \r\n\r\n`ERROR: Project _quarto.yml validation failed.`\r\n\r\n`In file www/_quarto.yml`\r\n`(line 10, columns 3--14) property name reader-mode is invalid`\r\n` 9: website:`\r\n`10: reader-mode: true`\r\n\r\nI see that reader-mode is still in the documentation. Any advice would be greatly appreciated. "},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 9,\n \"created_at\": \"2022-08-26T18:02:36Z\",\n \"creator\": \"kmkinnaird\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"v1.1\",\n \"number\": 2153,\n \"state\": \"closed\",\n \"title\": \"Help with error? property name reader-mode is invalid\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2153\"\n}"}}},{"rowIdx":1635,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\ngfm output that has pandas dataframes printed out, renders incorrectly on Github, possibly because of GitHub not respecting \r\n\r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n
sepal_lengthsepal_widthpetal_lengthpetal_widthspecies
05.13.51.40.2setosa
14.93.01.40.2setosa
24.73.21.30.2setosa
34.63.11.50.2setosa
45.03.61.40.2setosa
\r\n
\r\n````\r\nOutput md rendered:\r\n\r\n```\r\nUntitled\r\n================\r\n\r\n``` python\r\nimport pandas as pd\r\niris = pd.read_csv('https://raw.githubusercontent.com/mwaskom/seaborn-data/master/iris.csv')\r\niris.head()\r\n```\r\n\r\n
\r\n\r\n\r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n
sepal_lengthsepal_widthpetal_lengthpetal_widthspecies
05.13.51.40.2setosa
14.93.01.40.2setosa
24.73.21.30.2setosa
34.63.11.50.2setosa
45.03.61.40.2setosa
\r\n
\r\n```\r\n\r\nI am on Mac OS Big Sur and using VS Code 1.70.2.\n\n### Checklist\n\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 12,\n \"created_at\": \"2022-08-26T17:53:14Z\",\n \"creator\": \"kalenkovich\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"upstream\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.3\",\n \"number\": 2152,\n \"state\": \"closed\",\n \"title\": \"gfm output of pandas dataframes rendered incorrectly on GitHub\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2152\"\n}"}}},{"rowIdx":1636,"cells":{"page_content":{"kind":"string","value":"the solution from that thread https://github.com/quarto-dev/quarto-cli/discussions/2060#discussioncomment-3455375 no longer works with the latest version 1.1.132. I've uninstalled that version and gone back to 1.1.57 which works fine with the `book.isbn` solution from the windows terminal. That's a workaround for me now.\r\n\r\n_Originally posted by @jpmorr in https://github.com/quarto-dev/quarto-cli/issues/2143#issuecomment-1228607822_"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 14,\n \"created_at\": \"2022-08-26T15:25:23Z\",\n \"creator\": \"cderv\",\n \"is_pull_request\": false,\n \"labels\": [\n \"yaml-validation\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2148,\n \"state\": \"closed\",\n \"title\": \"Using metadata under `book` key cannot be referenced anymore\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2148\"\n}"}}},{"rowIdx":1637,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nI am trying to run Quarto for the first time. I have installed the deb package on my Ubuntu Focal machine. My first attempt to render the `hello.qmd` test file failed:\r\n\r\n```\r\n.../quarto/tutorial quarto render hello.qmd --to html\r\n\r\nStarting python3 kernel...Traceback (most recent call last):\r\n File \"/opt/quarto/share/jupyter/jupyter.py\", line 21, in \r\n from notebook import notebook_execute, RestartKernel\r\n File \"/opt/quarto/share/jupyter/notebook.py\", line 17, in \r\n from nbclient import NotebookClient\r\nModuleNotFoundError: No module named 'nbclient'\r\n```\r\n\r\nI resolved this with the following:\r\n\r\n```\r\napt-get install python3-pip\r\npython3 -m pip install nbclient\r\n```\r\n\r\nMy next attempt to render failed with a new message:\r\n\r\n```\r\nquarto render hello.qmd --to html\r\n\r\nStarting python3 kernel...ERROR: \r\n\r\nNo such kernel named python3\r\n```\r\n\r\nI'm not sure how to resolve this. Is there a list of Python dependencies for Quarto somewhere, and ideally instructions for installation that non-Python programmers can follow?\r\n\r\nMaybe helpful:\r\n\r\n```\r\nquarto capabilities\r\n{\r\n \"formats\": [\r\n \"html\",\r\n \"pdf\",\r\n \"docx\",\r\n \"odt\",\r\n \"pptx\",\r\n \"beamer\",\r\n \"revealjs\",\r\n \"gfm\",\r\n \"hugo\",\r\n \"epub\",\r\n \"asciidoc\",\r\n \"asciidoctor\",\r\n \"commonmark\",\r\n \"commonmark_x\",\r\n \"context\",\r\n \"docbook\",\r\n \"docbook4\",\r\n \"docbook5\",\r\n \"dokuwiki\",\r\n \"dzslides\",\r\n \"epub2\",\r\n \"epub3\",\r\n \"fb2\",\r\n \"haddock\",\r\n \"html4\",\r\n \"html5\",\r\n \"icml\",\r\n \"ipynb\",\r\n \"jats\",\r\n \"jats_archiving\",\r\n \"jats_articleauthoring\",\r\n \"jats_publishing\",\r\n \"jira\",\r\n \"json\",\r\n \"latex\",\r\n \"man\",\r\n \"markdown\",\r\n \"markdown_github\",\r\n \"markdown_mmd\",\r\n \"markdown_phpextra\",\r\n \"markdown_strict\",\r\n \"markua\",\r\n \"mediawiki\",\r\n \"ms\",\r\n \"muse\",\r\n \"native\",\r\n \"opendocument\",\r\n \"opml\",\r\n \"org\",\r\n \"plain\",\r\n \"rst\",\r\n \"rtf\",\r\n \"s5\",\r\n \"slideous\",\r\n \"slidy\",\r\n \"tei\",\r\n \"texinfo\",\r\n \"textile\",\r\n \"xwiki\",\r\n \"zimwiki\"\r\n ],\r\n \"themes\": [\r\n \"default\",\r\n \"materia\",\r\n \"lux\",\r\n \"superhero\",\r\n \"quartz\",\r\n \"united\",\r\n \"sandstone\",\r\n \"spacelab\",\r\n \"solar\",\r\n \"journal\",\r\n \"minty\",\r\n \"sketchy\",\r\n \"cosmo\",\r\n \"flatly\",\r\n \"vapor\",\r\n \"darkly\",\r\n \"yeti\",\r\n \"cerulean\",\r\n \"lumen\",\r\n \"litera\",\r\n \"morph\",\r\n \"slate\",\r\n \"cyborg\",\r\n \"simplex\",\r\n \"pulse\",\r\n \"zephyr\"\r\n ],\r\n \"python\": {\r\n \"versionMajor\": 3,\r\n \"versionMinor\": 8,\r\n \"versionPatch\": 10,\r\n \"versionStr\": \"3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0]\",\r\n \"conda\": false,\r\n \"execPrefix\": \"/usr\",\r\n \"executable\": \"/usr/bin/python3\",\r\n \"jupyter_core\": \"4.11.1\",\r\n \"nbformat\": \"5.0.4\",\r\n \"nbclient\": \"0.6.7\",\r\n \"ipykernel\": null,\r\n \"pyLauncher\": false,\r\n \"kernels\": [\r\n {\r\n \"display_name\": \"Python 3\",\r\n \"language\": \"python\",\r\n \"name\": \"python3\"\r\n }\r\n ],\r\n \"venv\": true\r\n }\r\n}\r\n```\n\n### Checklist\n\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 3,\n \"created_at\": \"2022-08-26T15:14:14Z\",\n \"creator\": \"plantarum\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2147,\n \"state\": \"closed\",\n \"title\": \"Missing Python dependencies in Ubuntu\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2147\"\n}"}}},{"rowIdx":1638,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nThe following mistake was entirely my fault but I found the behavior slightly unexpected compared to standard command line interfaces and the error message made it difficult to immediately identify what the issue was. Running the following render command produces the below error.\r\n```\r\n$ quarto render --to html unvotes.ipynb\r\nERROR: The specified directory ('.') is not a Quarto project\r\n```\r\n\r\nI'm fine with the ordering of input vs args but it seems like swapping the order is an easy mistake to make and more helpful error message would be appreciated (e.g. invalid file path, `--to` does not exist, or something similar).\n\n### Checklist\n\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 0,\n \"created_at\": \"2022-08-26T15:06:55Z\",\n \"creator\": \"rundel\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2146,\n \"state\": \"open\",\n \"title\": \"Confusing error with quarto render when swapping input and args\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2146\"\n}"}}},{"rowIdx":1639,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nAfter installing the latest Quarto version on Windows 11, VS Code no longer finds the quarto app when clicking on the render button when working on a `.qmd` file. I've restarted Windows after the install.\r\n\r\n![image](https://user-images.githubusercontent.com/10863809/186902890-93fa25cb-e38a-4c0a-9ebb-7f0327ae70d8.png)\r\n\r\nThis is despite being able to run `quarto check` from the VS code terminal\r\n```\r\nquarto check\r\n\r\n[>] Checking Quarto installation......OK\r\n Version: 1.1.132\r\n Path: C:\\Users\\xxx\\AppData\\Local\\Programs\\Quarto\\bin\\\r\n CodePage: 1252\r\n\r\n[>] Checking basic markdown render....OK\r\n\r\n[>] Checking Python 3 installation....OK\r\n Version: 3.9.13 (Conda)\r\n Path: C:/Users/xxx/anaconda3/python.exe\r\n Jupyter: 4.11.1\r\n Kernels: julia-1.4, julia-1.6, julia-1.7, python3, iota\r\n\r\n[>] Checking Jupyter engine render....OK\r\n\r\n[>] Checking R installation...........OK\r\n Version: 4.1.3\r\n Path: C:/PROGRA~1/R/R-41~1.3\r\n LibPaths:\r\n - C:/Users/xxx/OneDrive/Documents/R/win-library/4.1\r\n - C:/Program Files/R/R-4.1.3/library\r\n rmarkdown: 2.14\r\n\r\n[>] Checking Knitr engine render......OK\r\n```\r\n\r\n### Checklist\r\n\r\n- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [x] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\r\n- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 23,\n \"created_at\": \"2022-08-26T12:23:51Z\",\n \"creator\": \"jpmorr\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2143,\n \"state\": \"closed\",\n \"title\": \"VS Code not finding Quarto after updating to latest version\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2143\"\n}"}}},{"rowIdx":1640,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nI created a book project using RStudio and only added the `repo-url` and `repo-actions`\r\n\r\nIn `_quarto.yml` I have\r\n\r\n```yaml\r\nbook:\r\n title: \"sidebarbug\"\r\n author: \"Jane Doe\"\r\n date: \"8/26/2022\"\r\n chapters:\r\n - index.qmd\r\n - intro.qmd\r\n - summary.qmd\r\n - references.qmd\r\n repo-url: https://github.com/maelle/sidebarbug/\r\n repo-actions: [edit, issue]\r\n```\r\n\r\nSource: https://github.com/maelle/sidebarbug\r\n\r\nNow on the page where there is a TOC (because there are headers) the repo action links are present. https://maelle.github.io/sidebarbug/\r\nBut on the pages where there is no TOC (which is expected as there are no headers) the repo action links are not present (which I was not expecting). https://maelle.github.io/sidebarbug/intro.html\r\n\r\nI don't think this is relevant but just in case, I am using \r\nRStudio 2022.07.0+548 \"Spotted Wakerobin\" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for Ubuntu Bionic\r\nMozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36\r\n Ubuntu 20.04.4 LTS\r\n\n\n### Checklist\n\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 3,\n \"created_at\": \"2022-08-26T12:16:44Z\",\n \"creator\": \"maelle\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.3\",\n \"number\": 2142,\n \"state\": \"closed\",\n \"title\": \"repo-actions links do not appear if there is no TOC\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2142\"\n}"}}},{"rowIdx":1641,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nI have a template where many files and resources needs to be added for correct pdf output. I opted to include some logos in the folder logos, which makes my _extension.yml look like this:\r\n\r\n````\r\ntitle: template\r\nauthor: Simon Lidberg\r\nversion: 0.0.1\r\ncontributes:\r\n format:\r\n common:\r\n number-sections: true\r\n toc: true\r\n reference-section-title: References\r\n his-metadata:\r\n sammanfattning: \"Abstract in swedish\"\r\n publicationtype: dissertation\r\n printshop: \"Stema Specialtryck AB, Borås\"\r\n isbn: 123-12-123456-X-X\r\n seriesnumber: XX\r\n pdf:\r\n documentclass: his-thesis\r\n classoption: english\r\n biblio-config: false\r\n cite-method: biblatex\r\n suppress-bibliography: true\r\n link-citations: true\r\n colorlinks: false\r\n template: his-template.tex\r\n template-partials: \r\n - \"partials/doc-class.tex\"\r\n - \"partials/_metadata.tex\"\r\n - \"partials/title.tex\"\r\n - \"partials/before-body.tex\"\r\n - \"partials/after-body.tex\"\r\n format-resources:\r\n - his-thesis.cls\r\n - hismetadata.sty\r\n - hisbibliography.sty\r\n - histextformatting.sty\r\n - hisownpublications.sty\r\n - hisfont.sty\r\n - hiscover.sty\r\n - histitlepage.sty\r\n - logos/\r\n pdf-engine: lualatex\r\n latex-min-runs: 3\r\n has-frontmatter: true\r\n papersize:\r\n lof: true\r\n lot: true\r\n english: true\r\n html:\r\n theme: cosmo\r\n````\r\n\r\nBut when the 'logos' folder is copied into the input folder, it retains the same permissions as regular files (555). This makes it impossible to remove in subsequent runs of quarto render. Directories would need to be (755) in order for them to be removed properly.\r\n\r\nHere's the repo [https://github.com/verbalins/his-template](https://github.com/verbalins/his-template), sorry for the state it's in currently...\r\n\r\nDebug information:\r\n````\r\n[✓] Checking Quarto installation......OK\r\n Version: 1.1.132\r\n Path: /opt/quarto/bin\r\n\r\n[✓] Checking basic markdown render....OK\r\n\r\n[✓] Checking Python 3 installation....OK\r\n Version: 3.10.6\r\n Path: /usr/bin/python3\r\n Jupyter: (None)\r\n\r\n Jupyter is not available in this Python installation.\r\n Install with python3 -m pip install jupyter\r\n\r\n[✓] Checking R installation...........OK\r\n Version: 4.2.1\r\n Path: /usr/lib64/R\r\n LibPaths:\r\n - /home/verbalins/R/x86_64-pc-linux-gnu-library/4.2\r\n - /usr/lib/R/library\r\n rmarkdown: 2.14\r\n\r\n[✓] Checking Knitr engine render......OK\r\n````\r\nOutput showing the error:\r\n````\r\n[1/3] index.qmd\r\n[2/3] intro.qmd\r\n[3/3] summary.qmd\r\n\r\npandoc \r\n to: latex\r\n output-file: index.tex\r\n template: _extensions/his/his-template.tex\r\n standalone: true\r\n toc: true\r\n number-sections: true\r\n top-level-division: chapter\r\n pdf-engine: lualatex\r\n variables:\r\n graphics: true\r\n tables: true\r\n default-image-extension: pdf\r\n cite-method: biblatex\r\n \r\nmetadata\r\n crossref:\r\n chapters: true\r\n documentclass: his-thesis\r\n papersize: null\r\n block-headings: true\r\n reference-section-title: References\r\n his-metadata:\r\n sammanfattning: Abstract in swedish\r\n publicationtype: licentiate\r\n printshop: 'Stema Specialtryck AB, Borås'\r\n isbn: 123-12-123456-X-X\r\n seriesnumber: XX\r\n coverimage: foto.jpg\r\n coverphoto: face.jpg\r\n fullarticles: |\r\n \\fullarticle[scale=.9,trim={0mm 5mm 0mm 5mm},pages=-]{fischer2017doctoraldissertationmanual}{style-guide/manual.pdf}[\\href{https://creativecommons.org/licenses/by-nc-nd/4.0/}{\\ccbyncnd}]\r\n \\fullarticle[scale=.9,trim={0mm 5mm 0mm 5mm},pages=1]{fischer2017doctoraldissertationmanual}{style-guide/manual.pdf}[\\copyright{} 2018 University of Skövde. Reprinted, with permission, from]\r\n \\fullarticle[scale=.9,trim={0mm 5mm 0mm 5mm},pages=1]{fischer2017doctoraldissertationmanual}{style-guide/manual.pdf}[Reprinted from][with permission from University of Skövde.]\r\n acronyms: |\r\n \\newacronym{moo}{MOO}{Multi-Objective Optimization}\r\n \\newacronym{sbo}{SBO}{Simulation-Based Optimization}\r\n \\newacronym{ai}{AI}{Artificial Intelligence}\r\n \\newacronym{doe}{DOE}{Design of Experiments}\r\n ownpublications: |\r\n \\authorspublication{fischer2017doctoraldissertationmanual}\r\n \\authorspublication[Design, manuscript preparation, review]{fischer2017doctoraldissertationmanual}\r\n classoption:\r\n - english\r\n - final\r\n - cover\r\n biblio-config: false\r\n suppress-bibliography: true\r\n link-citations: true\r\n colorlinks: false\r\n has-frontmatter: true\r\n lof: true\r\n lot: true\r\n english: true\r\n bibliography:\r\n - references.bib\r\n title: Title for this example thesis\r\n author: Author Authorsson\r\n date: '2022-08-23'\r\n abstract: Testing abstract\r\n \r\n(ERROR) PermissionDenied: Permission denied (os error 13), remove '/path/to/folder/thesis/logos/laurelbranch-rubin.pdf'\r\n\r\n````\r\n\n\n### Checklist\n\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 2,\n \"created_at\": \"2022-08-26T11:02:09Z\",\n \"creator\": \"verbalins\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.3\",\n \"number\": 2141,\n \"state\": \"closed\",\n \"title\": \"quarto template format-resources folder not removed in linux\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2141\"\n}"}}},{"rowIdx":1642,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nChange the default contents of index.qmd created in a new book project to:\r\n\r\n````md\r\n::: {.content-visible when-format=\"html\"}\r\n# Preface {.unnumbered}\r\n\r\nThis is a Quarto book.\r\n\r\nTo learn more about Quarto books visit .\r\n:::\r\n````\r\nThe compiled pdf file shows the chapter heading \"Preface\" but not the contents (This is a Quarto book...). It is my understanding that the chapter title should also be ignored?\r\n\r\nquarto check:\r\n````\r\n[✓] Checking Quarto installation......OK\r\n Version: 1.1.132\r\n Path: /opt/quarto/bin\r\n\r\n[✓] Checking basic markdown render....OK\r\n\r\n[✓] Checking Python 3 installation....OK\r\n Version: 3.10.6\r\n Path: /usr/bin/python3\r\n Jupyter: (None)\r\n\r\n Jupyter is not available in this Python installation.\r\n Install with python3 -m pip install jupyter\r\n\r\n[✓] Checking R installation...........OK\r\n Version: 4.2.1\r\n Path: /usr/lib64/R\r\n LibPaths:\r\n - /home/verbalins/R/x86_64-pc-linux-gnu-library/4.2\r\n - /usr/lib/R/library\r\n rmarkdown: 2.14\r\n\r\n[✓] Checking Knitr engine render......OK\r\n````\r\nquarto render -t all output:\r\n````\r\n1/4] index.qmd\r\n[2/4] intro.qmd\r\n[3/4] summary.qmd\r\n[4/4] references.qmd\r\n\r\npandoc \r\n to: latex\r\n output-file: index.tex\r\n standalone: true\r\n toc: true\r\n number-sections: true\r\n top-level-division: chapter\r\n pdf-engine: xelatex\r\n variables:\r\n graphics: true\r\n tables: true\r\n default-image-extension: pdf\r\n \r\nmetadata\r\n crossref:\r\n chapters: true\r\n documentclass: scrreprt\r\n papersize: letter\r\n classoption:\r\n - DIV=11\r\n - numbers=noendperiod\r\n header-includes:\r\n - '\\KOMAoption{captions}{tableheading}'\r\n block-headings: true\r\n bibliography:\r\n - references.bib\r\n title: repro\r\n author: Jane Doe\r\n date: 8/26/2022\r\n \r\nrunning xelatex - 1\r\n This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022/Arch Linux) (preloaded format=xelatex)\r\n restricted \\write18 enabled.\r\n entering extended mode\r\n \r\nrunning xelatex - 2\r\n This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022/Arch Linux) (preloaded format=xelatex)\r\n restricted \\write18 enabled.\r\n entering extended mode\r\n \r\n\r\nOutput created: _book/index.html\r\n````\n\n### Checklist\n\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 7,\n \"created_at\": \"2022-08-26T09:08:48Z\",\n \"creator\": \"verbalins\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"ast\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.4\",\n \"number\": 2140,\n \"state\": \"open\",\n \"title\": \"quarto book .content-visible ignored\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2140\"\n}"}}},{"rowIdx":1643,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nWhen using the chalkboard feature and adding some annotations in a speaker view setting, the annotations are not mirrored to the main presentation.\r\n\r\nThis is an issue as usually one looks at the speaker view during a presentation on the laptop while the main audience looks at the mirrored slides behind/beside the speaker. For speakers, it's not easy to spot that things are not synchronized.\r\n\r\nAdding annotations only on the main presentation view would require taking the mouse across screens which is fiddly and takes additional time.\r\n\r\nquarto v1.1.120\n\n### Checklist\n\n- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 3,\n \"created_at\": \"2022-08-26T07:58:52Z\",\n \"creator\": \"pat-s\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"upstream\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2139,\n \"state\": \"open\",\n \"title\": \"Chalkboard: annotations in speaker view are not mirrored to main presentation\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2139\"\n}"}}},{"rowIdx":1644,"cells":{"page_content":{"kind":"string","value":"I set up a connection to a database but Quarto throws an error when rendering (not if I execute the chunk). The same code in Rmarkdown works smoothly.\r\n\r\n```\r\nlibrary(dbplyr)\r\n\r\nconn <- DBI::dbConnect(RMySQL::MySQL(),\r\n host = \"my_hostname\",\r\n user = \"my_user\",\r\n password = Sys.getenv(\"PASSWORD_DB\"),\r\n dbname = \"my_db\",\r\n port=3306)\r\n\r\nmy_table <- tbl(conn, \"my_table\")\r\n```\r\nThis is the error:\r\n```\r\n#> Quitting from lines 11-28 (ECS_data_mining.qmd) \r\n#> Error in .local(drv, ...) : \r\n#> Failed to connect to database: Error: Access denied for user \r\n#> my_user'@'2a01:57a0:1608:6300:8818:75ea:8b53:6933' (using password: NO)\r\n#> Calls: .main ... eval -> -> -> .local -> .Call\r\n\r\n#> Execution halted\r\n```"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 7,\n \"created_at\": \"2022-08-26T07:37:35Z\",\n \"creator\": \"jospueyo\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2145,\n \"state\": \"closed\",\n \"title\": \"Problem when connecting to MySQL using environmental variables\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2145\"\n}"}}},{"rowIdx":1645,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nHello!\r\n\r\nI can't find functions for automating list of tables, list of figures and list of abbreviations in quarto book. These functionalities would be very useful for technical and academic reports.\r\n\r\nBest\r\n\r\nKo Ko Zaw \n\n### Checklist\n\n- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\n- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 7,\n \"created_at\": \"2022-08-26T07:23:59Z\",\n \"creator\": \"zawkzaw\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\",\n \"crossref\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.4\",\n \"number\": 2138,\n \"state\": \"open\",\n \"title\": \"list of tables, list of figures and list of abbreviations in quarto book \",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2138\"\n}"}}},{"rowIdx":1646,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nI'm redoing my website using a Quarto blog. When I have post set to eval: false with a SQL code chunk and an R code chunk, it looks fine. When I remove the R part, it changes formatting.\r\n\r\nTo reproduce, I have a blog post with each of these options:\r\n\r\n1) Blog post without R chunk.\r\n\r\n````\r\n---\r\ntitle: \"Test without R\"\r\ndate: \"2022-08-24\"\r\nexecute: \r\n eval: false\r\n---\r\n\r\n```{sql test}\r\nSELECT * FROM EXAMPLE;\r\n```\r\n\r\n![Test without R code](https://user-images.githubusercontent.com/15098268/186791358-28b8b09a-77f0-4d36-948d-79c68c563e9c.png)\r\n\r\n\r\n2) Same blog post, but with a blank R chunk at the end.\r\n---\r\ntitle: \"Test with R\"\r\ndate: \"2022-08-25\"\r\nexecute: \r\n eval: false\r\n---\r\n\r\n```{sql test}\r\nSELECT * FROM EXAMPLE;\r\n```\r\n\r\n```{r}\r\n```\r\n````\r\n\r\n![Test with R code](https://user-images.githubusercontent.com/15098268/186791368-8af62e5e-f6c7-4464-80a9-a8f811d75fd3.png)\r\n\r\n-----\r\n\r\nThe SQL section outputs are different.\r\n\r\nScreenshot of the first blog post. Formatting does not have syntax highlighting.\r\n![Test without R](https://user-images.githubusercontent.com/15098268/186791434-1f7e5381-3e22-4a58-bbee-35ac129e6188.png)\r\n\r\nScreenshot of the second blog post. This does have highlighting.\r\n![Test with R](https://user-images.githubusercontent.com/15098268/186791455-eba33902-20e5-4047-80d0-088abe085f3a.png)\r\n\r\nScreenshot of the home page. \r\n![Home page](https://user-images.githubusercontent.com/15098268/186791458-124f7373-b639-42ac-ac07-49a69f6d49e2.png)\r\n\r\nI don't know why they don't match. I just updated to the newest Quarto version (but I think it was happening on the previous one too). This is on RStudio 2022.07.1 Build 554. \"Spotted Wakerobin\" for macOS, on Monterey.\r\n\r\n\r\n\r\n### Checklist\r\n\r\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\r\n- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 2,\n \"created_at\": \"2022-08-26T00:37:26Z\",\n \"creator\": \"WilliamTylerBradley\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2137,\n \"state\": \"open\",\n \"title\": \"SQL chucks appear different with R chunks when eval is false\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2137\"\n}"}}},{"rowIdx":1647,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nUsing MS code, Anaconda with python 3.9.12, when selecting 'file new' if I select a .ipynb file it does nothing, however if I create a .qmb file, and then create a .ipynb it then appears. The MS code extensions I have installed are:\r\n\r\nms-toolsai.jupyter\r\nms-toolsai.jupyter-keymap\r\nms-toolsai.jupyter-renderers\r\nms-python.vscode-pylance\r\nms-python.python\r\nquarto.quarto\r\nREditorSupport.r\r\nRDebugger.r-debugger\r\n\r\nThis occurs on more than one machine, windows 10 professional:\r\n\r\nEdition\tWindows 10 Pro\r\nVersion\t20H2\r\nInstalled on\t‎03/‎08/‎2022\r\nOS build\t19042.1706\r\nExperience\tWindows Feature Experience Pack 120.2212.4170.0\r\n\r\n\r\n### Checklist\r\n\r\n- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\r\n- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 2,\n \"created_at\": \"2022-08-25T21:50:08Z\",\n \"creator\": \"Eclecticdata\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"needs-repro\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2135,\n \"state\": \"closed\",\n \"title\": \"new ipynb file not appearing until a new .qmd file is created\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2135\"\n}"}}},{"rowIdx":1648,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\ntest code\r\n\r\n````md\r\n---\r\ntitle: 'debug code fold'\r\nformat:\r\n html:\r\n code-fold: true\r\n embed-resources: true\r\n standalone: true\r\nexecute:\r\n cache: false\r\n echo: false\r\n---\r\n\r\n```{ojs}\r\n1+1\r\n```\r\n````\r\n\r\noutput:\r\n\r\n![image](https://user-images.githubusercontent.com/5415510/186770778-d1a1f1b3-6f8a-45f1-9c4c-5bf27c3ced5c.png)\r\n\r\n\r\nThis bug is caused by `code-fold: true` in the header. When remove this line, the rendering is ok. But it would better to check if echo == Ture before display the code fold mark.\r\n\r\n### Checklist\r\n\r\n- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.\r\n- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 1,\n \"created_at\": \"2022-08-25T21:18:23Z\",\n \"creator\": \"y9c\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2134,\n \"state\": \"closed\",\n \"title\": \"code-fold still exist even if `echo` is set as false\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2134\"\n}"}}},{"rowIdx":1649,"cells":{"page_content":{"kind":"string","value":"I've been doing a lot of work on the shell scripts, and there's been some headache around platform-specific syntax. I saw some of that in my conda days. The only real way to avoid the headache is to strive for POSIX compliance, which can be something of a headache unto itself.\r\n\r\nThe first part of this proposal is to:\r\n* Add a shellcheck step to our CI to show our status\r\n* Make an effort to get our scripts into POSIX compliance\r\n\r\nThe second part of this proposal is to create native, standalone executables to replace our shell scripts. This is really only relevant to the `quarto` and `quarto.cmd` scripts. Native executables are not mutually exclusive with POSIX compatibility. Each part should be considered in terms of what goes into installers/packages and what only developers use. \r\n\r\nThe argument for POSIX compliance in our dev scripts is much weaker than the argument for it in the end-user scripts. It's reasonable to establish some BASH requirement for our dev scripts.\r\n\r\nWhat this really boils down to is that it would be good to have the end-user scripts be POSIX compliant or be replaced by a standalone compiled executable (go, rust, whatever is easiest and most completely standalone)."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 3,\n \"created_at\": \"2022-08-25T17:19:01Z\",\n \"creator\": \"msarahan\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2128,\n \"state\": \"closed\",\n \"title\": \"Proposal: posix compliance in shell scripts; native compiled launcher\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2128\"\n}"}}},{"rowIdx":1650,"cells":{"page_content":{"kind":"string","value":"
\r\n\r\nOriginally posted by **cbrnr** August 25, 2022\r\nI created a website with `quarto create-project website --type website`. In `_quarto.yml` I changed the `theme` to `flatly` because the issue is more pronounced with this theme (but it also occurs with the default `cosmo` theme).\r\n\r\nThen after `quarto preview`, repeatedly click on \"Home\" in the navbar (or switch between \"Home\" and \"About\"). Notice when the corresponding page is rendered, the main text jumps down a little. Here's a screen recording to show what I mean:\r\n\r\nhttps://user-images.githubusercontent.com/4377312/186645355-abfbcc48-3137-4889-97ad-01a7e666f004.mov\r\n\r\nAny ideas how to fix this behavior? I'm using Quarto 1.0.36 (part of RStudio) on macOS.
"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 1,\n \"created_at\": \"2022-08-25T16:09:46Z\",\n \"creator\": \"cscheid\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2126,\n \"state\": \"closed\",\n \"title\": \"Website text \\\"jumps\\\" when rendered\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2126\"\n}"}}},{"rowIdx":1651,"cells":{"page_content":{"kind":"string","value":"e.g.\r\n\r\n````markdown\r\n```{python}\r\n#| output: asis\r\n%%javascript\r\n\r\n// some JS code\r\n```\r\n````\r\n\r\nThis is because cell magics need to be the first line of the cell. \r\n\r\nNote that the `keep-ipynb` feature is really designed for debugging rather than for producing a final notebook for distribution (e.g. markdown constructs like citations and crossrefs are not resolved in this version). We should either resolve this or make it more clear in the documentation that `keep-ipynb` is for debugging intermediate representations (we could even change the filename to make this more clear).\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 7,\n \"created_at\": \"2022-08-25T12:25:17Z\",\n \"creator\": \"jjallaire\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.4\",\n \"number\": 2123,\n \"state\": \"open\",\n \"title\": \"keep-ipynb notebook with cell magics and yaml options can't be executed\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2123\"\n}"}}},{"rowIdx":1652,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nCurrently in the doc for engine binding regarding computation chunk (https://quarto.org/docs/computations/execution-options.html#engine-binding) we have mention of two things regarding Markdown file : \r\n\r\n* The table about auto-binding shows `.md` is supported, and no engine will be used \r\n![image](https://user-images.githubusercontent.com/6791940/186656973-e298287c-2c38-482e-806b-5c14fdbbd647.png)\r\n\r\n\r\n* `engine: markdown` can be used to deactivate engine\r\n > You can also specify that no execution engine should be used via engine: markdown.\r\n\r\n\r\nHowever, we have a check for computation chunk inside `.md` document that prevent any rendering at all \r\nhttps://github.com/quarto-dev/quarto-cli/blob/71310bfd92ce7240042dd29f96a6f305690feb23/src/execute/markdown.ts#L67-L75\r\n\r\nWhich leads to \r\n````\r\n> quarto render test.md --to html\r\nERROR: You must use the .qmd extension for documents with executable code.\r\n````\r\n\r\nAs discussed with @jjallaire \r\n> That error is I think more helpful than not because if you have code cells in your .md you definitely aren't getting what you expected (the code won't execute). We could indeed silently send this to pandoc but I sort of view that as similar to eating bad YAML schema. Longer term its better for the user to clean this up.\r\n\r\nShould we maybe update the documentation to clearly state that `.md` document works with quarto only if there is no computation chunk ? Or at least remove the `.md` line from the table ? "},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 1,\n \"created_at\": \"2022-08-25T11:54:31Z\",\n \"creator\": \"cderv\",\n \"is_pull_request\": false,\n \"labels\": [\n \"documentation\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2122,\n \"state\": \"closed\",\n \"title\": \"Adapt the documentation about .md document with computation chunk\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2122\"\n}"}}},{"rowIdx":1653,"cells":{"page_content":{"kind":"string","value":""},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 1,\n \"created_at\": \"2022-08-25T11:34:32Z\",\n \"creator\": \"jjallaire\",\n \"is_pull_request\": false,\n \"labels\": [\n \"books\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.3\",\n \"number\": 2120,\n \"state\": \"closed\",\n \"title\": \"support globs for book chapter lists\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2120\"\n}"}}},{"rowIdx":1654,"cells":{"page_content":{"kind":"string","value":"Issue https://github.com/quarto-dev/quarto-cli/issues/2113 is a problem that I caused by not considering that symlinks to the quarto binary may be relative. Our dev configuration makes absolute path symlinks, and we don't otherwise have a check for this use case. It seems like we should add something to the CI process to test this behavior."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 0,\n \"created_at\": \"2022-08-25T00:54:18Z\",\n \"creator\": \"msarahan\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2114,\n \"state\": \"open\",\n \"title\": \"Need test for relative symlinks to Quarto\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2114\"\n}"}}},{"rowIdx":1655,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nI am currently maintaining a set of homebrew formulae (for MacOS) for both quarto and quarto-dev, a user just reported (rundel/homebrew-quarto-cli#37) that as of v1.1.113 they are getting an error when running quarto installed using this formula. Specifically,\r\n```\r\n> quarto preview\r\nusage: basename string [suffix]\r\n basename [-a] [-s suffix] string [...]\r\nERROR: Cannot determine the Quarto source path. This script must be run from the bin or common folder.\r\n```\r\nthis is still occurring with the latest pre-release (v1.1.119).\r\n\r\nThese formulae are installing the files from the `quarto-1.1.119-macos.tar.gz` assest into a homebrew cellar which are then symlinked into `/opt/homebrew`. The issue appears to be with how the primary quarto shell script is handling the construction of [`SCRIPT_PATH`](https://github.com/quarto-dev/quarto-cli/blob/1fbd4124cc00101f19601adbccd3ccc3474f6e1e/package/scripts/common/quarto#L4-L13) when the symlink is a relative path.\r\n\r\n```\r\n> ls -la /opt/homebrew/bin/quarto \r\nlrwxr-xr-x 1 rundel admin 39 Aug 24 17:54 /opt/homebrew/bin/quarto -> ../Cellar/quarto-dev/1.1.119/bin/quarto\r\n```\r\n\r\nFor this case it appears that https://github.com/quarto-dev/quarto-cli/blob/1fbd4124cc00101f19601adbccd3ccc3474f6e1e/package/scripts/common/quarto#L8\r\ndoes not work as a relative path is not handled properly by `cd` since this is relative to where the script was invoked and not where the script lives.\r\n\r\nThe breaking changes seem to be part of #2015.\r\n\r\n\r\n\n\n### Checklist\n\n- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 6,\n \"created_at\": \"2022-08-25T00:03:55Z\",\n \"creator\": \"rundel\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2113,\n \"state\": \"closed\",\n \"title\": \"SCRIPT_PATH discovery is broken for relative symlinks \",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2113\"\n}"}}},{"rowIdx":1656,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nThis bug is essentially #1141 but applied to citations in captions when using footnote citation styles. This Markdown doesn't work:\r\n\r\n```md\r\n---\r\ncsl: oxford-university-press-note.csl\r\n---\r\n![A schematic diagram of known types of viroid-like agents. This figure was published in [@Lee2021a].](figures/viroid-like-schematic.png)\r\n```\r\n\r\nThe error message also parallels #1141:\r\n\r\n```\r\ncompilation failed- error\r\nArgument of \\caption@ydblarg has an extra }.\r\n\r\n \\par\r\nl.324 ...1093/nar/gkab974}{10.1093/nar/gkab974}.}}\r\n```\r\n\r\n### Checklist\r\n\r\n- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?\r\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\r\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 1,\n \"created_at\": \"2022-08-24T22:54:16Z\",\n \"creator\": \"Benjamin-Lee\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2112,\n \"state\": \"closed\",\n \"title\": \"Footnote-style citation in figure caption crashed PDF render\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2112\"\n}"}}},{"rowIdx":1657,"cells":{"page_content":{"kind":"string","value":"Per previous conversations @cscheid --\r\nQuarto websites are fantastic for individual websites, but features are lacking for group or organization websites. The Hugo Academic framework enabled a taxonomy across the site for aggregating publications by author in a seamless manner. Quarto Listings are a start to this but need some ability to flag authors on publication entries and then aggregate each respective authors' publications on their individual page within the site. \r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 6,\n \"created_at\": \"2022-08-24T20:56:34Z\",\n \"creator\": \"kmasiello\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"v1.4\",\n \"number\": 2110,\n \"state\": \"open\",\n \"title\": \"Better frameworks for organization-centric websites \",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2110\"\n}"}}},{"rowIdx":1658,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nCode:\r\n\r\n````md\r\n---\r\ntitle: \"test webpage\"\r\nformat:\r\n html:\r\n code-fold: true\r\nexecute:\r\n cache: true\r\njupyter: python3\r\n---\r\n\r\n\r\n```{python}\r\n#| label: fig-demo\r\n#| fig-cap: \"This is a demo figure for debug\"\r\n\r\nfrom bokeh.io import output_notebook\r\noutput_notebook(hide_banner=True)\r\n\r\nfrom bokeh.palettes import Spectral5\r\nfrom bokeh.plotting import figure, show\r\nfrom bokeh.sampledata.autompg import autompg as df\r\nfrom bokeh.transform import factor_cmap\r\n\r\ndf.cyl = df.cyl.astype(str)\r\ngroup = df.groupby('cyl')\r\ncyl_cmap = factor_cmap('cyl', palette=Spectral5, factors=sorted(df.cyl.unique()))\r\np = figure(height=350, x_range=group, title=\"MPG by # Cylinders\", toolbar_location=None, tools=\"\")\r\np.vbar(x='cyl', top='mpg_mean', width=1, source=group, line_color=cyl_cmap, fill_color=cyl_cmap)\r\nshow(p)\r\n```\r\n````\r\n\r\nOutput:\r\n\r\n![image](https://user-images.githubusercontent.com/5415510/186504610-7b9a4437-45b5-461d-b2bc-570ee8a45dd0.png)\r\n\r\n\r\nThe subfigure 1b and 1c is empty and should be exist. \r\n\r\n### Checklist\r\n\r\n- [x] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?\r\n- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\r\n- [x] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 9,\n \"created_at\": \"2022-08-24T19:19:42Z\",\n \"creator\": \"y9c\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"needs-discussion\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.3\",\n \"number\": 2107,\n \"state\": \"closed\",\n \"title\": \"A single bokeh plot will be wrongly identified as several subfigures. \",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2107\"\n}"}}},{"rowIdx":1659,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nThe ipynb may be there from keep-ipynb or just not cleaned up from a previous render error\n\n### Checklist\n\n- [ ] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?\n- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 1,\n \"created_at\": \"2022-08-24T17:02:21Z\",\n \"creator\": \"jjallaire\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2101,\n \"state\": \"closed\",\n \"title\": \"index.qmd and index.ipynb causes rendering error in website\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2101\"\n}"}}},{"rowIdx":1660,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nHi, thank you for your amazing work.\r\n\r\nI'm trying to add an audio file to my blog, and I get a Babushka-like bug: The audio is being rendered but every time a get another copy of \"_site\" inside the previous \"_site\" file.\r\n\r\nI made a reprex of the problem:\r\n\r\n### Rendered Blog (everything is working well here):\r\nhttps://reproduce-bug-audio.netlify.app/about.html\r\n\r\n### Github Links:\r\n- Reprex of the blog: https://github.com/uriahf/reproduce_bug_audio\r\n- YMAL call for resources: https://github.com/uriahf/reproduce_bug_audio/blob/a262d13fced8ab6010b33bdb1c6527d434db35f5/about.qmd#L16-L19\r\n- Babushka-like _site files https://github.com/uriahf/reproduce_bug_audio/tree/main/_site/_site/_site/_site/_site/_site/_site/_site\r\n- Commits (one for each time I rendered the quarto file): https://github.com/uriahf/reproduce_bug_audio/commits/main\r\n\r\n### My Rstudio IDE version:\r\nRStudio 2022.07.1+554 \"Spotted Wakerobin\" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows\r\nMozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36\r\n\r\nMy OS is windows.\r\n\r\n![](https://images.rawpixel.com/image_800/cHJpdmF0ZS9zdGF0aWMvaW1hZ2Uvd2Vic2l0ZS8yMDIyLTA0L2xyL2ZybWF0cmlvc2hrYV93b29kZW5fY3VsdHVyZV9zeW1ib2xfMC1pbWFnZS1reWJiMHRrdi5qcGc.jpg)\n\n### Checklist\n\n- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 0,\n \"created_at\": \"2022-08-24T14:03:38Z\",\n \"creator\": \"uriahf\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2097,\n \"state\": \"closed\",\n \"title\": \"Adding audio file to quarto-blog creates \\\"_site\\\" new nested file each time that the site is being rendered.\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2097\"\n}"}}},{"rowIdx":1661,"cells":{"page_content":{"kind":"string","value":"I've seen many users put document level YAML options in the `project` and `website` keys. This does not get reported as an error b/c those schemas aren't closed. I think we need to close up schemas that can be right away as the longer we wait the more projects/documents will be broken when we do (or at the limit we can never close them)."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 2,\n \"created_at\": \"2022-08-24T13:53:16Z\",\n \"creator\": \"jjallaire\",\n \"is_pull_request\": false,\n \"labels\": [\n \"yaml-validation\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.1\",\n \"number\": 2096,\n \"state\": \"closed\",\n \"title\": \"close yaml schemas that can be closed\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2096\"\n}"}}},{"rowIdx":1662,"cells":{"page_content":{"kind":"string","value":"I've created a new Quarto book project. When I render the provided example in HTML format (without having made any changes), the search index appears to be incomplete.\r\n\r\nExample: The file `intro.qmd` begins like this:\r\n\r\n```\r\n# Introduction\r\n\r\nThis is a book created from markdown and executable code.\r\n\r\nSee @knuth84 for additional discussion of literate programming.\r\n\r\n```\r\n\r\nThe corresponding part in `search.json` however looks like this:\r\n\r\n```\r\n {\r\n \"objectID\": \"intro.html\",\r\n \"href\": \"intro.html\",\r\n \"title\": \"1  Introduction\",\r\n \"section\": \"\",\r\n \"text\": \"See Knuth (1984) for additional discussion of literate programming.\"\r\n }\r\n```\r\n\r\nThe same issue occurs with `summary.qmd`.\r\n\r\n```\r\nR version 4.2.1 (2022-06-23)\r\nPlatform: aarch64-apple-darwin20 (64-bit)\r\nRunning under: macOS Big Sur 11.6.8\r\nRStudio version: 2022.07.1 Build 554\r\nQuarto version: 1.1.113\r\n```\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 0,\n \"created_at\": \"2022-08-24T13:22:07Z\",\n \"creator\": \"jderrfuss\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2095,\n \"state\": \"closed\",\n \"title\": \"search.json appears to be incomplete\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2095\"\n}"}}},{"rowIdx":1663,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nTake this example where we have a very wide code chunk\r\n\r\n`````markdown\r\n---\r\ntitle: \"Untitled\"\r\nformat: revealjs\r\nexecute: \r\n echo: true\r\n---\r\n\r\n## Slides 1\r\n\r\n```{r}\r\n#| output-location: column\r\n\r\nlibrary(ggplot2)\r\nggplot(airquality, aes(Temp, Ozone)) + geom_point() + geom_smooth(method = \"loess\")\r\n```\r\n`````\r\n\r\nThis is what we get with stable quarto \r\n![image](https://user-images.githubusercontent.com/6791940/186413711-3f269b45-da48-459f-8c44-adf240d7e58c.png)\r\n\r\n\r\nThis is what we get with pre-release\r\n\r\n![image](https://user-images.githubusercontent.com/6791940/186413399-f17f574a-7668-49a9-90d0-16b782be1b1b.png)\r\n\r\nThe second column is outside the slide\r\n![image](https://user-images.githubusercontent.com/6791940/186413522-c76a638d-0441-4259-bf5a-e25f3b7051bc.png)\r\n\r\n\r\nPossibly related to this change: https://github.com/quarto-dev/quarto-cli/commit/a43090353c454860dca50164f06896dec5a48968 to try fixing https://github.com/quarto-dev/quarto-cli/issues/1940 as `flex` is replacing `width`\r\n\r\n![image](https://user-images.githubusercontent.com/6791940/186413851-d41ded98-4296-4dda-9c25-d854aff5bc58.png)\r\n\r\nThis came up from a discussion in https://github.com/quarto-dev/quarto-cli/discussions/2088#discussioncomment-3464422\r\n\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 1,\n \"created_at\": \"2022-08-24T12:05:30Z\",\n \"creator\": \"cderv\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.1\",\n \"number\": 2093,\n \"state\": \"closed\",\n \"title\": \"output-location to column does not work anymore for revealjs\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2093\"\n}"}}},{"rowIdx":1664,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nI don't know what `xfun::session_info()` is, hopefully the GH issue works without that?? (from the link with instructions to follow...)\r\n\r\nI am following this tutorial:\r\n\r\nhttps://quarto.org/docs/get-started/authoring/jupyter.html\r\n\r\nand am using `nb_conda_kernel` to manage my Jupyter kernels from different environments.\r\nThis leads to notebook metadata having different kernelspec metadata than what are available.\r\n\r\nHowever, this should not matter, as the YAML doc options should precede those kind of findings, but I find that that is not the case.\r\n\r\nHere's my whole notebook:\r\n\r\n```json\r\n{\r\n \"cells\": [\r\n {\r\n \"cell_type\": \"raw\",\r\n \"id\": \"563ca2fc-b9a0-4e94-ab33-a511b79debe4\",\r\n \"metadata\": {},\r\n \"source\": [\r\n \"---\\n\",\r\n \"title: \\\"Quarto Document\\\"\\n\",\r\n \"author: \\\"Michael Aye\\\"\\n\",\r\n \"toc: true\\n\",\r\n \"number-sections: true\\n\",\r\n \"highlight-style: pygments\\n\",\r\n \"format:\\n\",\r\n \" html:\\n\",\r\n \" code-fold: false\\n\",\r\n \" html-math-method: katex\\n\",\r\n \" pdf:\\n\",\r\n \" geometry:\\n\",\r\n \" - top=30mm\\n\",\r\n \" - left=20mm\\n\",\r\n \" docx: default \\n\",\r\n \"jupyter: python3\\n\",\r\n \"---\"\r\n ]\r\n },\r\n {\r\n \"cell_type\": \"markdown\",\r\n \"id\": \"86065445-3aab-4e52-ad26-2edf63ff1670\",\r\n \"metadata\": {},\r\n \"source\": [\r\n \"# Test\\n\",\r\n \"\\n\",\r\n \"This is a test.\"\r\n ]\r\n },\r\n {\r\n \"cell_type\": \"code\",\r\n \"execution_count\": null,\r\n \"id\": \"a5fa2a9c-093f-4558-a4b9-686e684c6d59\",\r\n \"metadata\": {},\r\n \"outputs\": [],\r\n \"source\": [\r\n \"2+2\"\r\n ]\r\n }\r\n ],\r\n \"metadata\": {\r\n \"kernelspec\": {\r\n \"display_name\": \"Python [conda env:py310] *\",\r\n \"language\": \"python\",\r\n \"name\": \"conda-env-py310-py\"\r\n }\r\n },\r\n \"nbformat\": 4,\r\n \"nbformat_minor\": 5\r\n}\r\n```\r\n\r\nHere are the available kernels, note the matching `python3` kernel name, fitting the doc options.\r\n\r\n```bash\r\n/Dropbox/src/quarto_hello ❯ jupyter kernelspec list\r\n[ListKernelSpecs] WARNING | Config option `kernel_spec_manager_class` not recognized by `ListKernelSpecs`.\r\nAvailable kernels:\r\n python3 /home/ayek72/mambaforge/envs/py310/share/jupyter/kernels/python3\r\n xonsh /usr/share/jupyter/kernels/xonsh\r\n```\r\nand here's what `quarto` says:\r\n\r\n```\r\n~/Dropbox/src/quarto_hello ❯ quarto render formats.ipynb --to html --execute\r\nERROR: \r\n\r\nNo such kernel named conda-env-py310-py\r\n```\r\n\r\nFor reference, here's my output of `quarto check`:\r\n```bash\r\n~/Dropbox/src/quarto_hello ❯ quarto check\r\n\r\n[✓] Checking Quarto installation......OK\r\n Version: 1.0.37\r\n Path: /opt/quarto/bin\r\n\r\n[✓] Checking basic markdown render....OK\r\n\r\n[✓] Checking Python 3 installation....OK\r\n Version: 3.10.5 (Conda)\r\n Path: /home/ayek72/mambaforge/envs/py310/bin/python\r\n Jupyter: 4.11.1\r\n Kernels: python3, xonsh\r\n\r\n[✓] Checking Jupyter engine render....OK\r\n\r\n[✓] Checking R installation...........(None)\r\n\r\n Unable to locate an installed version of R.\r\n Install R from https://cloud.r-project.org/\r\n\r\n```\r\n\r\nI don't know what a QMD file is, but with above notebook json and the commands, it should be easily reproducible. It simply seems to be the case that `quarto` looks at the notebook metadata first instead of looking at the YAML docoptions first.\r\n\r\n## OS\r\n\r\n```\r\n~/Dropbox/src/quarto_hello ❯ uname -a\r\nLinux apollo.planet.fu-berlin.de 5.15.0-46-generic #49~20.04.1-Ubuntu SMP Thu Aug 4 19:15:44 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux\r\n```\r\nRunning a KDE Neon : \r\n![image](https://user-images.githubusercontent.com/69774/186401244-b94bbd27-83eb-40d3-af9d-050bfd04aa3b.png)\r\n\n\n### Checklist\n\n- [ ] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 1,\n \"created_at\": \"2022-08-24T10:55:16Z\",\n \"creator\": \"michaelaye\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2091,\n \"state\": \"closed\",\n \"title\": \"quarto --execute ignores jupyter kernel name in yaml doc options\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2091\"\n}"}}},{"rowIdx":1665,"cells":{"page_content":{"kind":"string","value":"At https://quarto.org/docs/presentations/revealjs/presenting.html, there is a section on the Navigation Menu. It gives an example of the `side`, `width` and `number` options:\r\n\r\n``` \r\nformat:\r\n revealjs:\r\n side: right\r\n width: wide\r\n```\r\n\r\nHowever, this does not seem to work. Autocompletion in the yaml header also doesn't mention these options. Well, it does mention the `width` option, but that's for the overall presentation, not the nav menu.\r\n\r\nBorrowing from the documentation for revealjs in RMarkdown (https://github.com/rstudio/revealjs), this does seem to work:\r\n\r\n``` \r\nformat:\r\n revealjs:\r\n menu:\r\n side: right\r\n width: wide\r\n```\r\n\r\nHowever, this implementation seems to obliviate the option to not show the hamburger, which is done as follows:\r\n\r\n``` \r\nformat:\r\n revealjs:\r\n menu: false\r\n```\r\n\r\nbecause you can either give `menu: false` OR `menu: <>` in the yaml section. There is no option for not showing the hamburger thingy AND having options for the case where you do want to open the menu (hitting the `M` key).\r\n\r\nSo, two things: \r\n* There's an error in the documentation\r\n* A suboption in the `menu` option list (besides `side`, `width`, `numbers` and `use-text-content-for-missing-titles`) for not showing the hamburger would be nice (e.g., `show-hamburger: true/false`).\r\n\r\nTo be clear, the second bullet refers to something like this:\r\n\r\n```\r\nformat:\r\n revealjs:\r\n menu:\r\n side: right\r\n width: wide\r\n show-hamburger: false\r\n```\r\n\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 1,\n \"created_at\": \"2022-08-24T07:48:45Z\",\n \"creator\": \"mathijsdeen\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\",\n \"revealjs\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 3376,\n \"state\": \"open\",\n \"title\": \"documentation error on navigation menu in revealjs\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/3376\"\n}"}}},{"rowIdx":1666,"cells":{"page_content":{"kind":"string","value":"Really excited about quarto, but coming from blogdown/hugo world I'm struggling to understand how custom SASS themes work. In particular, I've read https://quarto.org/docs/output-formats/html-themes-more.html#bootswatch-sass-theme-files, which says:\r\n\r\n> We’ve merged Bootswatch themes for Bootstrap 5 into this single file theme format in our repo here:\r\n> https://github.com/twbs/bootstrap/blob/main/scss/_variables.scss\r\n\r\nerr... is that the correct link? That appears to be the (unmerged?) official bootstrap-5 sources of the Bootstrap team, not a merged scss file in \"our repo\"? (trying to better understand this single-file format deal). \r\n\r\nMore generally, it's not clear how I would go about bringing in external bootstrap-based SASS themes. For instance, I rather like the MIT-licensed bootstrap-5 themes from CreativeTim, like https://github.com/creativetimofficial/material-kit. It seems like to work with quarto, I need to refactor that whole sass stack into a single .scss file, ordered specifically as quarto expects, with the five decorations described in the above link? (e.g. ` /*-- scss:uses --*/`, `/*-- scss:functions --*/`). Is that correct? Or do I just need to convert my sass theme to a bootswatch theme (al al https://bootswatch.com/help/#customization) ?\r\n\r\nMaybe just my ignorance here in these things, but manually refactoring perfectly good SASS code seems like a significant and somewhat cumbersome and needless design -- e.g. compared to converting material-kit or other bootstrap-based SASS templates into hugo themes which was super straight-forward. Maybe the answer is that users who want lower-level customization should just stick with hugo and this is out of scope for quarto? All the same, I had hoped that quarto would lower rather than raise the barrier for user-contributed themes. Sorry if I'm just confused?\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 2,\n \"created_at\": \"2022-08-24T00:35:56Z\",\n \"creator\": \"cboettig\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2086,\n \"state\": \"closed\",\n \"title\": \"Questions/ need more advice on extending themes ?\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2086\"\n}"}}},{"rowIdx":1667,"cells":{"page_content":{"kind":"string","value":"This came up in https://github.com/quarto-ext/code-filename/issues/4\r\n\r\nQuarto allows to install from a file (https://quarto.org/docs/extensions/distributing.html#archive-files) but expect a specific structure. When downloading from Github source, there is a parent folder to the repo folder. \r\n\r\nWe could maybe check for that structure instead of just directly looking for the `_extensions` folder.\r\n\r\nSee discussion in the issue link\r\n\r\ncc @dragonstyle \r\n\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 2,\n \"created_at\": \"2022-08-23T19:11:17Z\",\n \"creator\": \"cderv\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"extensions\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2081,\n \"state\": \"closed\",\n \"title\": \"Installing extension from Git archive repo does not work\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2081\"\n}"}}},{"rowIdx":1668,"cells":{"page_content":{"kind":"string","value":"Tag @dragonstyle per discussion, here are the pre-release references. It might be helpful to formalize the strategy of if y'all do or do not want to indicate a minimum version when introducing new features that aren't backported.\r\n\r\nReference to 0.9: [Mermaid Diagrams](https://github.com/quarto-dev/quarto-web/blob/5a79cba1d466d55da139cd447c9f3fe1fc812d4d/docs/authoring/diagrams.qmd#L22)\r\nReference to 1.0.15: [Shortcodes](https://github.com/quarto-dev/quarto-web/blob/5a79cba1d466d55da139cd447c9f3fe1fc812d4d/docs/extensions/shortcodes.qmd#L105)\r\nReference to 0.9: [YAML Intelligence](https://github.com/quarto-dev/quarto-web/blob/5a79cba1d466d55da139cd447c9f3fe1fc812d4d/docs/tools/vscode.qmd#L124)\r\n\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 5,\n \"created_at\": \"2022-08-23T18:44:20Z\",\n \"creator\": \"jthomasmock\",\n \"is_pull_request\": false,\n \"labels\": [\n \"documentation\",\n \"needs-discussion\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.3\",\n \"number\": 4463,\n \"state\": \"closed\",\n \"title\": \"Reference to old or pre-release RStudio/Quarto versions\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/4463\"\n}"}}},{"rowIdx":1669,"cells":{"page_content":{"kind":"string","value":"Allowing variable overrides in batch scripts is hairy because of the need for complicated `startlocal enabledelayedexpansion` stuff. It makes our scripts fragile and limits the number of people who are willing to work on them. I propose that we cut `configure.cmd` completely, and run configure.sh on all platforms.\r\n\r\nWhat this requires is the use of msys2 or git for windows. WSL is not useful here, it behaves like a linux system for the sake of our scripts instead of a bash-on-windows thing.\r\n\r\nWe clearly can't require this on end user systems for our quarto.cmd script. This proposal is only for development. The quarto.cmd script doesn't present the same override headaches anyway, so it's not a big deal there.\r\n\r\nI will put up a PR showing that configure.sh can run fine on windows. If that is satisfactory, then maybe we can consider removing configure.cmd."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 3,\n \"created_at\": \"2022-08-23T13:47:26Z\",\n \"creator\": \"msarahan\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2071,\n \"state\": \"open\",\n \"title\": \"Proposal: use bash on windows for configure\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2071\"\n}"}}},{"rowIdx":1670,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nI'm unable to schedule a cron job to automatically render/publish a quarto website. The command get executed but the log just shows an empty line (like the output you get when you just execute quarto without any parameter).\r\n\r\nThis is the entry in my cron schedule file (linux/debian). The exact same command works when executed in the terminal.\r\n\r\n`*/10 * * * * /usr/local/bin/quarto publish --no-prompt --no-browser quarto-pub '/home/rstudio/mine_2022/' >> '/home/rstudio/mine_2022/siteupdate.log' 2>&1`\r\n\r\nI was not able to find documentation on how to schedule such a command.\r\n\r\nThank you in advance for your help. Best, Fabio\n\n### Checklist\n\n- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 2,\n \"created_at\": \"2022-08-23T09:42:54Z\",\n \"creator\": \"fabiogiglietto\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2066,\n \"state\": \"closed\",\n \"title\": \"Schedule quarto publish with cron\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2066\"\n}"}}},{"rowIdx":1671,"cells":{"page_content":{"kind":"string","value":"When using `quarto` to build websites, some static site generators, for instance `mkdocs`, create sites with \"pretty\" URLs by default. It would be great if Quarto also did this.\r\n\r\nFor instance, in a project containing the file `science.md`, `quarto render` will generate that as `science.html`, resulting in a URL like, `https://example.com/science.html`. In contrast, `mkdocs build` would generate it as `science/index.html`, meaning that, when published, it could be accessed at `https://example.com/science/`.\r\n\r\nThe current workaround would be to create the original file at `science/index.md`, in which case, both `quarto` and `mkdocs` would generate the same HTML in the same places.\r\n\r\nThis is important for sites that might be considering migrating to `quarto` that are not currently structured along the lines of the workaround."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 1,\n \"created_at\": \"2022-08-23T09:02:29Z\",\n \"creator\": \"sellorm\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2065,\n \"state\": \"open\",\n \"title\": \"Quarto should output websites with \\\"pretty\\\" URLs\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2065\"\n}"}}},{"rowIdx":1672,"cells":{"page_content":{"kind":"string","value":"I find the ability to insert tikz pictures by simply calling `![caption](tikz_code.tex){#label}` when rendering to PDF to be extremely elegant and practical, unfortunately the pictures do not seem to render for HTML outputs.\r\n\r\nTrying to find a workaround I found the [TikZJax](https://github.com/kisonecat/tikzjax) library. It looks like it could be helpfu for this. "},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 0,\n \"created_at\": \"2022-08-23T07:41:08Z\",\n \"creator\": \"Matrsz\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2064,\n \"state\": \"open\",\n \"title\": \"Feature Request: Rendering TikZ pictures for HTML output\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2064\"\n}"}}},{"rowIdx":1673,"cells":{"page_content":{"kind":"string","value":"Currently the callout blocks visible text stays the same if the block is collapsed or expanded, like here:\r\nCollapsed:\r\n\"image\"\r\nExpanded:\r\n\"image\"\r\n\r\nWould it make sense to have different text for when be block is collapsed: \"Expand to see me\" and different when it's expanded: \"Collapse to hide me\"?"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 0,\n \"created_at\": \"2022-08-23T06:10:17Z\",\n \"creator\": \"miwojc\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2063,\n \"state\": \"open\",\n \"title\": \"[feature request] change visible text for callout blocks when collapsed/expanded\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2063\"\n}"}}},{"rowIdx":1674,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nWhen I choose `revealjs` as a `format` for a `qmd` document, it does not render `width` variable from `ojs` properly.\r\n````{qmd}\r\n---\r\nformat: revealjs\r\n---\r\n## DEMO\r\n\r\n```{ojs}\r\nmd`${width}`\r\n```\r\n````\r\n![image](https://user-images.githubusercontent.com/10469752/186004708-b1e97dbf-8c70-4f34-8035-35b9c0de83e2.png)\r\n\r\n\r\nWhen I render it as `html`, it works well.\r\n![image](https://user-images.githubusercontent.com/10469752/186004760-8875e7bd-91be-424c-bcf8-f6d1a42ad4ff.png)\r\n\r\nOS: mac air m1 Venture 13.0 Beta 22A5321d\n\n### Checklist\n\n- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?\n- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well."},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 3,\n \"created_at\": \"2022-08-22T19:45:45Z\",\n \"creator\": \"kwangkim\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"ojs-engine\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2058,\n \"state\": \"closed\",\n \"title\": \"[revealjs] ojs runtime error: Cannot read properties of null (reading 'clientWidth') from width\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2058\"\n}"}}},{"rowIdx":1675,"cells":{"page_content":{"kind":"string","value":"### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2056\r\n\r\n
\r\n\r\nOriginally posted by **Hedonical** August 22, 2022\r\nHi everyone,\r\n\r\nI am trying to make it so only the header of a section is centered and center text as seen in the live editor view:\r\n![Screenshot from 2022-08-22 11-11-08](https://user-images.githubusercontent.com/91704211/185992668-ea435ec6-3cce-40d4-b481-c867d3f87091.png)\r\n\r\nBut when I render the HTML document, it applys the centering and color to the entire section:\r\n![Screenshot from 2022-08-22 14-24-18](https://user-images.githubusercontent.com/91704211/185992753-fd422d6e-5a8d-4162-947e-9a3ce3b2e9e4.png)\r\n\r\nIs there an easy way to make it so the css elements only apply to the header and not all of the text under?\r\n
"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 7,\n \"created_at\": \"2022-08-22T18:51:32Z\",\n \"creator\": \"cscheid\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2057,\n \"state\": \"closed\",\n \"title\": \"How to stop CSS styling of a header applying to entire section?\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2057\"\n}"}}},{"rowIdx":1676,"cells":{"page_content":{"kind":"string","value":"I have created a Blog and I use Github Pages to deploy it. \r\n\r\nHowever, my blog struggles to get updated on the web when I have modified something in an old post. \r\n\r\nWhat I do, is that I push the changes to the main repo and then I go to the terminal and just type the usual command: `quarto publish `\r\n\r\nI have tried to delete my cache in the browser, but the blog fails to update. \r\n\r\nI honestly cannot understand what is the process to update a blog manually, i.e. without GithubActions, when one is using Github Pages for deployment. \r\n\r\n\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 9,\n \"created_at\": \"2022-08-22T17:35:24Z\",\n \"creator\": \"ghost\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"needs-repro\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2055,\n \"state\": \"closed\",\n \"title\": \"Deployment with Github Pages \",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2055\"\n}"}}},{"rowIdx":1677,"cells":{"page_content":{"kind":"string","value":"Fixes `colorlinks` issue in pdf output"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 0,\n \"created_at\": \"2022-08-22T17:08:11Z\",\n \"creator\": \"dragonstyle\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.1\",\n \"number\": 2054,\n \"state\": \"closed\",\n \"title\": \"Update pandoc template to 2.19.1\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2054\"\n}"}}},{"rowIdx":1678,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nIt is [documented](https://quarto.org/docs/computations/r.html#chunk-options) that `!expr` works with `fig-cap`, but it doesn't work with `fig-subcap`.\r\n\r\n````md\r\n```{r}\r\n#| label: fig-charts\r\n#| fig-cap: Charts\r\n#| fig-subcap: !expr c(\"First\", \"Second\")\r\n\r\nplot(cars)\r\nplot(pressure)\r\n```\r\n````\r\n\r\nI get the following error when running `quarto render` on the file:\r\n\r\n```\r\nERROR: Validation of YAML cell metadata failed.\r\nIn file subfig-eval-yaml.qmd\r\n(line 4, columns 16--42) Key fig-subcap has value !expr c(\"First\", \"Second\"), which must be 'true'\r\n3: #| fig-cap: Charts\r\n4: #| fig-subcap: !expr c(\"First\", \"Second\")\r\n ~~~~~~~~~~~~~~~~~~~~~~~~~~\r\n\r\nERROR: Render failed due to invalid YAML.\r\n```\n\n### `quarto check` Output\n\n```\r\n[>] Checking Quarto installation......OK\r\n Version: 1.0.38\r\n Path: C:\\scoop\\apps\\quarto\\current\\bin\\\r\n CodePage: 1250\r\n\r\n[>] Checking basic markdown render....OK\r\n\r\n[>] Checking Python 3 installation....OK\r\n Version: 3.10.6\r\n Path: C:/msys64/mingw64/bin/python.exe\r\n Jupyter: (None)\r\n\r\n Jupyter is not available in this Python installation.\r\n Install with python -m pip install jupyter\r\n\r\n[>] Checking R installation...........OK\r\n Version: 4.2.1\r\n Path: C:/scoop/apps/r-release/current\r\n LibPaths:\r\n - C:/scoop/apps/r-release/4.2.1/library\r\n rmarkdown: 2.15\r\n\r\n[>] Checking Knitr engine render......OK\r\n```\n\n### `quarto tools check` Output\n\n```\r\n[>] Inspecting tools\r\n\r\nTool Status Installed Latest \r\nchromium Not installed --- 869685 \r\ntinytex External Installation --- v2022.08\r\n```\n\n### Checklist\n\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the \"Quarto Check Output\" text area?\n- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?\n- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.\n- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 6,\n \"created_at\": \"2022-08-22T15:25:06Z\",\n \"creator\": \"svraka\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"yaml-validation\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2047,\n \"state\": \"open\",\n \"title\": \"Evaluating R code with `!expr` in `fig-subcap` doesn't work\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2047\"\n}"}}},{"rowIdx":1679,"cells":{"page_content":{"kind":"string","value":"### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2043\r\n\r\n
\r\n\r\nOriginally posted by **maelle** August 22, 2022\r\nSay I have a chapter file called `abb-blurb.qmd`.\r\n\r\nHow can I make the corresponding HTML file something else than `abb-blurb.HTML`? Do I need to use a YAML field in the file?
"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 2,\n \"created_at\": \"2022-08-22T15:13:09Z\",\n \"creator\": \"jjallaire\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2045,\n \"state\": \"closed\",\n \"title\": \"How to change the rendered file path in Quarto books\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2045\"\n}"}}},{"rowIdx":1680,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nThis is a minimal sample project.\r\n\r\n[quarto_minimal.zip](https://github.com/quarto-dev/quarto-cli/files/9394347/quarto_minimal.zip)\r\n\r\nThe post content is simply:\r\n\r\n````qmd\r\n---\r\ntitle: test\r\n---\r\n\r\n```{r}\r\nplot(1)\r\n```\r\n````\r\n\r\nThe rendered site will not display the picture stated in post.\r\n\r\n![image](https://user-images.githubusercontent.com/13306020/185921680-8b47fdce-27c0-496e-96de-dc0658b0cb6b.png)\r\n\r\nError message from console is as follows:\r\n\r\n```r\r\n#> GET: /\r\n#> /index_files/figure-html/unnamed-chunk-1-1.png (404: Not Found)\r\n#> /index_files/figure-html/unnamed-chunk-1-1.png (404: Not Found)\r\n```\r\n\r\nCreated on 2022-08-22 with [reprex v2.0.2](https://reprex.tidyverse.org)\r\n\r\n
\r\n\r\nSession info\r\n\r\n\r\n``` r\r\nsessioninfo::session_info()\r\n#> ─ Session info ───────────────────────────────────────────────────────────────\r\n#> setting value\r\n#> version R version 4.2.1 (2022-06-23 ucrt)\r\n#> os Windows 10 x64 (build 22000)\r\n#> system x86_64, mingw32\r\n#> ui RTerm\r\n#> language (EN)\r\n#> collate Chinese (Simplified)_China.utf8\r\n#> ctype Chinese (Simplified)_China.utf8\r\n#> tz Asia/Taipei\r\n#> date 2022-08-22\r\n#> pandoc 2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)\r\n#> \r\n#> ─ Packages ───────────────────────────────────────────────────────────────────\r\n#> package * version date (UTC) lib source\r\n#> cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.1)\r\n#> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.1)\r\n#> evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.1)\r\n#> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1)\r\n#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)\r\n#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.1)\r\n#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)\r\n#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.1)\r\n#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)\r\n#> knitr 1.39 2022-04-26 [1] CRAN (R 4.2.1)\r\n#> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.1)\r\n#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)\r\n#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)\r\n#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1)\r\n#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.1)\r\n#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.1)\r\n#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)\r\n#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)\r\n#> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.1)\r\n#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)\r\n#> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.1)\r\n#> rmarkdown 2.15 2022-08-16 [1] CRAN (R 4.2.1)\r\n#> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.1)\r\n#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)\r\n#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)\r\n#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.1)\r\n#> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.1)\r\n#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)\r\n#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1)\r\n#> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.1)\r\n#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)\r\n#> xfun 0.32 2022-08-10 [1] CRAN (R 4.2.1)\r\n#> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.1)\r\n#> \r\n#> [1] C:/Users/lenovo/AppData/Local/R/win-library/4.2\r\n#> [2] C:/Program Files/R/R-4.2.1/library\r\n#> \r\n#> ──────────────────────────────────────────────────────────────────────────────\r\n```\r\n\r\n
\r\n\r\n\n\n### `quarto check` Output\n\n```bash\r\n[>] Checking Quarto installation......OK\r\n Version: 1.0.38\r\n Path: C:\\PROGRA~1\\Quarto\\bin\\\r\n CodePage: 936\r\n\r\n[>] Checking basic markdown render....OK\r\n\r\n[>] Checking Python 3 installation....OK\r\n Version: 3.9.5 (Conda)\r\n Path: C:/Users/lenovo/miniconda3/python.exe\r\n Jupyter: (None)\r\n\r\n Jupyter is not available in this Python installation.\r\n Install with conda install jupyter\r\n\r\n(/) Checking R installation...........\r\n```\n\n### `quarto tools check` Output\n\n```bash\r\n[>] Inspecting tools\r\n\r\nTool Status Installed Latest \r\nchromium Not installed --- 869685 \r\ntinytex Not installed --- v2022.08\r\n```\n\n### Checklist\n\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the \"Quarto Check Output\" text area?\n- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?\n- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.\n- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 9,\n \"created_at\": \"2022-08-22T12:40:13Z\",\n \"creator\": \"psychelzh\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.3\",\n \"number\": 2042,\n \"state\": \"closed\",\n \"title\": \"For website project, images generated by R code does not display normally in listing page\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2042\"\n}"}}},{"rowIdx":1681,"cells":{"page_content":{"kind":"string","value":"See discussion and example in https://github.com/quarto-dev/quarto-cli/issues/1581\r\n\r\nIn short, some **knitr** option could be useful with other computation engine and this require broader Quarto support\r\n\r\nThis could maybe even be done using Lua filter in an extension (TBC)"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 0,\n \"created_at\": \"2022-08-22T07:49:51Z\",\n \"creator\": \"cderv\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2040,\n \"state\": \"open\",\n \"title\": \" Consider support for `class.source` `class.output` `attr.source` `attr.output` equivalent (not only available for knitr cells)\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2040\"\n}"}}},{"rowIdx":1682,"cells":{"page_content":{"kind":"string","value":"### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2003\r\n\r\n
\r\n\r\nOriginally posted by **andrewcstewart** August 19, 2022\r\nLooking under the list of formats under https://quarto.org/docs/output-formats/all-formats.html, one format that would be nice to add is Confluence's. I think there are probably a few different options there, but one would be https://confluence.atlassian.com/doc/confluence-storage-format-790796544.html \r\n\r\nJust starting this conversation to see if there is similar interest out there.
"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"allenmanning\",\n \"comments\": 3,\n \"created_at\": \"2022-08-22T07:05:16Z\",\n \"creator\": \"allenmanning\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.3\",\n \"number\": 2038,\n \"state\": \"closed\",\n \"title\": \"Publish to Confluence\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2038\"\n}"}}},{"rowIdx":1683,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\n````markdown\r\n---\r\ntitle: \"test\"\r\nformat: \r\n html:\r\n self-contained: true\r\nkeep-md: true\r\n---\r\n\r\n```{r}\r\nplot(mtcars)\r\n```\r\n\r\n````\r\n\r\nThis will produce with quarto 1.1.107 on the RStudio Viewer preview pane on Windows\r\n![image](https://user-images.githubusercontent.com/6791940/185857724-7c6225f6-7960-4c3e-b9d2-e06938f6d060.png)\r\n\r\nThis is due to a bug in Pandoc introduced in version 2.19.1 when base64 package was changed. \r\n\r\nSee https://github.com/jgm/pandoc/issues/8239\r\n\r\nWe should probably wait for new Pandoc release before new Quarto release \r\n\r\nFWIW I check with R Markdown document that using Pandoc 2.19 works, and 2.19.1 does not."},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 2,\n \"created_at\": \"2022-08-22T06:56:20Z\",\n \"creator\": \"cderv\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2037,\n \"state\": \"closed\",\n \"title\": \"self-contained document have broken images\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2037\"\n}"}}},{"rowIdx":1684,"cells":{"page_content":{"kind":"string","value":"Hi,\r\n\r\nI was running a simple Quarto document that just takes the mean of `c(1,2,3)` and wanted to know how `code-link` and `code-line-numbers` work. \r\nThe versions are Quarto 1.0.11, R 4.2.1 and RStudio 2022.07.1 Build 554. \r\n\r\nHopefully the issue reported can be reproduced.\r\n\r\nI understand that both R packages `downlit` and `xml2` need to be installed.\r\n\r\nBelow is the content of the Quarto document.\r\n\r\n```\r\n---\r\ntitle: \"CodeNumberVSCodeLink\"\r\nformat:\r\n html:\r\n code-link: true\r\n code-line-numbers: true\r\n---\r\n\r\n## Quarto\r\n\r\nQuarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see .\r\n\r\n```{r}\r\nmean(c(1,2,3))\r\n```\r\n\r\nIf I set `code-link: true` and `code-line-numbers: false` and click render, the hyperlink works \r\n\r\n![image](https://user-images.githubusercontent.com/9066508/185841447-780f55c9-9928-43e4-a8de-98a1ec7a0339.png)\r\n\r\nIf I set `code-link: false` and `code-line-numbers: true` and click render, the code numbering works\r\n\r\n![image](https://user-images.githubusercontent.com/9066508/185841533-b4f56945-578d-448d-82ba-0306f2ada545.png)\r\n\r\nHowever when I set both `code-link: true` and `code-line-numbers: true` and click render, **only** the the code numbering works.\r\n\r\n![image](https://user-images.githubusercontent.com/9066508/185841667-cfa72099-7f39-4f26-8bc8-6e9e57876909.png)\r\n\r\nIs there a reason for this behaviour ?\r\n\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 2,\n \"created_at\": \"2022-08-22T04:55:25Z\",\n \"creator\": \"JauntyJJS\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"upstream\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2036,\n \"state\": \"open\",\n \"title\": \"`code-link` and `code-line-numbers` does not work together when both set to true\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2036\"\n}"}}},{"rowIdx":1685,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nI keep getting the error \"\\Quarto\\bin\\ was unexpected at this time\" when trying to use a fresh install of Quarto. \r\n\r\nThe only command I have found so far that works is \"quarto -- version\" which outputs:\r\n\r\n\"1.0.38\"\r\n\r\n\r\n\r\nWindows 10 \r\nVersion\t10.0.19044 Build 19044\r\n\r\nI have verified that quarto is in my path. \n\n### `quarto check` Output\n\n\\Quarto\\bin\\ was unexpected at this time.\n\n### `quarto tools check` Output\n\n\\Quarto\\bin\\ was unexpected at this time.\n\n### Checklist\n\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the \"Quarto Check Output\" text area?\n- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?\n- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.\n- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 2,\n \"created_at\": \"2022-08-22T04:37:27Z\",\n \"creator\": \"kpjmcg\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2035,\n \"state\": \"closed\",\n \"title\": \"\\\"\\\\Quarto\\\\bin\\\\ was unexpected at this time\\\" error for all commands\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2035\"\n}"}}},{"rowIdx":1686,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nMore a question than a bug but wondering if I have multiple Jupyter Notebooks in my project, each of those with different figures that I would like to reference from other notebook, how can I do that?\r\n\r\nIn the \"testing copy.ipynb\" notebook I put two cross references: @fig-plot and @fig-plot-copy\r\nfig-plot belongs to testin.ipynb and as shown in the image below, not rendering. Also getting `WARNING: Unable to resolve crossref @fig-plot`\r\n\r\nMinimal Reproducible Example here:\r\nhttps://lgonzalezsa.github.io/hello_quarto/cross_copy.html\r\nhttps://github.com/lgonzalezsa/hello_quarto/blob/main/test/testing%20copy.ipynb\r\n![image](https://user-images.githubusercontent.com/704686/185818466-69459ec2-5c8e-4b90-8178-ad9f7f5d63f4.png)\r\n\r\n\r\n### `quarto check` Output\r\n\r\n_No response_\r\n\r\n### `quarto tools check` Output\r\n\r\n_No response_\r\n\r\n### Checklist\r\n\r\n- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\r\n- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the \"Quarto Check Output\" text area?\r\n- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?\r\n- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.\r\n- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 1,\n \"created_at\": \"2022-08-22T00:43:47Z\",\n \"creator\": \"lgonzalezsa\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2034,\n \"state\": \"closed\",\n \"title\": \"How to cross reference figures from distinct Jupyter Notebooks ?\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2034\"\n}"}}},{"rowIdx":1687,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nCreating quarto website with a Jupyter Notebook using Python [Holoviz](https://holoviz.org/) plot but getting `Unable to display output for mime type(s):`\r\n\r\nI also tested seaborn package and the plots render properly. \r\n\r\nDo I need to configure a property for Holoviz plots to render properly with Quarto?\r\n\r\nPlease check my minimal reproducible example here:\r\nhttps://lgonzalezsa.github.io/hello_quarto/testing.html#fig-plot\r\nhttps://github.com/lgonzalezsa/hello_quarto/blob/main/test/testing.ipynb \r\n\r\n### `quarto check` Output\r\n\r\n```bash\r\n[✓] Checking Quarto installation......OK\r\n Version: 1.0.38\r\n Path: /opt/quarto/bin\r\n\r\n[✓] Checking basic markdown render....OK\r\n\r\n[✓] Checking Python 3 installation....OK\r\n Version: 3.9.12 (Conda)\r\n Path: /home/gonluisr/miniconda3/envs/conda_dev/bin/python\r\n Jupyter: 4.10.0\r\n Kernels: julia-(8-threads)-1.7, julia-1.7, python3\r\n\r\n[✓] Checking Jupyter engine render....OK\r\n\r\n[✓] Checking R installation...........(None)\r\n\r\n Unable to locate an installed version of R.\r\n Install R from https://cloud.r-project.org/\r\n```\r\n\r\n### `quarto tools check` Output\r\n\r\n```bash\r\n[✓] Inspecting tools\r\n\r\nTool Status Installed Latest \r\nchromium Not installed --- 869685 \r\ntinytex Not installed --- v2022.08\r\n```\r\nLinux OS:\r\n```bash\r\nOS: Pop!_OS 22.04 LTS x86_64 \r\nKernel: 5.19.0-76051900-generic \r\n```\r\n\r\n### Checklist\r\n\r\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\r\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the \"Quarto Check Output\" text area?\r\n- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?\r\n- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.\r\n- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 2,\n \"created_at\": \"2022-08-22T00:07:04Z\",\n \"creator\": \"lgonzalezsa\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2033,\n \"state\": \"closed\",\n \"title\": \"Quarto not rendering Holoviz plots | Unable to display output for mime type(s):\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2033\"\n}"}}},{"rowIdx":1688,"cells":{"page_content":{"kind":"string","value":"### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2030\r\n\r\n
\r\n\r\nOriginally posted by **lukefullard** August 21, 2022\r\nHi,\r\n\r\nI'm trying to add a table to my quarto document using the [Panel Tabulator widget](https://panel.holoviz.org/reference/widgets/Tabulator.html). \r\nWhile the table displays nicely and is interactive, I get a warning printed into my pdf:\r\n\r\n_Unable to display output for mime type(s)_\r\n\r\nI googled and found [another document with a similar warning](https://nasa-openscapes.github.io/2021-Cloud-Hackathon/tutorials/05_Data_Access_Direct_S3.html#plot-the-hls-s3-object).\r\nI tried adding \r\n\r\n#| warning: false\r\n#| error: false\r\n\r\nto my Python block, bit the warning text still appeared.\r\nCould anyone tell me how to suppress this warning?\r\nThanks.\r\n
"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 3,\n \"created_at\": \"2022-08-21T21:09:33Z\",\n \"creator\": \"jjallaire\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"v1.1\",\n \"number\": 2031,\n \"state\": \"closed\",\n \"title\": \"Warning: \\\"Unable to display output for mime type(s)\\\"\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2031\"\n}"}}},{"rowIdx":1689,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\n````markdown\r\n---\r\ntitle: \"test\"\r\nformat: docx\r\n---\r\n\r\n\r\n:::{.callout-caution}\r\n## Running Code\r\n\r\n```{r}\r\n1 + 1\r\n```\r\n\r\n:::\r\n````\r\n\r\nThis causes this issue : \r\n````bash\r\nAn error occurred\r\nFound a nested callout in the document. Please fix this issue and try again.\r\n````\r\n\r\nThis does not happen in PDF and HTML. \r\n\r\nThis error is thrown from \r\nhttps://github.com/quarto-dev/quarto-cli/blob/852c9bb99e54e0163575ceecf7dde372b4b73321/src/resources/filters/quarto-pre/callout.lua#L533-L538\r\n\r\nwhere we check for nested Divs. \r\n\r\nThe Markdown generated by Quarto before Pandoc rendering is the following\r\n\r\n````markdown\r\n:::{.callout-caution}\r\n## Running Code\r\n\r\n\r\n::: {.cell}\r\n\r\n```{.r .cell-code}\r\n1 + 1\r\n```\r\n\r\n::: {.cell-output .cell-output-stdout}\r\n```\r\n[1] 2\r\n```\r\n:::\r\n:::\r\n\r\n\r\n:::\r\n````\r\n\r\nHence the error thrown. \r\n\r\nI believe this should be fixed - not sure about the context of nested Divs not allowed in Docx @dragonstyle (https://github.com/quarto-dev/quarto-cli/commit/688fd1c070739e3d629d65773da6760ad1d74e41) but it does seem something we should allow for our own expected div right ? \r\n\r\nInitially reported in https://community.rstudio.com/t/quarto-render-to-docx-word-fails-if-callout-has-a-code-chunk/145189\r\n\r\n### `quarto check` Output\r\n\r\n````\r\nquarto check\r\n\r\n[>] Checking Quarto installation......OK\r\n Version: 1.1.80\r\n Path: C:\\Users\\chris\\scoop\\apps\\quarto-prerelease\\current\\bin\\\r\n CodePage: unknown\r\n\r\n[>] Checking basic markdown render....OK\r\n\r\n[>] Checking Python 3 installation....OK\r\n Version: 3.9.13\r\n Path: C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.13/python3.exe\r\n Jupyter: 4.11.1\r\n Kernels: bash, julia-1.7, python3\r\n\r\n[>] Checking Jupyter engine render....OK\r\n\r\n(-) Checking R installation...........++ Activating rlang global_entrace\r\n\r\n++ Setting QUARTO_PYTHON\r\n\r\n[>] Checking R installation...........OK\r\n Version: 4.2.0\r\n Path: C:/PROGRA~1/R/R-42~1.0\r\n LibPaths:\r\n - C:/Users/chris/AppData/Local/R/win-library/4.2\r\n - C:/Program Files/R/R-4.2.0/library\r\n rmarkdown: 2.14.3\r\n\r\n[>] Checking Knitr engine render......OK\r\n````\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 0,\n \"created_at\": \"2022-08-21T15:38:13Z\",\n \"creator\": \"cderv\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"verify-fixed\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2027,\n \"state\": \"closed\",\n \"title\": \"Nested callout error in Docx when include code chunk in callout block\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2027\"\n}"}}},{"rowIdx":1690,"cells":{"page_content":{"kind":"string","value":"Tracking issue for this PR: https://github.com/quarto-dev/quarto-cli/pull/2015"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jjallaire\",\n \"comments\": 1,\n \"created_at\": \"2022-08-21T13:12:42Z\",\n \"creator\": \"jjallaire\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"v1.1\",\n \"number\": 2025,\n \"state\": \"closed\",\n \"title\": \"merge conda PR\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2025\"\n}"}}},{"rowIdx":1691,"cells":{"page_content":{"kind":"string","value":"### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2009\r\n\r\n@dragonstyle You should read to the bottom of the discussion to see the clearest explanation of what the bug is.\r\n\r\n
\r\n\r\nOriginally posted by **sammo3182** August 19, 2022\r\nRecently I asked a question about varying the reference allocation with Quarto in #1728. Then I find the problem that made the old rmarkdown tricks not work was because I used the [`article-format-template`](https://github.com/quarto-journals/article-format-template). The reference was in the right place I want when rendering the plain pdf but then moved to the very end of the document when rendering the `aft`. \r\n\r\nA replicable example:\r\n\r\n```qmd\r\n---\r\nformat:\r\n pdf:\r\n number-sections: true\r\n aft-pdf:\r\n keep-tex: true \r\n aft-html: default\r\n\r\nbibliography: bio.bib\r\ntitle: A test\r\n---\r\n\r\ncontent @Hu2020\r\n\r\n# Reference\r\n\r\n::: {#refs}\r\n:::\r\n\r\n# Online Supplementary Materials\r\n\r\n```\r\n[bio.zip](https://github.com/quarto-dev/quarto-cli/files/9386033/bio.zip)\r\n\r\nSee the difference of the reference when choosing the following options respectively:\r\n\r\n![image](https://user-images.githubusercontent.com/6463211/185724871-cd89a2f3-24d7-4787-8515-d2aba80475e6.png)\r\n\r\n\r\nHow could I allow the `aft` to recognize my reference setting? Any suggestion will be very helpful.\r\nMoreover, a more detailed instruction and examples about how to customize the template than the current [brief version](https://github.com/quarto-journals/article-format-template/blob/main/README.md) under aft repo and Quarto.org will be super welcomed---details like how to arrange the author area, showing the corresponding author, adding the key words and acknowledge, etc.
"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 5,\n \"created_at\": \"2022-08-21T13:04:30Z\",\n \"creator\": \"jjallaire\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"v1.4\",\n \"number\": 2024,\n \"state\": \"open\",\n \"title\": \"Varying the reference position in `quarto-journals` template\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2024\"\n}"}}},{"rowIdx":1692,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\nWould be great if collapsed sections would be accessible for follow hints, for example in qutebrowser or vimium/vimium-FF \r\nIn this screenshot the collapsed section doesn't get it's own follow hint, making it not possible to navigate to it without mose. This website was generated by quarto from markdown files using github workflow actions from this repo: https://github.com/miwojc/mlq\r\nWebsite is built to `gh-pages` branch as per quarto instructions.\r\n\r\n\"image\"\r\n\r\n\r\n### `quarto check` Output\r\n\r\n```bash\r\nquarto check\r\n\r\n[✓] Checking Quarto installation......OK\r\n Version: 0.9.476\r\n Path: /Applications/quarto/bin\r\n\r\n[✓] Checking basic markdown render....OK\r\n\r\n[✓] Checking Python 3 installation....OK\r\n Version: 3.9.13 (Conda)\r\n Path: /Users/username/mambaforge/bin/python\r\n Jupyter: 4.10.0\r\n Kernels: python3, dyalog-kernel\r\n\r\n[✓] Checking Jupyter engine render....OK\r\n\r\n[✓] Checking R installation...........(None)\r\n\r\n Unable to locate an installed version of R.\r\n Install R from https://cloud.r-project.org/\r\n```\r\n\r\n### `quarto tools check` Output\r\n\r\n```bash\r\nquarto tools check\r\n(\\) Reading Tool DataDownload https://deno.land/x/cache@0.2.12/directories.ts\r\n(|) Reading Tool DataDownload https://deno.land/x/cache@0.2.12/deps.ts\r\n[✓] Reading Tool Data\r\nTool Status Installed Latest\r\ntinytex Not installed ---- v2022.08\r\nchromium Not installed ---- 869685\r\n```\r\n\r\n### Checklist\r\n\r\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\r\n- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the \"Quarto Check Output\" text area?\r\n- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?\r\n- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.\r\n- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"jooyoungseo\",\n \"comments\": 0,\n \"created_at\": \"2022-08-21T12:10:32Z\",\n \"creator\": \"miwojc\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"accessibility\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.4\",\n \"number\": 2023,\n \"state\": \"open\",\n \"title\": \"Add follow hint to collapsed section\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2023\"\n}"}}},{"rowIdx":1693,"cells":{"page_content":{"kind":"string","value":"It's fairly common for data scientists to produce reports which end up in Google Slides and it would be great if there were a pattern which let them use quarto to generate these slides. I know that people have asked for this in the Rmarkdown world and it was tricky to implement, but I was wondering if it would be possible to implement it in quarto. \r\n\r\nThe only project that I'm aware of that kind of helps is this [md2googleslides](https://github.com/googleworkspace/md2googleslides) project. "},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 6,\n \"created_at\": \"2022-08-20T23:13:26Z\",\n \"creator\": \"GShotwell\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2022,\n \"state\": \"open\",\n \"title\": \"Feature request: Google slides output\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2022\"\n}"}}},{"rowIdx":1694,"cells":{"page_content":{"kind":"string","value":"Hi,\r\njust getting started with quarto (thanks), and not sure I've got the jupyter side of things sorted out. I think I've installed the irkernel for R okay. but am struggling to convert a .qmd file to .ipynb. \r\n\r\nRunning 'quarto check' in the folder I see the error (at bottom):\r\n\r\n```\r\nstephen@blur estimateq % quarto check \r\n\r\n[✓] Checking Quarto installation......OK\r\n Version: 1.0.38\r\n Path: /Applications/quarto/bin\r\n\r\n[✓] Checking basic markdown render....OK\r\n\r\n[✓] Checking Python 3 installation....OK\r\n Version: 3.10.6\r\n Path: /opt/homebrew/opt/python@3.10/bin/python3.10\r\n Jupyter: 4.11.1\r\n Kernels: ir\r\n\r\n[✓] Checking Jupyter engine render....OK\r\n\r\nERROR: Invalid jupyter YAML metadata found in file (must be string or object)\r\n```\r\n\r\nwhere might I find the invalid YAML? If the check script knows the location (file/line number) of the error, is there any chance it could report that?\r\n\r\nAs far as I can tell, the only yaml file I've got in the folder is the following\r\n\r\n```\r\n---\r\ntitle: \"Example quarto document: estimating PI\"\r\nauthor: \"Stephen J Eglen\"\r\ndate: \"2022-08-20\"\r\nbibliography: refs.bib\r\nformat: \r\n html:\r\n code-fold: false\r\n---\r\n```\r\n\r\n(what I'd like to do is specify the ir kernel).\r\n\r\n(As a minor aside, when I saw the rstudioconf talk that quarto was 'batteries included', I had falsely assumed that it would include all the python/jupyter machinery. but I don't think it did, so I've done the following:\r\n\r\n```\r\npython3 -m pip install jupyter\r\n```\r\n\r\nand from the R side, installed the irkernel package and installed the kernel\r\n\r\n```\r\ninstall.packages('IRkernel') # Don’t forget step 2/3!\r\nIRkernel::installspec()\r\n```\r\n)"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 5,\n \"created_at\": \"2022-08-20T22:28:04Z\",\n \"creator\": \"sje30\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2020,\n \"state\": \"closed\",\n \"title\": \"ERROR: Invalid jupyter YAML metadata found in file (must be string or object)\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2020\"\n}"}}},{"rowIdx":1695,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nThe \"On this page\" table of contents drop down menu sometimes glitches in and out when scrolling through a part of the page with margin elements.\r\n\r\nHere's an example from the Quarto website: [https://quarto.org/docs/authoring/article-layout.html]()\r\n\r\nwith a screen recording of the behavior:\r\n\r\nhttps://user-images.githubusercontent.com/25734232/185762861-22533a12-ac99-4b67-9fdf-993ec86a120c.mov\r\n\n\n### `quarto check` Output\n\n```\r\n[✓] Checking Quarto installation......OK\r\n Version: 1.0.38\r\n Path: /Applications/quarto/bin\r\n\r\n[✓] Checking basic markdown render....OK\r\n\r\n[✓] Checking Python 3 installation....OK\r\n Version: 3.9.12\r\n Path: /usr/local/opt/python@3.9/bin/python3.9\r\n Jupyter: 4.10.0\r\n Kernels: ir, julia-1.6, juliapro_v1.5.0-1-1.5, julia-1.5, python3\r\n\r\n[✓] Checking Jupyter engine render....OK\r\n\r\n[✓] Checking R installation...........OK\r\n Version: 4.1.2\r\n Path: /Library/Frameworks/R.framework/Resources\r\n LibPaths:\r\n - /Library/Frameworks/R.framework/Versions/4.1/Resources/library\r\n rmarkdown: 2.14\r\n\r\n[✓] Checking Knitr engine render......OK\r\n```\n\n### `quarto tools check` Output\n\n```\r\n[✓] Inspecting tools\r\n\r\nTool Status Installed Latest\r\nchromium Not installed --- 869685\r\ntinytex Not installed --- v2022.08\r\n```\n\n### Checklist\n\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the \"Quarto Check Output\" text area?\n- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?\n- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.\n- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 2,\n \"created_at\": \"2022-08-20T19:18:01Z\",\n \"creator\": \"maxdrohde\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\",\n \"duplicate\",\n \"verify-fixed\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.1\",\n \"number\": 2019,\n \"state\": \"closed\",\n \"title\": \"\\\"On this page\\\" menu glitches when scrolling through margin elements on page\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2019\"\n}"}}},{"rowIdx":1696,"cells":{"page_content":{"kind":"string","value":"RStudio 2022.07.1 Build 554\r\nOS Mac M1 Air\r\n\r\n### Bug description\r\n\r\nWhat happens depends on the document class. Described below.\r\n\r\nIf one passes in `hyperrefoptions: `\r\n\r\n```\r\n pdf:\r\n documentclass: scrbook\r\n keep-tex: true\r\n hyperrefoptions: \r\n - \"colorlinks=true\"\r\n - \"linkcolor=blue\"\r\n - \"urlcolor=cyan\"\r\n```\r\nThis is correctly passed to hyperref in the tex output. At top of generated tex:\r\n```\r\n\\PassOptionsToPackage{unicode,colorlinks=true,linkcolor=blue,urlcolor=cyan}{hyperref}\r\n```\r\nBut below that (after line 100 in the generated tex) is this `\\hypersetup` command which overrides that.\r\n\r\n**`documentclass: scrbook` and `book`**\r\n\r\nNo hyperlink color are seen because the `\\hyperref` setup is not changed and includes `hidelinks`.\r\n```\r\n\\hypersetup{\r\n pdftitle={title},\r\n pdfauthor={author},\r\n hidelinks,\r\n pdfcreator={LaTeX via pandoc}}\r\n```\r\n\r\n**`documentclass: scrarticle`, `article`, `krantz`, `svmono`, `report`, `memoir`**\r\n\r\nPassing in any `hyperrefoptions: `, including `colorlinks=false`, triggers a change to `\\hypersetup` to turn on colorlinks but none of the info in `hyperrefoptions` is used.\r\n\r\nThe code the generated tex is this\r\n```\r\n\\hypersetup{\r\n pdftitle={title},\r\n pdfauthor={the author},\r\n colorlinks=true,\r\n linkcolor={blue},\r\n filecolor={Maroon},\r\n citecolor={Blue},\r\n urlcolor={Blue},\r\n pdfcreator={LaTeX via pandoc}}\r\n```\r\nwhether one puts this\r\n```\r\n hyperrefoptions: \r\n - \"colorlinks=false\"\r\n```\r\nor this (or anything else)\r\n```\r\n hyperrefoptions: \r\n - \"colorlinks=true\"\r\n - \"urlcolor=red\"\r\n```\r\nin the format pdf YAML.\r\n\r\nNote in all cases the hyperref options are passed to hyperref at the top of the tex file, it's just that they are being overridden later by `\\hypersetup`\r\n\r\nPersonally as a LaTeX user, I find this preferable\r\n\r\n```\r\n hyperrefoptions: \r\n - \"colorlinks=true\"\r\n - \"linkcolor=blue\"\r\n - \"urlcolor=cyan\"\r\n```\r\nover this \r\n```\r\n colorlinks: true\r\n linkcolor: blue\r\n urlcolor: cyan\r\n```\r\nThe former is what I use for `classoptions` and `geometry` and it is 100% clear what I am doing, i.e. I am setting the hyperref package options and I can look up all the possible options for that package. But the can co-exist just need the `\\hyperrefoptions` commands to make it into `\\hypersetup`.\r\n\r\n\r\n### `quarto check` Output\r\n\r\n```\r\n[✓] Checking Quarto installation......OK\r\n Version: 1.0.38\r\n Path: /Applications/quarto/bin\r\n\r\n[✓] Checking basic markdown render....OK\r\n\r\n[✓] Checking Python 3 installation....OK\r\n Version: 3.9.12\r\n Path: /opt/homebrew/opt/python@3.9/bin/python3.9\r\n Jupyter: (None)\r\n\r\n Jupyter is not available in this Python installation.\r\n Install with python3 -m pip install jupyter\r\n\r\n[✓] Checking R installation...........OK\r\n Version: 4.1.1\r\n Path: /Library/Frameworks/R.framework/Resources\r\n LibPaths:\r\n - /Users/eli.holmes/Library/R/x86_64/4.1/library\r\n - /Library/Frameworks/R.framework/Versions/4.1/Resources/library\r\n rmarkdown: 2.14\r\n\r\n[✓] Checking Knitr engine render......OK\r\n```\r\n\r\n### `quarto tools check` Output\r\n\r\n```\r\n[✓] Inspecting tools\r\n\r\nTool Status Installed Latest \r\nchromium Not installed --- 869685 \r\ntinytex External Installation --- v2022.08\r\n```\r\n\r\nMWE qmd\r\n```\r\n---\r\ntitle: title\r\nauthor:\r\n - name: the author\r\neditor: source\r\nformat:\r\n pdf:\r\n documentclass: scrbook\r\n keep-tex: true\r\n hyperrefoptions: \r\n - \"colorlinks=true\"\r\n - \"linkcolor=blue\"\r\n - \"urlcolor=cyan\"\r\n---\r\n\r\n# Intro\r\n\r\n[Quarto](https://quarto.org/) is great.\r\n\r\n```\r\n\r\n### Checklist\r\n\r\n- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\r\n- [x] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\r\n- [x] documented the quarto version you're running, by pasting the output from running `quarto check` in the \"Quarto Check Output\" text area?\r\n- [x] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?\r\n- [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\r\n- [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well.\r\n- [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"dragonstyle\",\n \"comments\": 10,\n \"created_at\": \"2022-08-20T16:48:21Z\",\n \"creator\": \"eeholmes\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2017,\n \"state\": \"closed\",\n \"title\": \"For PDF, hyperrefoptions being overridden by \\\\hypersetup\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2017\"\n}"}}},{"rowIdx":1697,"cells":{"page_content":{"kind":"string","value":"I am trying to replicate the example shown here : https://quarto.org/docs/interactive/ojs/ but instead of using the csv file I am using the penguins data set and I am not able to get the plots showing up when I used the transpose function but it work when I use the csv file found [here](https://github.com/quarto-dev/quarto-web/blob/main/docs/interactive/ojs/palmer-penguins.csv) . \r\n\r\n````\r\n---\r\ntitle: \"test observ\"\r\nformat: html\r\nexecute:\r\n echo: false\r\n---\r\n\r\n## Quarto\r\n``` {r, include=FALSE}\r\nlibrary(\"palmerpenguins\")\r\nojs_define(data = penguins)\r\n```\r\n\r\n```{ojs}\r\n\r\nviewof bill_length_min = Inputs.range(\r\n [32, 50], \r\n {value: 35, step: 1, label: \"Bill length (min):\"}\r\n)\r\n\r\nviewof islands = Inputs.checkbox(\r\n [\"Torgersen\", \"Biscoe\", \"Dream\"], \r\n { value: [\"Torgersen\", \"Biscoe\"], \r\n label: \"Islands:\"\r\n }\r\n)\r\n```\r\n\r\n```{ojs}\r\n\r\n\r\nfiltered = transpose(data).filter(function(penguin) {\r\n return bill_length_min < penguin.bill_length &&\r\n islands.includes(penguin.island);\r\n})\r\nPlot.rectY(filtered, \r\n Plot.binX(\r\n {y: \"count\"}, \r\n {x: \"body_mass\", fill: \"species\", thresholds: 20}\r\n ))\r\n .plot({\r\n facet: {\r\n data: filtered,\r\n x: \"sex\",\r\n y: \"species\",\r\n marginRight: 80\r\n },\r\n marks: [\r\n Plot.frame(),\r\n ]\r\n }\r\n)\r\n```\r\n````\r\n\r\n\r\nThis is what I get the plots are not showing. When I use the csv the plots show up. \r\n\r\n![image](https://user-images.githubusercontent.com/21668964/185757626-5390586d-64d4-4897-9968-9ef572be973c.png)\r\n"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 5,\n \"created_at\": \"2022-08-20T16:45:34Z\",\n \"creator\": \"meldarionqeusse\",\n \"is_pull_request\": false,\n \"labels\": [],\n \"locked\": false,\n \"milestone\": \"v1.2\",\n \"number\": 2018,\n \"state\": \"closed\",\n \"title\": \"ObservableJS penguins exmaple does not work with transpose but works if you load csv file.\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2018\"\n}"}}},{"rowIdx":1698,"cells":{"page_content":{"kind":"string","value":"### Bug description\n\nSetting either `none-in` or `none-out` results in fading instead of nothing. \r\n\r\nReprex:\r\n\r\n````md\r\n---\r\nformat: revealjs\r\n---\r\n\r\n## slide 1\r\n\r\n## slide 2 {transition=\"none-in none-out\"}\r\n\r\n## slide 3\r\n\r\n````\r\n\r\nresults:\r\n\r\n\r\n![Kapture 2022-08-20 at 18 22 37](https://user-images.githubusercontent.com/14034784/185756814-c45b403a-503d-4ba4-845f-674b80e402bc.gif)\r\n\r\n## RStudio about\r\n\r\nUsing MacOS\r\n\r\n\"Screen\r\n\r\n\n\n### `quarto check` Output\n\n```bash\r\n[✓] Checking Quarto installation......OK\r\n Version: 1.0.38\r\n Path: /Applications/quarto/bin\r\n\r\n[✓] Checking basic markdown render....OK\r\n\r\n[✓] Checking Python 3 installation....OK\r\n Version: 3.8.9\r\n Path: /Library/Developer/CommandLineTools/usr/bin/python3\r\n Jupyter: (None)\r\n\r\n Jupyter is not available in this Python installation.\r\n Install with python3 -m pip install jupyter\r\n\r\n[✓] Checking R installation...........OK\r\n Version: 4.2.1\r\n Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources\r\n LibPaths:\r\n - /Users/emilhvitfeldt/Library/R/arm64/4.2/library\r\n - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library\r\n rmarkdown: 2.14\r\n\r\n[✓] Checking Knitr engine render......OK\r\n```\n\n### `quarto tools check` Output\n\n```bash\r\n[✓] Inspecting tools\r\n\r\nTool Status Installed Latest \r\nchromium Not installed --- 869685 \r\ntinytex Update available v2021.12 v2022.08\r\n```\n\n### Checklist\n\n- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?\n- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.\n- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the \"Quarto Check Output\" text area?\n- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?\n- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the \"About RStudio\" main menu dialog?\n- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.\n- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?"},"metadata":{"kind":"string","value":"{\n \"assignee\": null,\n \"comments\": 2,\n \"created_at\": \"2022-08-20T16:27:23Z\",\n \"creator\": \"EmilHvitfeldt\",\n \"is_pull_request\": false,\n \"labels\": [\n \"bug\"\n ],\n \"locked\": false,\n \"milestone\": null,\n \"number\": 2016,\n \"state\": \"closed\",\n \"title\": \"Setting transition=\\\"none-*\\\" turns on fading\",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2016\"\n}"}}},{"rowIdx":1699,"cells":{"page_content":{"kind":"string","value":"### Bug description\r\n\r\n**distill** has also a `layout` option, and for now if the option is not correctly converted to Quarto supported one then there is an useful error \r\n\r\n* Content from distill without using YAML syntax\r\n````markdown\r\n---\r\ntitle: \"A small example\"\r\nformat: html\r\npage-layout: article\r\n---\r\n\r\n```{r setup, layout=\"l-body-outset\"}\r\nmtcars[,1:3] |> head()\r\n```\r\n````\r\n\r\n* After conversion using `knitr::convert_chunk_header()`\r\n````markdown\r\n---\r\ntitle: \"A small example\"\r\nformat: html\r\npage-layout: article\r\n---\r\n\r\n```{r}\r\n#| layout: l-body-outset\r\nmtcars[,1:3] |> head()\r\n```\r\n````\r\n\r\nin both case, we'll have this issue \r\n````\r\nError running filter C:/Users/chris/scoop/apps/quarto-prerelease/current/share/filters/layout/layout.lua:\r\n...prerelease\\current\\bin\\..\\share\\pandoc\\datadir\\_json.lua:167: bad 'for' initial value (number expected, got nil)\r\nstack traceback:\r\n\t...prerelease\\current\\bin\\..\\share\\pandoc\\datadir\\_json.lua:381: in function '_json.decode'\r\n\t...uarto-prerelease/current/share/filters/layout/layout.lua:3641: in function 'parseLayoutWidths'\r\n\t...uarto-prerelease/current/share/filters/layout/layout.lua:4274: in function 'layoutCells'\r\n\t...uarto-prerelease/current/share/filters/layout/layout.lua:4098: in function <...uarto-prerelease/current/share/filters/layout/layout.lua:4091>\r\nERROR: unexpected character 'l' at line 1 col 1\r\n`````\r\n\r\nNot so useful. \r\nAnd in the second case, YAML validation does not help to detect that. No error detected for the `layout` field in the chunk for me. \r\n\r\nCan we do better in the error or at least in the validation ? \r\n\r\n### `quarto check` Output\r\n\r\n````\r\n$ quarto check\r\n\r\n[>] Checking Quarto installation......OK\r\n Version: 1.1.80\r\n Path: C:\\Users\\chris\\scoop\\apps\\quarto-prerelease\\current\\bin\\\r\n CodePage: unknown\r\n\r\n[>] Checking basic markdown render....OK\r\n\r\n[>] Checking Python 3 installation....OK\r\n Version: 3.9.13\r\n Path: C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.13/python3.exe\r\n Jupyter: 4.11.1\r\n Kernels: bash, julia-1.7, python3\r\n\r\n[>] Checking Jupyter engine render....OK\r\n\r\n(\\) Checking R installation...........++ Activating rlang global_entrace\r\n\r\n++ Setting QUARTO_PYTHON\r\n\r\n[>] Checking R installation...........OK\r\n Version: 4.2.0\r\n Path: C:/PROGRA~1/R/R-42~1.0\r\n LibPaths:\r\n - C:/Users/chris/AppData/Local/R/win-library/4.2\r\n - C:/Program Files/R/R-4.2.0/library\r\n rmarkdown: 2.14.3\r\n\r\n[>] Checking Knitr engine render......OK\r\n````"},"metadata":{"kind":"string","value":"{\n \"assignee\": \"cscheid\",\n \"comments\": 8,\n \"created_at\": \"2022-08-20T13:21:25Z\",\n \"creator\": \"cderv\",\n \"is_pull_request\": false,\n \"labels\": [\n \"enhancement\",\n \"yaml-validation\"\n ],\n \"locked\": false,\n \"milestone\": \"Future\",\n \"number\": 2013,\n \"state\": \"open\",\n \"title\": \"Improve validation for layout to help distill conversion ? \",\n \"url\": \"https://github.com/quarto-dev/quarto-cli/issues/2013\"\n}"}}}],"truncated":false,"partial":false},"paginationData":{"pageIndex":16,"numItemsPerPage":100,"numTotalItems":2841,"offset":1600,"length":100}},"jwt":"eyJhbGciOiJFZERTQSJ9.eyJyZWFkIjp0cnVlLCJwZXJtaXNzaW9ucyI6eyJyZXBvLmNvbnRlbnQucmVhZCI6dHJ1ZX0sImlhdCI6MTc1NjAyNTk5OSwic3ViIjoiL2RhdGFzZXRzL2hhbWVsL3F1YXJ0by1pc3N1ZXMiLCJleHAiOjE3NTYwMjk1OTksImlzcyI6Imh0dHBzOi8vaHVnZ2luZ2ZhY2UuY28ifQ.-4YOhp9i590Bz1Hc0IH-Nz6wJeD9giO_4M-ZYWqwgPGhhE9X8lylDU6yYn5SKW8qIlNWUTGzdNChWxaVFQyeDA","displayUrls":true},"discussionsStats":{"closed":0,"open":0,"total":0},"fullWidth":true,"hasGatedAccess":true,"hasFullAccess":true,"isEmbedded":false,"savedQueries":{"community":[],"user":[]}}">
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### Bug description The [title-block html template](https://github.com/quarto-dev/quarto-cli/blob/af5c051e8251d3a0535f2e8dcf62d011259c8fb2/src/resources/formats/html/templates/title-block.html) is applied to every page of an HTML book. It would be nice to have (partial) template which runs only on the book's title page and one which runs only on the other pages. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "dragonstyle", "comments": 11, "created_at": "2022-08-31T14:44:39Z", "creator": "ThierryO", "is_pull_request": false, "labels": [ "bug", "enhancement", "books" ], "locked": false, "milestone": "v1.4", "number": 2235, "state": "open", "title": "different template for html book title page", "url": "https://github.com/quarto-dev/quarto-cli/issues/2235" }
### Bug description It's been a while since I reported a bug, here is a new one introduced in v1.1 (introduced between v1.1.67 and v1.1.149, and still in v1.1.165 or v1.2.15, likely to be c56d23e7690a5aec4e99b26310ffe12783807709). This issue is platform/IDE independent. Issue possibly related to #2166. ```` --- format: html --- ::: {#thm-line} ## Line (with or without the Lua filter error occurs) ``` 1+1 ``` ::: ```` ```bash pandoc to: html output-file: Untitled-1.html standalone: true section-divs: true html-math-method: mathjax wrap: none default-image-extension: png metadata document-css: false link-citations: true date-format: long lang: en Error running filter /Applications/quarto/share/filters/crossref/crossref.lua: /Applications/quarto/share/filters/crossref/crossref.lua:97: bad argument #1 to 'insert' (table expected, got nil) stack traceback: /Applications/quarto/share/filters/crossref/crossref.lua:97: in function 'tprepend' /Applications/quarto/share/filters/crossref/crossref.lua:2057: in local 'fn' /Applications/quarto/share/filters/crossref/crossref.lua:1154: in function </Applications/quarto/share/filters/crossref/crossref.lua:1148> ``` Currently the only way to use "Theorems and Proofs", is to fully specify those. ```` ::: {#thm-line} ## Label Some text ``` 1+1 ``` ::: ```` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "cscheid", "comments": 0, "created_at": "2022-08-31T12:24:15Z", "creator": "mcanouil", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2228, "state": "closed", "title": "Theorems and Proofs with code blocks and no header/label cause Lua filter to error out", "url": "https://github.com/quarto-dev/quarto-cli/issues/2228" }
### Bug description Pandoc offers two ways to create a block image, ``` ![My Caption](file.png) ``` and ``` ![My Caption][ref] [ref]: file.png ``` BUT, if you want to cross-reference these only the first works. See this testcase: ~~~markdown --- title: "Crossref Test" author: Jane Doe lang: en verbose: true --- # Introduction # Sed illum minimum, est mægna alienum mentitum ne. ![This is a medieval conception of an elephant fighting a dragon.](Elephant.jpg){#fig-elephant} Sint meis quo et (see @fig-elephant), vis ad fæcete dolorem! ![This is a medieval conception of an elephant fighting a dragon.][Elephant]{#fig-elephant2} Ad pro quod definitiønem (see @fig-elephant2), mel no laudem delectus, te mei prompta maiorum pønderum! [Elephant]: Elephant.jpg ~~~ Image used: ![Elephant](https://user-images.githubusercontent.com/153905/187661004-57cad992-0fa5-45f5-96f9-ad69f2c1f275.jpg) The result is this: ![Screenshot 2022-08-31 at 11 42 15 copy](https://user-images.githubusercontent.com/153905/187661175-b123884d-b921-4740-8c1e-379b42249421.png) ----- macOS 12.5.1 and Quarto Version: 1.1.165 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 1, "created_at": "2022-08-31T10:46:29Z", "creator": "iandol", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2227, "state": "closed", "title": "Allow cross-referencing to work with reference-link images", "url": "https://github.com/quarto-dev/quarto-cli/issues/2227" }
### Bug description Hello, After creating a new Quarto blog project, I immediately get a permissions error (OS Error 5) when attempting to render `index.qmd` or `about.rmq`. Sometimes it'll render the website fine, but then I'll get the same error when clicking "About." Both R and RStudio are up to date. (RStudio 2022.07.1+554; R 4.2.1) I am the administrator on my PC, which shouldn't cause any permission issues. I didn't make any changes to the default template of the blog, this happened on my first attempt to render. ![accessdenied](https://user-images.githubusercontent.com/56735792/187577584-65b17798-c3c2-4377-86d1-fc6270050810.jpg) ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 2, "created_at": "2022-08-31T02:23:20Z", "creator": "dinanajiarch", "is_pull_request": false, "labels": [ "bug", "needs-repro" ], "locked": false, "milestone": "Future", "number": 2225, "state": "closed", "title": "\"Access is denied\" (os error 5) when rendering. ", "url": "https://github.com/quarto-dev/quarto-cli/issues/2225" }
### Bug description A previously working document just failed after upgrading via `git pull` and `./configure.sh`. Then I used the installer, and it has the same error (v 1.1.165). This was working 2 days ago. When I do `quarto preview` the error I see is: ``` ~/.../R_Pkgs/CSR(master ✗)> quarto preview ERROR: Project _quarto.yml validation failed. In file _quarto.yml (line 9, columns 3--13) property name prefs-text is invalid 8: cookie-consent: true 9: prefs-text: "Cookies are used to track visits only" ~~~~~~~~~~ 10: body-footer: <script data-goatcounter="https://chemospec.goatcounter.com/count" async src="//gc.zgo.at/count.js"></script> ℹ The error happened in location website:prefs-text. ``` This is on MacOS 12.5.1. `quarto check` responds OK at each point. The full repo should you need it is [here](https://github.com/bryanhanson/CSR).
{ "assignee": null, "comments": 1, "created_at": "2022-08-31T02:18:02Z", "creator": "bryanhanson", "is_pull_request": false, "labels": [], "locked": false, "milestone": null, "number": 2224, "state": "closed", "title": "Property name prefs-text is invalid", "url": "https://github.com/quarto-dev/quarto-cli/issues/2224" }
Our changes to override gt's default styles are over-eager and also change custom styles.
{ "assignee": "cscheid", "comments": 1, "created_at": "2022-08-30T19:54:42Z", "creator": "cscheid", "is_pull_request": false, "labels": [ "bug", "needs-repro" ], "locked": false, "milestone": "v1.2", "number": 2222, "state": "closed", "title": "fix style override for gt", "url": "https://github.com/quarto-dev/quarto-cli/issues/2222" }
It is probably a pandoc issue. but would it be possible that the ```yaml tbl-cap-location: top fig-cap-location: top ``` work for docx output? For the moment, they don't have any effect.
{ "assignee": "cscheid", "comments": 3, "created_at": "2022-08-30T18:32:32Z", "creator": "olivroy", "is_pull_request": false, "labels": [ "bug", "crossref", "tables", "docx" ], "locked": false, "milestone": "v1.4", "number": 2221, "state": "open", "title": "Add possibility to change the table, figure captions (docx)", "url": "https://github.com/quarto-dev/quarto-cli/issues/2221" }
### Bug description Hello I was trying to change the font of a Reveal presentation following the themes in GitHub. I was doing it by adding: ```scss /*-- scss:defaults --*/ @import url(http://fonts.googleapis.com/css?family=Montserrat:300,300italic,800,800italic); ``` to my SCSS file. Unfortunately, when Quarto renders the presentation it creates a `Quarto.css` file in `./rppresentation_files/libs/revealjs/dist/theme` with all the CSS rules adding another importing rule after mine, like this: ```css @import"http://fonts.googleapis.com/css?family=Montserrat:300,300i,800,800i";@import"./fonts/source-sans-pro/source-sans-pro.css";:root{ ... ``` This overrules my Montserrat font. I am running Linux Mint 21, with Quarto 1.1.163 and RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Ubuntu Jammy ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 5, "created_at": "2022-08-30T18:14:15Z", "creator": "rgouveiamendes", "is_pull_request": false, "labels": [], "locked": false, "milestone": null, "number": 2219, "state": "closed", "title": "Font import through SCSS file", "url": "https://github.com/quarto-dev/quarto-cli/issues/2219" }
### Bug description Trying to render any document with cache is not possible resulting in the message ``` The jupyter-cache package is required for cached execution ``` from [here](https://github.com/quarto-dev/quarto-cli/blob/9f91bdb4fbcc326944f8aea560f3a86797e2459e/src/resources/jupyter/notebook.py#L103) The .qmd has nothing except for containing only Julia cells: ```` --- title: "test_quarto" execute: cache: true --- ## Quarto Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>. ```{julia} 1 ``` ```` I use Windows. I do not know how to debug the error as I do have jupyter_cache, and my own python installation can find it without issue. The directory containing `jcache` is also in PATH ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "jjallaire", "comments": 4, "created_at": "2022-08-30T16:13:07Z", "creator": "justanothergithubber", "is_pull_request": false, "labels": [ "bug", "windows" ], "locked": false, "milestone": "v1.2", "number": 2217, "state": "closed", "title": "Julia cache does not seem to work", "url": "https://github.com/quarto-dev/quarto-cli/issues/2217" }
Via Max Kuhn: > Does quarto have built-in environmental variables (or similar) during qmd compilation that reflects the output type? Similar to knitr::is_html_output() but cross-language and more specific about the output type? > I’m trying to write single qmd files for books that get compiled in different formats. Any tools (e.g. chunk options etc) that make that easier would be fantastic.
{ "assignee": "cscheid", "comments": 3, "created_at": "2022-08-30T16:04:27Z", "creator": "cscheid", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": "v1.4", "number": 2216, "state": "open", "title": "communicate format output to all engines ", "url": "https://github.com/quarto-dev/quarto-cli/issues/2216" }
### Bug description Hi, I use [BasicTeX](https://tug.org/mactex/morepackages.html), a small TeX Live 2022 install for macOS. When rendering to PDF I get a permission error when `tlmgr` tries to install a required package. It would be nice if **I could enter my password when required**. I can also manually run `tlmgr` based on the output from quarto, but I do appreciate the fact quarto tries to do this for me so I just wish it could handle authorisation... ``` ▶︎ quarto render Quarto.qmd --to pdf pandoc to: latex output-file: Quarto.tex standalone: true pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf toc: true number-sections: true metadata documentclass: scrartcl classoption: - DIV=11 - numbers=noendperiod papersize: letter header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true title: Quarto author: Jane Doe lang: en bibliography: - /Users/ian/.local/share/pandoc/Core.json title-block-banner: true colorlinks: true running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode updating tlmgr updating existing packages finding package for tcolorbox.sty > 1 package to install > installing tcolorbox (1 of 1) ERROR: tlmgr returned a non zero status code You don't have permission to change the installation in any way, specifically, the directory /usr/local/texlive/2022basic/tlpkg/ is not writable. Please run this program as administrator, or contact your local admin. tlmgr: An error has occurred. See above messages. Exiting. ``` ------------ Quarto version: ``` ▶︎ quarto check [✓] Checking Quarto installation......OK Version: 1.1.163 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.3 Path: /Users/ian/.pyenv/versions/3.10.3/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "dragonstyle", "comments": 0, "created_at": "2022-08-30T16:01:29Z", "creator": "iandol", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "Future", "number": 2215, "state": "open", "title": "tlmgr cannot install using macOS 12.5.1 and a BasicTeX install", "url": "https://github.com/quarto-dev/quarto-cli/issues/2215" }
### Bug description I had a document with a graphviz chart, and when I rendered to PDF I got the following error: ``` ▷ quarto render Quarto.qmd --to pdf ERROR: NotFound: No such file or directory (os error 2) Exception: quarto exited with 1 [tty 150], line 1: quarto render Quarto.qmd --to pdf ``` Rendering to HTML and there was no problem, and rereading the docs I realised I needed to install Chromium. After installing (`quarto install tool chromium`) then the error message goes away. It would be good if Quarto could offer a more descriptive error message when chromium is required. ``` ▶︎ quarto check [✓] Checking Quarto installation......OK Version: 1.1.163 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.3 Path: /Users/ian/.pyenv/versions/3.10.3/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` macOS 12.5.1 ### Checklist - [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "cscheid", "comments": 34, "created_at": "2022-08-30T15:54:35Z", "creator": "iandol", "is_pull_request": false, "labels": [ "bug", "mermaid", "chromium" ], "locked": false, "milestone": "v1.3", "number": 2214, "state": "closed", "title": "Cryptic error message when chromium is not yet installed", "url": "https://github.com/quarto-dev/quarto-cli/issues/2214" }
### Bug description In a quarto website/blog project, I put this in `_quarto.yml` to set the "default" author: ```yaml format: html: author: someAuthor ``` And I don't want to display it on the main page, so I put `author: Null` in `index.qmd`. This worked well with quarto ported with RStudio 2022.07.1 (seems to be v1.0.36), but after I installed quarto 1.1.163 in my system (Kubuntu 22.04.1), the project refuses to render, saying ``` ERROR: Validation of YAML front matter failed. ERROR: In file index.qmd (line 3, columns 9--12) Key author has value Null, which must be an object 2: title: "test" 3: author: Null ~~~ 4: --- ✖ The value Null is a null value. ℹ The error happened in location author. ``` I installed the 1.2.15 official pre-release and the problem remains. The problem can be minimally reproduced by 1. Open a new quarto website project in RStudio 2. In `_quarto.yml`, set ```yaml format: html: author: someAuthor ``` 3. And set `author` to be `Null`, `null` or `~` in `index.qmd`. (BTW I remember having `author: null` renders as if `null` is a string with quarto 1.0.36, unsure though) I guess it's the YAML validator that blocks the page from rendering. Since it worked fine in the earlier version, I suppose it's valid YAML... ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "cscheid", "comments": 4, "created_at": "2022-08-30T13:23:16Z", "creator": "mksinicus", "is_pull_request": false, "labels": [ "bug", "yaml-validation" ], "locked": false, "milestone": "v1.3", "number": 2210, "state": "closed", "title": "Project-wide YAML metadata cannot be suppressed", "url": "https://github.com/quarto-dev/quarto-cli/issues/2210" }
### Bug description I have see this type of issue several time already: https://github.com/quarto-ext/lightbox/issues/9 ```` Error running filter lightbox: Could not find executable lightbox ```` It seems it is confusing for user what this means, especially as they tried to use an extension and the error does not mention anything. When you know filter can also be JSON filter, the error message makes sense: Extension was not found somehow. What about making this error more clear to user ? We don't have specific syntax to know the filter asked is supposed to be in an extension, but we can assume most of the time that will be the usage (instead of JSON filter for Pandoc). Maybe we can improve the error message saying. "If you tried to use an extension, please do check the extension is correctly installed for your project", or something like that. Just an idea and opening this issue to get feedback on this situation when that happens. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 2, "created_at": "2022-08-30T09:06:26Z", "creator": "cderv", "is_pull_request": false, "labels": [ "duplicate" ], "locked": false, "milestone": null, "number": 2207, "state": "closed", "title": "Better error when extension filter is not found", "url": "https://github.com/quarto-dev/quarto-cli/issues/2207" }
### Context In looking to develop a [Format for Confluence](https://github.com/quarto-dev/quarto-cli/issues/2038), I've been investigating a minimal HTML reset format. It seems that some `link`s can't currently be removed from the HTML format when `minimal=true`. These scripts would be stripped out by Confluence so it seems wise to update the CLI to support a true HTML reset. ### Steps to Reproduce 1. Build the following example format _extension.yml ```yaml title: Min HTML Format author: Al Manning version: 0.0.1 contributes: format: html: theme: none minimal: true template: min-template.html ``` min-template.html ```html $body$ ``` min-example.qmd ``` quarto --- title: "Min HTML Format" format: min-html --- ``` 2. Expected Render min-example.html ``` html <html><body></body></html> ``` 3. Actual Render min-example.html ``` html <html><head> <link href="example_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light"> <link href="example_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"></head><body></body></html> ```
{ "assignee": "allenmanning", "comments": 4, "created_at": "2022-08-30T08:03:49Z", "creator": "allenmanning", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": null, "number": 2206, "state": "closed", "title": "Enhancement: Min HTML Template / full reset with no scripts", "url": "https://github.com/quarto-dev/quarto-cli/issues/2206" }
I followed the following wizard in RStudio: 1) `New Project` 2) `New Directory` 3) `Quarto book` 4) typed in the directory name Create project as subdirectory of: [on a local drive] D:/directoryname 5) select "use renv with this project" 6) click `Create Project` I got this: 'C:/Program' is not recognized as an internal or external command, operable program or batch file.
{ "assignee": "jjallaire", "comments": 11, "created_at": "2022-08-30T04:16:22Z", "creator": "linlennypinawa", "is_pull_request": false, "labels": [ "bug", "upstream" ], "locked": false, "milestone": "v1.2", "number": 2208, "state": "closed", "title": "problem with creation of quarto book in RStudio IDE", "url": "https://github.com/quarto-dev/quarto-cli/issues/2208" }
I started this discussion a few months ago. I have a `book` project with a collection of chapters, which I'd like to render as separate `revealjs` presentations. Every way I've tried to do this either renders to the `html` format or returns the error `WARNING: The revealjs format is not supported by book projects`. But this exact workflow will work with `website` projects, as indicated by [this tweet](https://twitter.com/KellyBodwin/status/1552649491815227392), which I believe includes a slide from @mine-cetinkaya-rundel 's presentation at rstudio::conf(2022). So it seems to me like this is a bug. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1433 <div type='discussions-op-text'> <sup>Originally posted by **dhicks** July 16, 2022</sup> I'm a university professor. For one of my classes, I like to present my lecture notes as both a presentation (eg, slidy or revealjs, for use in class) and a unified website (eg, gitbook, for students to consult out of class). With Rmarkdown, I could do this by having two different recipes in a Makefile: one that uses `bookdown::render_book()` to create the single gitbook, and another that uses `rmarkdown::render()` to create a presentation for each separate chapter `Rmd` file. I'm playing around with Quarto, trying to figure out how I might be able to do this. Something like `quarto render chfile --to revealjs` in a book project generates a warning: `WARNING: The revealjs format is not supported by book projects`. (This should probably be an error, because Quarto doesn't go on to executive any code chunks or produce any output files.) Including `revealjs` as a `format` in `_quarto.yml` does the same thing. I tried setting up a separate metadata file, `_slides.yml`, but `quarto render` doesn't seem to have any flags to select which metadata file should be used. So currently the best option seems to be to stick with `rmarkdown::render()` for the slides? </div>
{ "assignee": "dragonstyle", "comments": 3, "created_at": "2022-08-30T00:36:49Z", "creator": "dhicks", "is_pull_request": false, "labels": [ "bug", "needs-discussion" ], "locked": false, "milestone": "v1.2", "number": 2200, "state": "closed", "title": "book chapters can't be rendered as separate revealjs presentations", "url": "https://github.com/quarto-dev/quarto-cli/issues/2200" }
We should have a `lst-cap-location` to control the location of listing captions in the same way that we control figure and table caption locations. While we're at it, `lst-cap-location` should also be controllable from `cap-location`.
{ "assignee": "cscheid", "comments": 0, "created_at": "2022-08-29T20:25:31Z", "creator": "cscheid", "is_pull_request": false, "labels": [ "bug", "crossref" ], "locked": false, "milestone": "v1.4", "number": 2196, "state": "open", "title": "`lst-cap-location`", "url": "https://github.com/quarto-dev/quarto-cli/issues/2196" }
```` ```{#lst-prefs .python lst-cap="Sum Function" filename=sum.py} def sum(a, b): sum = a + b print(f'Sum: {sum}`) return sum ``` ```` <img width="896" alt="image" src="https://user-images.githubusercontent.com/285675/187291268-12dd5601-c98f-4502-8b6a-3517c5b949a0.png"> (Thanks, @jpmorr)
{ "assignee": "cscheid", "comments": 1, "created_at": "2022-08-29T20:22:27Z", "creator": "cscheid", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.3", "number": 2195, "state": "closed", "title": "listing caption interacts badly with listing filename", "url": "https://github.com/quarto-dev/quarto-cli/issues/2195" }
![image](https://user-images.githubusercontent.com/285675/187241684-5065beee-8c67-4e57-bfd5-c031e3da0281.png) The following error message is very hard to read: ``` Key sidebar has value background: primary logo: "images/logo.png" ... - href: schedule.qmd text: Schedule, which must be `true` or `false` ``` There are two problems here. ## Formatting We can improve formatting in at least three ways. If we're going to print object values that violate the schema, we should always print them by themselves instead of wrapping text around them. That error should then read like so: ``` Key sidebar has value background: primary logo: "images/logo.png" ... - href: schedule.qmd text: Schedule which must be `true` or `false` ``` I think we also shouldn't use the work `key`, we should use the word `field`. Finally, when we're emitting error messages in contexts that have no color formatting, we should consistently use quotes (as we already do in `'true'` and `'false'`). The error should read ``` Field "sidebar" has value background: primary logo: "images/logo.png" ... - href: schedule.qmd text: Schedule which must be "true" or "false" ``` ## Better information in the case of short suggestions This error is especially bad, though, in that it suggests that the replacement value _has_ to be `true` or `false`. The problem is that although these replacements work, they are not the only options. The other alternatives, though, are more complicated schemas, and our short error report doesn't show that. Our error heuristics should try to offer short suggestions, but they should not mislead.
{ "assignee": "cscheid", "comments": 1, "created_at": "2022-08-29T15:59:58Z", "creator": "cscheid", "is_pull_request": false, "labels": [ "enhancement", "yaml-validation" ], "locked": false, "milestone": "v1.2", "number": 2191, "state": "closed", "title": "Improve YAML validation error messages", "url": "https://github.com/quarto-dev/quarto-cli/issues/2191" }
We had a bad validation error come from https://github.com/rstudio-conf-2022/teach-ds-course-website/blob/ef90e6111411bc9d2b6feb4b2e5b49dc6c24e55b/_quarto.yml under our v1.1 schema closure. ![image](https://user-images.githubusercontent.com/285675/187238631-8f177300-c23d-4136-8e7b-340704c41b22.png) ### Context We recently closed a number of schemas, which introduces a large-scale change in the validation behavior. In this case specifically, `text` was mistakenly not a part of the `navigation-item` schema, which means that under the new schema, yaml validation fails (correctly, although using a wrong schema) : - every array entry in `website:sidebar:contents` fails - same for every array entry in `website:sidebar:tools` - as a result, the entries `website:sidebar` and `website` fail ### Heuristics gone bad We have heuristics that try to find "small" changes to fix the problem. Unfortunately, in this case, the small change suggested is to replace the `website:sidebar` object with `true` or `false`. It does this because we have a heuristic that says "a lot of internal errors to one object probably mean a single larger error in a containing object". That heuristic is good in the case of interactive editing, where we expect errors to show up one at a time. But in this case, the schema change caused all errors to show up at once. ## Possible solutions (All of these are a significant amount of work, but I'm writing them here so I don't need to keep them in my head for when I come back to this problem later.) - We have a mechanism for identifying the "type" of error (`schemaPath`). Many errors with the same `schemaPath` should be an indication that it's actually the same error, and we should consider reporting that one instead. - The bad heuristic comes from looking at the entire YAML at once. In this case, if we forced ourselves to look at "the first error to happen", then the error would be better, as long as we had a good definition of "first". Currently, we scan the full YAML object for errors. Instead, we could run the entire validation procedure on a sequence of YAML objects, from empty object to full YAML object, and then report the errors as they come. This is an attempt to mimic the "incremental typing" behavior, under which our validation works well. - The logic of this is that there's always a path from a valid YAML (the empty object `{}`) to an invalid YAML (this object, `this`). Finding an error on a simpler partial YAML on the path from `{}` to `this` might make better validation errors.
{ "assignee": "cscheid", "comments": 1, "created_at": "2022-08-29T15:45:46Z", "creator": "cscheid", "is_pull_request": false, "labels": [ "bug", "yaml-validation" ], "locked": false, "milestone": "Future", "number": 2190, "state": "open", "title": "yaml validation error heuristics are not tuned for schema changes", "url": "https://github.com/quarto-dev/quarto-cli/issues/2190" }
### Bug description This was encounter in https://community.rstudio.com/t/quarto-unable-to-locate-r-installation/144340/5 In some installation, it is possible that R defaults packages are not loaded. See https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html > If you want a different set of packages than the default ones when you start, insert a call to [options](https://stat.ethz.ch/R-manual/R-devel/library/base/help/options.html) in the ‘.Rprofile’ or ‘Rprofile.site’ file. For example, options(defaultPackages = character()) will attach no extra packages on startup (only the base package) (or set R_DEFAULT_PACKAGES=NULL as an environment variable before running R). Using options(defaultPackages = "") or R_DEFAULT_PACKAGES="" enforces the R system default. Setting that and not loading **utils** will make Quarto fail the check https://github.com/quarto-dev/quarto-cli/blob/2430b604b7651f9d40ee98bdd7b479208290eac0/src/resources/capabilities/knitr.R#L10-L11 Reprex: ````powershell # No ENV set > $env:R_DEFAULT_PACKAGES=$null > quarto check knitr (-) Checking R installation........... [>] Checking R installation...........OK Version: 4.2.1 Path: C:/PROGRA~1/R/R-42~1.1 LibPaths: - C:/Users/chris/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.1/library rmarkdown: 2.16.1 [>] Checking Knitr engine render......OK # Setting the env var > $env:R_DEFAULT_PACKAGES="NULL" > quarto check knitr (-) Checking R installation........... Error in `packageVersion()`: ! could not find function "packageVersion" Backtrace: ▆ 1. ├─base::cat(...) 2. └─base::paste0(...) Execution halted [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ```` By just namespacing our usage of `packageVersion()` we could avoid that ```r > Rscript --vanilla -e "packageVersion('rmarkdown')" Error in packageVersion("rmarkdown") : could not find function "packageVersion" Execution halted > Rscript --vanilla -e "utils::packageVersion('rmarkdown')" [1] '2.16.1' ```
{ "assignee": "cderv", "comments": 0, "created_at": "2022-08-29T13:32:17Z", "creator": "cderv", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2187, "state": "closed", "title": "Correctly namespace usage of R default package functions like utils", "url": "https://github.com/quarto-dev/quarto-cli/issues/2187" }
Would it be possible to enable the quarto options for code folding and linking to the hugo format (as per html)? ``` format: hugo: code-fold: true code-link: true ```
{ "assignee": "jjallaire", "comments": 7, "created_at": "2022-08-29T13:30:41Z", "creator": "cgoo4", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": "v1.2", "number": 2186, "state": "closed", "title": "Hugo code folding and linking", "url": "https://github.com/quarto-dev/quarto-cli/issues/2186" }
### Bug description <img width="960" alt="image" src="https://user-images.githubusercontent.com/786803/187203159-ab45f23a-5612-483e-8006-b719c47350dd.png"> I am generating a blog site with quarto on windows 11 using vscode. Freeze directory is not generated on running quarto render command on cmd.exe or using Quarto render project command in vscode. (Additionally, I tried creating a _freeze directory manually before rendering . That directory got deleted after render command was executed) My _quarto.yml is as follows ``` project: type: website pre-render: custom2qmd.py website: title: "qblog" navbar: right: - about.qmd - icon: github href: https://github.com/ - icon: twitter href: https://twitter.com format: html: theme: cosmo css: styles.css execute: freeze: auto ``` and _metadata.yml in posts directory is as follows:- ``` # options specified here will apply to all posts in this folder # freeze computational output # (see https://quarto.org/docs/projects/code-execution.html#freeze) freeze: auto # Enable banner style title blocks title-block-banner: true comments: utterances: repo: quarto-dev/quarto-docs ``` ### Checklist - [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "dragonstyle", "comments": 3, "created_at": "2022-08-29T12:46:46Z", "creator": "Rahuketu86", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2185, "state": "closed", "title": "Freeze directory not formed on windows 11", "url": "https://github.com/quarto-dev/quarto-cli/issues/2185" }
I was not able to create quarto document. When I tped `quarto check` in cmd,an error occorred . ``` C:\Users\yuliang18\Documents>quarto check [>] Checking Quarto installation......OK Version: 1.1.149 Path: C:\Users\yuliang18\AppData\Local\Programs\Quarto\bin\ CodePage: unknown [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.8.13 (Conda) Path: D:/programfiles/anaconda/python.exe Jupyter: 4.9.2 Kernels: ir, javascript, python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.1 Path: D:/Program Files/R/R-4.2.1 LibPaths: - D:/Program Files/R/R-4.2.1/library rmarkdown: 2.16 (\) Checking Knitr engine render......ERROR: Error in source(file.path(res_dir, "hooks.R"), local = TRUE) : C:\Users\yuliang18\AppData\Local\Programs\Quarto\share/rmd/hooks.R:787:3: unexpected symbol 786: comment_chars <- knitr_engine_comment_chars[[engine]] %||% "#" 787: comment_start ^ Calls: .main -> source ͣ�� [>] Checking Knitr engine render......OK ```
{ "assignee": null, "comments": 3, "created_at": "2022-08-29T02:22:59Z", "creator": "antonio-yu", "is_pull_request": false, "labels": [ "needs-repro" ], "locked": false, "milestone": null, "number": 2184, "state": "closed", "title": ">quarto check . Knitr engine render error.", "url": "https://github.com/quarto-dev/quarto-cli/issues/2184" }
### Bug description Render this document fails using the latest nightly release of Quarto ``` --- format: pdf --- ``` Example in R ``` r file.create("test.qmd") #> [1] TRUE writeLines(c("---", "format: pdf", "---"), "test.qmd") tryCatch(quarto::quarto_render("test.qmd"), error = function(cnd) { cnd$stderr }) #> pandoc  #> to: latex #> output-file: test.tex #> standalone: true #> pdf-engine: xelatex #> variables: #> graphics: true #> tables: true #> default-image-extension: pdf #> #> metadata #> documentclass: scrartcl #> classoption: #> - DIV=11 #> - numbers=noendperiod #> papersize: letter #> header-includes: #> - '\KOMAoption{captions}{tableheading}' #> block-headings: true #> #> running xelatex - 1 #> This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex) #> restricted \write18 enabled. #> entering extended mode #> #> updating tlmgr #> #> updating existing packages #>  #> compilation failed- error #> see test.log for more information. #> [1] "\033[1mpandoc \033[22m\n to: latex\n output-file: test.tex\n standalone: true\n pdf-engine: xelatex\n variables:\n graphics: true\n tables: true\n default-image-extension: pdf\n \n\033[1mmetadata\033[22m\n documentclass: scrartcl\n classoption:\n - DIV=11\n - numbers=noendperiod\n papersize: letter\n header-includes:\n - '\\KOMAoption{captions}{tableheading}'\n block-headings: true\n \n\033[1mrunning xelatex - 1\033[22m\n This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)\n restricted \\write18 enabled.\n entering extended mode\n \n\033[1mupdating tlmgr\033[22m\n\n\033[1mupdating existing packages\033[22m\n\033[1m\ncompilation failed- error\033[22m\nsee test.log for more information.\n" quarto::quarto_version() #> [1] '1.1.149' tinytex::tlmgr_version() #> tlmgr revision 63068 (2022-04-18 07:58:07 +0200) #> tlmgr using installation: /Users/qiushi/Library/TinyTeX #> TeX Live (https://tug.org/texlive) version 2022 xfun::session_info() #> R version 4.2.0 (2022-04-22) #> Platform: aarch64-apple-darwin20 (64-bit) #> Running under: macOS Monterey 12.5 #> #> Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8 #> #> Package version: #> askpass_1.1 base64enc_0.1.3 bslib_0.4.0 cachem_1.0.6 #> callr_3.7.2 cli_3.3.0 clipr_0.8.0 compiler_4.2.0 #> curl_4.3.2 digest_0.6.29 evaluate_0.16 fansi_1.0.3 #> fastmap_1.1.0 fs_1.5.2 glue_1.6.2 graphics_4.2.0 #> grDevices_4.2.0 highr_0.9 htmltools_0.5.3 jquerylib_0.1.4 #> jsonlite_1.8.0 knitr_1.40 later_1.3.0 lifecycle_1.0.1 #> magrittr_2.0.3 memoise_2.0.1 methods_4.2.0 openssl_2.0.2 #> packrat_0.8.1 pillar_1.8.1.9000 pkgconfig_2.0.3 processx_3.7.0 #> ps_1.7.1 purrr_0.3.4 quarto_1.2.0.9000 R.cache_0.16.0 #> R.methodsS3_1.8.2 R.oo_1.25.0 R.utils_2.12.0 R6_2.5.1 #> rappdirs_0.3.3 Rcpp_1.0.9.1 rematch2_2.1.2 reprex_2.0.2 #> rlang_1.0.4 rmarkdown_2.16 rprojroot_2.0.3 rsconnect_0.8.27 #> rstudioapi_0.14 sass_0.4.2 stats_4.2.0 stringi_1.7.8 #> stringr_1.4.1 styler_1.7.0.9001 sys_3.4 tibble_3.1.8 #> tinytex_0.41 tools_4.2.0 utf8_1.2.2 utils_4.2.0 #> vctrs_0.4.1 withr_2.5.0 xfun_0.32 yaml_2.3.5 ``` <sup>Created on 2022-08-28 with [reprex v2.0.2](https://reprex.tidyverse.org)</sup> [log file](https://gist.github.com/qiushiyan/97d9df61aa2ff1bf571f52af6dafa56f) Although it is expected that tinytex produce no output with empty content, the quarto error could be improved to indicate this.
{ "assignee": null, "comments": 0, "created_at": "2022-08-28T23:45:35Z", "creator": "qiushiyan", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2183, "state": "closed", "title": "Render PDF fails with empty content", "url": "https://github.com/quarto-dev/quarto-cli/issues/2183" }
### Bug description ```md Watching files for changes Browse at http://localhost:3849/chapter/part01/myfile.html GET: /chapter/part01/myfile.html ERROR: AlreadyExists: Cannot create a file when that file already exists. (os error 183), mkdir 'H:\My Drive\...\site_libs\quarto-nav' System: windows IDE: Vscode Type quarto: book to directory in google drive ``` ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "dragonstyle", "comments": 8, "created_at": "2022-08-28T12:55:55Z", "creator": "jefferds", "is_pull_request": false, "labels": [ "bug", "file-systems" ], "locked": false, "milestone": "v1.4", "number": 2174, "state": "open", "title": "ERROR: AlreadyExists: (os error 183), mkdir 'H:\\My Drive\\...\\site_libs\\quarto-nav' on Google Drive", "url": "https://github.com/quarto-dev/quarto-cli/issues/2174" }
I was sketching a theorem using a bullet point list inside a div and stumbled upon the following issue. The following minimal example using (un-)ordered lists inside a theorem div ```markdown --- title: "unexpected caption item" --- ::: {#thm-unordered-list} ## This heading shouldn't have a bullet point * This * unordered list (unexpectedly) includes the caption ::: ::: {#thm-ordered-list} ## This heading shouldn't have a bullet point 1. This 2. ordered list (unexpectedly) includes the caption ::: ``` renders the theorem caption as part of the list: ![unexpected_caption_item](https://user-images.githubusercontent.com/1757177/187035748-f024d444-d095-4b39-8627-c5dd787b311d.png)
{ "assignee": "cscheid", "comments": 1, "created_at": "2022-08-27T15:05:16Z", "creator": "vmichals", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2166, "state": "closed", "title": "Heading in theorem is included as item in list in theorem body", "url": "https://github.com/quarto-dev/quarto-cli/issues/2166" }
Mermaid allows theming / styling diagrams with - ready-made built-in themes - user-provided CSS - combination of both above If this can already be used through Quarto, please document how. (I didn't find anything about it in the documentation.) If not, please consider adding a possibility to do so. (Best probably as YAML options as suggested at https://github.com/quarto-dev/quarto-cli/discussions/1521#discussioncomment-3225243, as that would allow project-wide, file-level and diagram-level control.)
{ "assignee": "cscheid", "comments": 4, "created_at": "2022-08-27T13:21:31Z", "creator": "das-g", "is_pull_request": false, "labels": [ "enhancement", "mermaid" ], "locked": false, "milestone": "Future", "number": 2165, "state": "closed", "title": "allow theming & styling Mermaid diagrams", "url": "https://github.com/quarto-dev/quarto-cli/issues/2165" }
### Bug description With the new quarto 1.1.147 release we see the following error when rendering a book (https://github.com/mlr-org/mlr3book/runs/8047883939?check_suite_focus=true#step:13:16) ```bash In file book/_quarto.yml (line 67, column 7 through line 68, column 23) Key code-tools has value toggle: true code-fold: false, which must be `true` or `false` 66: code-tools: 67: toggle: true ~~~~~~~~~~~~ 68: code-fold: false ~~~~~~~~~~~~~~~~~~~~~~ 69: highlight-style: printing ✖ The value toggle: true code-fold: false is object. ℹ The error happened in location format:html:code-tools. ``` AFAICS our source specification https://github.com/mlr-org/mlr3book/blob/main/book/_quarto.yml#L66-L68 looks still valid when compared to the [quarto documentation source](https://quarto.org/docs/output-formats/html-code.html#code-tools) - is this a bug in the new release? ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 1, "created_at": "2022-08-27T08:56:27Z", "creator": "pat-s", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2161, "state": "closed", "title": "`code-tools` options mapping buggy in v1.1?", "url": "https://github.com/quarto-dev/quarto-cli/issues/2161" }
I tried to create a new quarto document in Rstudio, through `File >> new file >> quarto document .` Error occoured as mentioned in the title,
{ "assignee": null, "comments": 3, "created_at": "2022-08-27T08:47:51Z", "creator": "antonio-yu", "is_pull_request": false, "labels": [], "locked": false, "milestone": null, "number": 2160, "state": "closed", "title": "an error occourred when parsing json : offset :2", "url": "https://github.com/quarto-dev/quarto-cli/issues/2160" }
### Bug description Hi, I _think_ this is a bug and not a case of user error (if it's the latter, sorry!). I am using the pre-release CLI 1.2.15 on an intel Mac (running 12.5.1) from the command line. This happens with both R and python posts. I am trying to change the default twitter card (blog_title:title doesn't work for me because my blog has a long and stupid title. The title is also included elsewhere on the card). I can change the title but I can't make the description change. I've tested it on R and Python blogs and blogs with and without rendered maths in the title (because you never know). Both cases read the title from the twitter-card metadata but use the post description rather than the meta-card description. A minimal reprex is here https://github.com/dpsimpson/blog/tree/quarto_bug The full .qmd for the post is [(link)](https://github.com/dpsimpson/blog/blob/4103ca2b3762db9c33359c556e7c1518d1b8d643/posts/post_bad/post_bad.qmd) ``` --- title: "$(n-1)$-sane in the membrane (bad twitter card)" subtitle: | Windmills? Tilted. Topic? Boring. (n-1)? No. date: 10-14-2021 categories: [Teaching, Fundamentals, Opinionated] twitter-card: title: "twitter title" description: "twitter description" creator: "@dan_p_simpson" citation: url: https://dansblog.netlify.app/n-sane-in-the-membrane --- Stuff ``` but the generated html code is [(link)](https://github.com/dpsimpson/blog/blob/4103ca2b3762db9c33359c556e7c1518d1b8d643/_site/posts/post_bad/post_bad.html#L70) ``` <meta name="twitter:title" content="twitter title"> <meta name="twitter:description" content="Windmills? Tilted. Topic? Boring. (n-1)? No."> <meta name="twitter:creator" content="@dan_p_simpson"> <meta name="twitter:card" content="summary"> ``` which is using the default description. I can't possibly imagine this being an important bug, but it's slightly odd behaviour. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 0, "created_at": "2022-08-27T08:07:45Z", "creator": "dpsimpson", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2159, "state": "closed", "title": "(Small) Bug: Twitter card description not copied from twitter-card metadata", "url": "https://github.com/quarto-dev/quarto-cli/issues/2159" }
### Bug description After pulling the commits today, I receive the following error on validation of the pre-render field in the project yaml file `_quarto.yml`: ```bash ERROR: Project _quarto.yml validation failed. In file _quarto.yml (line 4, columns 3--13) property name pre-render is invalid 3: output-dir: docs 4: pre-render: ~~~~~~~~~~ 5: - ./scripts/todo-pre.py ℹ The error happened in location project:pre-render. Error: Project _quarto.yml validation failed. In file _quarto.yml (line 4, columns 3--13) property name pre-render is invalid 3: output-dir: docs 4: pre-render: ~~~~~~~~~~ 5: - ./scripts/todo-pre.py ℹ The error happened in location project:pre-render. at readAndValidateYamlFromFile (file:///home/julian/quarto-cli/src/core/schema/val idated-yaml.ts:52:11) at async projectContext (file:///home/julian/quarto-cli/src/project/project-contex t.ts:123:28) at async Command.fn (file:///home/julian/quarto-cli/src/command/preview/cmd.ts:230 :23) at async Command.execute (file:///home/julian/quarto-cli/src/vendor/deno.land/x/cl [email protected]/command/command.ts:1275:7) at async quarto (file:///home/julian/quarto-cli/src/quarto.ts:104:3) at async file:///home/julian/quarto-cli/src/quarto.ts:124:5 ``` I am on Linux Ubuntu 22.04 ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 6, "created_at": "2022-08-26T20:02:07Z", "creator": "juliantao", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2155, "state": "closed", "title": "failed yaml validation on \"pre-render\"", "url": "https://github.com/quarto-dev/quarto-cli/issues/2155" }
### Bug description In chunk yaml, when I do "fig-cap-location: top" I still end up with the caption at the bottom. Setting it to "margin" works as expected. Published example is [here](https://quartopub.com/sites/356a4843-4b95-4082-9854-db5b0207f28f) on quarto-pub. Might this be related to [this issue](https://github.com/quarto-dev/quarto-cli/issues/1990)? I don't know. I have attached the qmd document that created the result linked to above that I published to quarto-pub: ```` --- title: "fig_caption_location_issue" author: "John Goldin" format: html editor: visual --- The fig-cap-location chunk option does not work as expected. I can do "bottom" or "margin" but "top" works the same way as "bottom". ```{r} #| label: fig-a #| fig-cap: "A Sample Figure" #| fig-cap-location: top plot(pressure) ``` Here is yaml for the code chunk: #| label: fig-a #| fig-cap: "A Sample Figure" #| fig-cap-location: top (I tried to find a function that would allow me to fetch these values, but I didn't see one so I've pasted them here.) RStudio version: RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_5_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36 quarto --version 1.1.140 When I run this I get the fig-cap at the bottom of the figure even if I try to specify "top". ## "Top" May Not Work, But "Margin" Does Next I'll show I am able to change the location to "margin" and that works as expected (provided the html window is wide enough to allow for the caption to appear in the margin). #| label: fig-b #| fig-cap: "Another Sample Figure" #| fig-cap-location: margin ```{r} #| label: fig-b #| fig-cap: "Another Sample Figure" #| fig-cap-location: margin plot(pressure) ``` I wonder whether there is something else going on that I don't understand. The typography when I use "margin" seems to be a smaller font. And when I use either "bottom" or "top" there seems to be a lot of space between the bottom of the figure and the caption. session_info: ```{r} print(devtools::session_info()) ``` ```` My system and session version info is all in the [published example](https://quartopub.com/sites/356a4843-4b95-4082-9854-db5b0207f28f) . I also tried with quarto --version 1.2.8 I submit this with trepidation because it is a small, simple thing so the simplest explanation is that I made a simple mistake. But just in case I didn't, here's the report. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "cscheid", "comments": 4, "created_at": "2022-08-26T18:47:41Z", "creator": "johngoldin", "is_pull_request": false, "labels": [ "bug", "crossref" ], "locked": false, "milestone": "v1.4", "number": 2154, "state": "open", "title": "fig-cap-location:top does place the caption above the figure", "url": "https://github.com/quarto-dev/quarto-cli/issues/2154" }
I just updated my quarto (to 1.1.140) and got the following error: `ERROR: Project _quarto.yml validation failed.` `In file www/_quarto.yml` `(line 10, columns 3--14) property name reader-mode is invalid` ` 9: website:` `10: reader-mode: true` I see that reader-mode is still in the documentation. Any advice would be greatly appreciated.
{ "assignee": "dragonstyle", "comments": 9, "created_at": "2022-08-26T18:02:36Z", "creator": "kmkinnaird", "is_pull_request": false, "labels": [], "locked": false, "milestone": "v1.1", "number": 2153, "state": "closed", "title": "Help with error? property name reader-mode is invalid", "url": "https://github.com/quarto-dev/quarto-cli/issues/2153" }
### Bug description gfm output that has pandas dataframes printed out, renders incorrectly on Github, possibly because of GitHub not respecting <style scoped> tags. Input qmd: ````md --- title: "Untitled" format: gfm --- ```{python} import pandas as pd iris = pd.read_csv('https://raw.githubusercontent.com/mwaskom/seaborn-data/master/iris.csv') iris.head() ``` ```` Output md raw: ```` Untitled ================ ``` python import pandas as pd iris = pd.read_csv('https://raw.githubusercontent.com/mwaskom/seaborn-data/master/iris.csv') iris.head() ``` <div> <style scoped> .dataframe tbody tr th:only-of-type { vertical-align: middle; } .dataframe tbody tr th { vertical-align: top; } .dataframe thead th { text-align: right; } </style> <table border="1" class="dataframe"> <thead> <tr style="text-align: right;"> <th></th> <th>sepal_length</th> <th>sepal_width</th> <th>petal_length</th> <th>petal_width</th> <th>species</th> </tr> </thead> <tbody> <tr> <th>0</th> <td>5.1</td> <td>3.5</td> <td>1.4</td> <td>0.2</td> <td>setosa</td> </tr> <tr> <th>1</th> <td>4.9</td> <td>3.0</td> <td>1.4</td> <td>0.2</td> <td>setosa</td> </tr> <tr> <th>2</th> <td>4.7</td> <td>3.2</td> <td>1.3</td> <td>0.2</td> <td>setosa</td> </tr> <tr> <th>3</th> <td>4.6</td> <td>3.1</td> <td>1.5</td> <td>0.2</td> <td>setosa</td> </tr> <tr> <th>4</th> <td>5.0</td> <td>3.6</td> <td>1.4</td> <td>0.2</td> <td>setosa</td> </tr> </tbody> </table> </div> ```` Output md rendered: ``` Untitled ================ ``` python import pandas as pd iris = pd.read_csv('https://raw.githubusercontent.com/mwaskom/seaborn-data/master/iris.csv') iris.head() ``` <div> <style scoped> .dataframe tbody tr th:only-of-type { vertical-align: middle; } .dataframe tbody tr th { vertical-align: top; } .dataframe thead th { text-align: right; } </style> <table border="1" class="dataframe"> <thead> <tr style="text-align: right;"> <th></th> <th>sepal_length</th> <th>sepal_width</th> <th>petal_length</th> <th>petal_width</th> <th>species</th> </tr> </thead> <tbody> <tr> <th>0</th> <td>5.1</td> <td>3.5</td> <td>1.4</td> <td>0.2</td> <td>setosa</td> </tr> <tr> <th>1</th> <td>4.9</td> <td>3.0</td> <td>1.4</td> <td>0.2</td> <td>setosa</td> </tr> <tr> <th>2</th> <td>4.7</td> <td>3.2</td> <td>1.3</td> <td>0.2</td> <td>setosa</td> </tr> <tr> <th>3</th> <td>4.6</td> <td>3.1</td> <td>1.5</td> <td>0.2</td> <td>setosa</td> </tr> <tr> <th>4</th> <td>5.0</td> <td>3.6</td> <td>1.4</td> <td>0.2</td> <td>setosa</td> </tr> </tbody> </table> </div> ``` I am on Mac OS Big Sur and using VS Code 1.70.2. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "cscheid", "comments": 12, "created_at": "2022-08-26T17:53:14Z", "creator": "kalenkovich", "is_pull_request": false, "labels": [ "bug", "upstream" ], "locked": false, "milestone": "v1.3", "number": 2152, "state": "closed", "title": "gfm output of pandas dataframes rendered incorrectly on GitHub", "url": "https://github.com/quarto-dev/quarto-cli/issues/2152" }
the solution from that thread https://github.com/quarto-dev/quarto-cli/discussions/2060#discussioncomment-3455375 no longer works with the latest version 1.1.132. I've uninstalled that version and gone back to 1.1.57 which works fine with the `book.isbn` solution from the windows terminal. That's a workaround for me now. _Originally posted by @jpmorr in https://github.com/quarto-dev/quarto-cli/issues/2143#issuecomment-1228607822_
{ "assignee": "cscheid", "comments": 14, "created_at": "2022-08-26T15:25:23Z", "creator": "cderv", "is_pull_request": false, "labels": [ "yaml-validation" ], "locked": false, "milestone": "v1.2", "number": 2148, "state": "closed", "title": "Using metadata under `book` key cannot be referenced anymore", "url": "https://github.com/quarto-dev/quarto-cli/issues/2148" }
### Bug description I am trying to run Quarto for the first time. I have installed the deb package on my Ubuntu Focal machine. My first attempt to render the `hello.qmd` test file failed: ``` .../quarto/tutorial quarto render hello.qmd --to html Starting python3 kernel...Traceback (most recent call last): File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module> from notebook import notebook_execute, RestartKernel File "/opt/quarto/share/jupyter/notebook.py", line 17, in <module> from nbclient import NotebookClient ModuleNotFoundError: No module named 'nbclient' ``` I resolved this with the following: ``` apt-get install python3-pip python3 -m pip install nbclient ``` My next attempt to render failed with a new message: ``` quarto render hello.qmd --to html Starting python3 kernel...ERROR: No such kernel named python3 ``` I'm not sure how to resolve this. Is there a list of Python dependencies for Quarto somewhere, and ideally instructions for installation that non-Python programmers can follow? Maybe helpful: ``` quarto capabilities { "formats": [ "html", "pdf", "docx", "odt", "pptx", "beamer", "revealjs", "gfm", "hugo", "epub", "asciidoc", "asciidoctor", "commonmark", "commonmark_x", "context", "docbook", "docbook4", "docbook5", "dokuwiki", "dzslides", "epub2", "epub3", "fb2", "haddock", "html4", "html5", "icml", "ipynb", "jats", "jats_archiving", "jats_articleauthoring", "jats_publishing", "jira", "json", "latex", "man", "markdown", "markdown_github", "markdown_mmd", "markdown_phpextra", "markdown_strict", "markua", "mediawiki", "ms", "muse", "native", "opendocument", "opml", "org", "plain", "rst", "rtf", "s5", "slideous", "slidy", "tei", "texinfo", "textile", "xwiki", "zimwiki" ], "themes": [ "default", "materia", "lux", "superhero", "quartz", "united", "sandstone", "spacelab", "solar", "journal", "minty", "sketchy", "cosmo", "flatly", "vapor", "darkly", "yeti", "cerulean", "lumen", "litera", "morph", "slate", "cyborg", "simplex", "pulse", "zephyr" ], "python": { "versionMajor": 3, "versionMinor": 8, "versionPatch": 10, "versionStr": "3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0]", "conda": false, "execPrefix": "/usr", "executable": "/usr/bin/python3", "jupyter_core": "4.11.1", "nbformat": "5.0.4", "nbclient": "0.6.7", "ipykernel": null, "pyLauncher": false, "kernels": [ { "display_name": "Python 3", "language": "python", "name": "python3" } ], "venv": true } } ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 3, "created_at": "2022-08-26T15:14:14Z", "creator": "plantarum", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2147, "state": "closed", "title": "Missing Python dependencies in Ubuntu", "url": "https://github.com/quarto-dev/quarto-cli/issues/2147" }
### Bug description The following mistake was entirely my fault but I found the behavior slightly unexpected compared to standard command line interfaces and the error message made it difficult to immediately identify what the issue was. Running the following render command produces the below error. ``` $ quarto render --to html unvotes.ipynb ERROR: The specified directory ('.') is not a Quarto project ``` I'm fine with the ordering of input vs args but it seems like swapping the order is an easy mistake to make and more helpful error message would be appreciated (e.g. invalid file path, `--to` does not exist, or something similar). ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 0, "created_at": "2022-08-26T15:06:55Z", "creator": "rundel", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": "Future", "number": 2146, "state": "open", "title": "Confusing error with quarto render when swapping input and args", "url": "https://github.com/quarto-dev/quarto-cli/issues/2146" }
### Bug description After installing the latest Quarto version on Windows 11, VS Code no longer finds the quarto app when clicking on the render button when working on a `.qmd` file. I've restarted Windows after the install. ![image](https://user-images.githubusercontent.com/10863809/186902890-93fa25cb-e38a-4c0a-9ebb-7f0327ae70d8.png) This is despite being able to run `quarto check` from the VS code terminal ``` quarto check [>] Checking Quarto installation......OK Version: 1.1.132 Path: C:\Users\xxx\AppData\Local\Programs\Quarto\bin\ CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.13 (Conda) Path: C:/Users/xxx/anaconda3/python.exe Jupyter: 4.11.1 Kernels: julia-1.4, julia-1.6, julia-1.7, python3, iota [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.1.3 Path: C:/PROGRA~1/R/R-41~1.3 LibPaths: - C:/Users/xxx/OneDrive/Documents/R/win-library/4.1 - C:/Program Files/R/R-4.1.3/library rmarkdown: 2.14 [>] Checking Knitr engine render......OK ``` ### Checklist - [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 23, "created_at": "2022-08-26T12:23:51Z", "creator": "jpmorr", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2143, "state": "closed", "title": "VS Code not finding Quarto after updating to latest version", "url": "https://github.com/quarto-dev/quarto-cli/issues/2143" }
### Bug description I created a book project using RStudio and only added the `repo-url` and `repo-actions` In `_quarto.yml` I have ```yaml book: title: "sidebarbug" author: "Jane Doe" date: "8/26/2022" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd repo-url: https://github.com/maelle/sidebarbug/ repo-actions: [edit, issue] ``` Source: https://github.com/maelle/sidebarbug Now on the page where there is a TOC (because there are headers) the repo action links are present. https://maelle.github.io/sidebarbug/ But on the pages where there is no TOC (which is expected as there are no headers) the repo action links are not present (which I was not expecting). https://maelle.github.io/sidebarbug/intro.html I don't think this is relevant but just in case, I am using RStudio 2022.07.0+548 "Spotted Wakerobin" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for Ubuntu Bionic Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36 Ubuntu 20.04.4 LTS ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "dragonstyle", "comments": 3, "created_at": "2022-08-26T12:16:44Z", "creator": "maelle", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.3", "number": 2142, "state": "closed", "title": "repo-actions links do not appear if there is no TOC", "url": "https://github.com/quarto-dev/quarto-cli/issues/2142" }
### Bug description I have a template where many files and resources needs to be added for correct pdf output. I opted to include some logos in the folder logos, which makes my _extension.yml look like this: ```` title: template author: Simon Lidberg version: 0.0.1 contributes: format: common: number-sections: true toc: true reference-section-title: References his-metadata: sammanfattning: "Abstract in swedish" publicationtype: dissertation printshop: "Stema Specialtryck AB, Borås" isbn: 123-12-123456-X-X seriesnumber: XX pdf: documentclass: his-thesis classoption: english biblio-config: false cite-method: biblatex suppress-bibliography: true link-citations: true colorlinks: false template: his-template.tex template-partials: - "partials/doc-class.tex" - "partials/_metadata.tex" - "partials/title.tex" - "partials/before-body.tex" - "partials/after-body.tex" format-resources: - his-thesis.cls - hismetadata.sty - hisbibliography.sty - histextformatting.sty - hisownpublications.sty - hisfont.sty - hiscover.sty - histitlepage.sty - logos/ pdf-engine: lualatex latex-min-runs: 3 has-frontmatter: true papersize: lof: true lot: true english: true html: theme: cosmo ```` But when the 'logos' folder is copied into the input folder, it retains the same permissions as regular files (555). This makes it impossible to remove in subsequent runs of quarto render. Directories would need to be (755) in order for them to be removed properly. Here's the repo [https://github.com/verbalins/his-template](https://github.com/verbalins/his-template), sorry for the state it's in currently... Debug information: ```` [✓] Checking Quarto installation......OK Version: 1.1.132 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /usr/lib64/R LibPaths: - /home/verbalins/R/x86_64-pc-linux-gnu-library/4.2 - /usr/lib/R/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ```` Output showing the error: ```` [1/3] index.qmd [2/3] intro.qmd [3/3] summary.qmd pandoc to: latex output-file: index.tex template: _extensions/his/his-template.tex standalone: true toc: true number-sections: true top-level-division: chapter pdf-engine: lualatex variables: graphics: true tables: true default-image-extension: pdf cite-method: biblatex metadata crossref: chapters: true documentclass: his-thesis papersize: null block-headings: true reference-section-title: References his-metadata: sammanfattning: Abstract in swedish publicationtype: licentiate printshop: 'Stema Specialtryck AB, Borås' isbn: 123-12-123456-X-X seriesnumber: XX coverimage: foto.jpg coverphoto: face.jpg fullarticles: | \fullarticle[scale=.9,trim={0mm 5mm 0mm 5mm},pages=-]{fischer2017doctoraldissertationmanual}{style-guide/manual.pdf}[\href{https://creativecommons.org/licenses/by-nc-nd/4.0/}{\ccbyncnd}] \fullarticle[scale=.9,trim={0mm 5mm 0mm 5mm},pages=1]{fischer2017doctoraldissertationmanual}{style-guide/manual.pdf}[\copyright{} 2018 University of Skövde. Reprinted, with permission, from] \fullarticle[scale=.9,trim={0mm 5mm 0mm 5mm},pages=1]{fischer2017doctoraldissertationmanual}{style-guide/manual.pdf}[Reprinted from][with permission from University of Skövde.] acronyms: | \newacronym{moo}{MOO}{Multi-Objective Optimization} \newacronym{sbo}{SBO}{Simulation-Based Optimization} \newacronym{ai}{AI}{Artificial Intelligence} \newacronym{doe}{DOE}{Design of Experiments} ownpublications: | \authorspublication{fischer2017doctoraldissertationmanual} \authorspublication[Design, manuscript preparation, review]{fischer2017doctoraldissertationmanual} classoption: - english - final - cover biblio-config: false suppress-bibliography: true link-citations: true colorlinks: false has-frontmatter: true lof: true lot: true english: true bibliography: - references.bib title: Title for this example thesis author: Author Authorsson date: '2022-08-23' abstract: Testing abstract (ERROR) PermissionDenied: Permission denied (os error 13), remove '/path/to/folder/thesis/logos/laurelbranch-rubin.pdf' ```` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "dragonstyle", "comments": 2, "created_at": "2022-08-26T11:02:09Z", "creator": "verbalins", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.3", "number": 2141, "state": "closed", "title": "quarto template format-resources folder not removed in linux", "url": "https://github.com/quarto-dev/quarto-cli/issues/2141" }
### Bug description Change the default contents of index.qmd created in a new book project to: ````md ::: {.content-visible when-format="html"} # Preface {.unnumbered} This is a Quarto book. To learn more about Quarto books visit <https://quarto.org/docs/books>. ::: ```` The compiled pdf file shows the chapter heading "Preface" but not the contents (This is a Quarto book...). It is my understanding that the chapter title should also be ignored? quarto check: ```` [✓] Checking Quarto installation......OK Version: 1.1.132 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /usr/lib64/R LibPaths: - /home/verbalins/R/x86_64-pc-linux-gnu-library/4.2 - /usr/lib/R/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ```` quarto render -t all output: ```` 1/4] index.qmd [2/4] intro.qmd [3/4] summary.qmd [4/4] references.qmd pandoc to: latex output-file: index.tex standalone: true toc: true number-sections: true top-level-division: chapter pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf metadata crossref: chapters: true documentclass: scrreprt papersize: letter classoption: - DIV=11 - numbers=noendperiod header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true bibliography: - references.bib title: repro author: Jane Doe date: 8/26/2022 running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022/Arch Linux) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode running xelatex - 2 This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022/Arch Linux) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode Output created: _book/index.html ```` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "cscheid", "comments": 7, "created_at": "2022-08-26T09:08:48Z", "creator": "verbalins", "is_pull_request": false, "labels": [ "bug", "ast" ], "locked": false, "milestone": "v1.4", "number": 2140, "state": "open", "title": "quarto book .content-visible ignored", "url": "https://github.com/quarto-dev/quarto-cli/issues/2140" }
### Bug description When using the chalkboard feature and adding some annotations in a speaker view setting, the annotations are not mirrored to the main presentation. This is an issue as usually one looks at the speaker view during a presentation on the laptop while the main audience looks at the mirrored slides behind/beside the speaker. For speakers, it's not easy to spot that things are not synchronized. Adding annotations only on the main presentation view would require taking the mouse across screens which is fiddly and takes additional time. quarto v1.1.120 ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 3, "created_at": "2022-08-26T07:58:52Z", "creator": "pat-s", "is_pull_request": false, "labels": [ "bug", "upstream" ], "locked": false, "milestone": "Future", "number": 2139, "state": "open", "title": "Chalkboard: annotations in speaker view are not mirrored to main presentation", "url": "https://github.com/quarto-dev/quarto-cli/issues/2139" }
I set up a connection to a database but Quarto throws an error when rendering (not if I execute the chunk). The same code in Rmarkdown works smoothly. ``` library(dbplyr) conn <- DBI::dbConnect(RMySQL::MySQL(), host = "my_hostname", user = "my_user", password = Sys.getenv("PASSWORD_DB"), dbname = "my_db", port=3306) my_table <- tbl(conn, "my_table") ``` This is the error: ``` #> Quitting from lines 11-28 (ECS_data_mining.qmd) #> Error in .local(drv, ...) : #> Failed to connect to database: Error: Access denied for user #> my_user'@'2a01:57a0:1608:6300:8818:75ea:8b53:6933' (using password: NO) #> Calls: .main ... eval -> <Anonymous> -> <Anonymous> -> .local -> .Call #> Execution halted ```
{ "assignee": null, "comments": 7, "created_at": "2022-08-26T07:37:35Z", "creator": "jospueyo", "is_pull_request": false, "labels": [], "locked": false, "milestone": null, "number": 2145, "state": "closed", "title": "Problem when connecting to MySQL using environmental variables", "url": "https://github.com/quarto-dev/quarto-cli/issues/2145" }
### Bug description Hello! I can't find functions for automating list of tables, list of figures and list of abbreviations in quarto book. These functionalities would be very useful for technical and academic reports. Best Ko Ko Zaw ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "cscheid", "comments": 7, "created_at": "2022-08-26T07:23:59Z", "creator": "zawkzaw", "is_pull_request": false, "labels": [ "enhancement", "crossref" ], "locked": false, "milestone": "v1.4", "number": 2138, "state": "open", "title": "list of tables, list of figures and list of abbreviations in quarto book ", "url": "https://github.com/quarto-dev/quarto-cli/issues/2138" }
### Bug description I'm redoing my website using a Quarto blog. When I have post set to eval: false with a SQL code chunk and an R code chunk, it looks fine. When I remove the R part, it changes formatting. To reproduce, I have a blog post with each of these options: 1) Blog post without R chunk. ```` --- title: "Test without R" date: "2022-08-24" execute: eval: false --- ```{sql test} SELECT * FROM EXAMPLE; ``` ![Test without R code](https://user-images.githubusercontent.com/15098268/186791358-28b8b09a-77f0-4d36-948d-79c68c563e9c.png) 2) Same blog post, but with a blank R chunk at the end. --- title: "Test with R" date: "2022-08-25" execute: eval: false --- ```{sql test} SELECT * FROM EXAMPLE; ``` ```{r} ``` ```` ![Test with R code](https://user-images.githubusercontent.com/15098268/186791368-8af62e5e-f6c7-4464-80a9-a8f811d75fd3.png) ----- The SQL section outputs are different. Screenshot of the first blog post. Formatting does not have syntax highlighting. ![Test without R](https://user-images.githubusercontent.com/15098268/186791434-1f7e5381-3e22-4a58-bbee-35ac129e6188.png) Screenshot of the second blog post. This does have highlighting. ![Test with R](https://user-images.githubusercontent.com/15098268/186791455-eba33902-20e5-4047-80d0-088abe085f3a.png) Screenshot of the home page. ![Home page](https://user-images.githubusercontent.com/15098268/186791458-124f7373-b639-42ac-ac07-49a69f6d49e2.png) I don't know why they don't match. I just updated to the newest Quarto version (but I think it was happening on the previous one too). This is on RStudio 2022.07.1 Build 554. "Spotted Wakerobin" for macOS, on Monterey. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": null, "comments": 2, "created_at": "2022-08-26T00:37:26Z", "creator": "WilliamTylerBradley", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": "Future", "number": 2137, "state": "open", "title": "SQL chucks appear different with R chunks when eval is false", "url": "https://github.com/quarto-dev/quarto-cli/issues/2137" }
### Bug description Using MS code, Anaconda with python 3.9.12, when selecting 'file new' if I select a .ipynb file it does nothing, however if I create a .qmb file, and then create a .ipynb it then appears. The MS code extensions I have installed are: ms-toolsai.jupyter ms-toolsai.jupyter-keymap ms-toolsai.jupyter-renderers ms-python.vscode-pylance ms-python.python quarto.quarto REditorSupport.r RDebugger.r-debugger This occurs on more than one machine, windows 10 professional: Edition Windows 10 Pro Version 20H2 Installed on ‎03/‎08/‎2022 OS build 19042.1706 Experience Windows Feature Experience Pack 120.2212.4170.0 ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "jjallaire", "comments": 2, "created_at": "2022-08-25T21:50:08Z", "creator": "Eclecticdata", "is_pull_request": false, "labels": [ "bug", "needs-repro" ], "locked": false, "milestone": "Future", "number": 2135, "state": "closed", "title": "new ipynb file not appearing until a new .qmd file is created", "url": "https://github.com/quarto-dev/quarto-cli/issues/2135" }
### Bug description test code ````md --- title: 'debug code fold' format: html: code-fold: true embed-resources: true standalone: true execute: cache: false echo: false --- ```{ojs} 1+1 ``` ```` output: ![image](https://user-images.githubusercontent.com/5415510/186770778-d1a1f1b3-6f8a-45f1-9c4c-5bf27c3ced5c.png) This bug is caused by `code-fold: true` in the header. When remove this line, the rendering is ok. But it would better to check if echo == Ture before display the code fold mark. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
{ "assignee": "cscheid", "comments": 1, "created_at": "2022-08-25T21:18:23Z", "creator": "y9c", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2134, "state": "closed", "title": "code-fold still exist even if `echo` is set as false", "url": "https://github.com/quarto-dev/quarto-cli/issues/2134" }
I've been doing a lot of work on the shell scripts, and there's been some headache around platform-specific syntax. I saw some of that in my conda days. The only real way to avoid the headache is to strive for POSIX compliance, which can be something of a headache unto itself. The first part of this proposal is to: * Add a shellcheck step to our CI to show our status * Make an effort to get our scripts into POSIX compliance The second part of this proposal is to create native, standalone executables to replace our shell scripts. This is really only relevant to the `quarto` and `quarto.cmd` scripts. Native executables are not mutually exclusive with POSIX compatibility. Each part should be considered in terms of what goes into installers/packages and what only developers use. The argument for POSIX compliance in our dev scripts is much weaker than the argument for it in the end-user scripts. It's reasonable to establish some BASH requirement for our dev scripts. What this really boils down to is that it would be good to have the end-user scripts be POSIX compliant or be replaced by a standalone compiled executable (go, rust, whatever is easiest and most completely standalone).
{ "assignee": null, "comments": 3, "created_at": "2022-08-25T17:19:01Z", "creator": "msarahan", "is_pull_request": false, "labels": [], "locked": false, "milestone": null, "number": 2128, "state": "closed", "title": "Proposal: posix compliance in shell scripts; native compiled launcher", "url": "https://github.com/quarto-dev/quarto-cli/issues/2128" }
<div type='discussions-op-text'> <sup>Originally posted by **cbrnr** August 25, 2022</sup> I created a website with `quarto create-project website --type website`. In `_quarto.yml` I changed the `theme` to `flatly` because the issue is more pronounced with this theme (but it also occurs with the default `cosmo` theme). Then after `quarto preview`, repeatedly click on "Home" in the navbar (or switch between "Home" and "About"). Notice when the corresponding page is rendered, the main text jumps down a little. Here's a screen recording to show what I mean: https://user-images.githubusercontent.com/4377312/186645355-abfbcc48-3137-4889-97ad-01a7e666f004.mov Any ideas how to fix this behavior? I'm using Quarto 1.0.36 (part of RStudio) on macOS.</div>
{ "assignee": "dragonstyle", "comments": 1, "created_at": "2022-08-25T16:09:46Z", "creator": "cscheid", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2126, "state": "closed", "title": "Website text \"jumps\" when rendered", "url": "https://github.com/quarto-dev/quarto-cli/issues/2126" }
e.g. ````markdown ```{python} #| output: asis %%javascript // some JS code ``` ```` This is because cell magics need to be the first line of the cell. Note that the `keep-ipynb` feature is really designed for debugging rather than for producing a final notebook for distribution (e.g. markdown constructs like citations and crossrefs are not resolved in this version). We should either resolve this or make it more clear in the documentation that `keep-ipynb` is for debugging intermediate representations (we could even change the filename to make this more clear).
{ "assignee": "jjallaire", "comments": 7, "created_at": "2022-08-25T12:25:17Z", "creator": "jjallaire", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": "v1.4", "number": 2123, "state": "open", "title": "keep-ipynb notebook with cell magics and yaml options can't be executed", "url": "https://github.com/quarto-dev/quarto-cli/issues/2123" }
### Bug description Currently in the doc for engine binding regarding computation chunk (https://quarto.org/docs/computations/execution-options.html#engine-binding) we have mention of two things regarding Markdown file : * The table about auto-binding shows `.md` is supported, and no engine will be used ![image](https://user-images.githubusercontent.com/6791940/186656973-e298287c-2c38-482e-806b-5c14fdbbd647.png) * `engine: markdown` can be used to deactivate engine > You can also specify that no execution engine should be used via engine: markdown. However, we have a check for computation chunk inside `.md` document that prevent any rendering at all https://github.com/quarto-dev/quarto-cli/blob/71310bfd92ce7240042dd29f96a6f305690feb23/src/execute/markdown.ts#L67-L75 Which leads to ```` > quarto render test.md --to html ERROR: You must use the .qmd extension for documents with executable code. ```` As discussed with @jjallaire > That error is I think more helpful than not because if you have code cells in your .md you definitely aren't getting what you expected (the code won't execute). We could indeed silently send this to pandoc but I sort of view that as similar to eating bad YAML schema. Longer term its better for the user to clean this up. Should we maybe update the documentation to clearly state that `.md` document works with quarto only if there is no computation chunk ? Or at least remove the `.md` line from the table ?
{ "assignee": null, "comments": 1, "created_at": "2022-08-25T11:54:31Z", "creator": "cderv", "is_pull_request": false, "labels": [ "documentation" ], "locked": false, "milestone": null, "number": 2122, "state": "closed", "title": "Adapt the documentation about .md document with computation chunk", "url": "https://github.com/quarto-dev/quarto-cli/issues/2122" }
{ "assignee": "dragonstyle", "comments": 1, "created_at": "2022-08-25T11:34:32Z", "creator": "jjallaire", "is_pull_request": false, "labels": [ "books" ], "locked": false, "milestone": "v1.3", "number": 2120, "state": "closed", "title": "support globs for book chapter lists", "url": "https://github.com/quarto-dev/quarto-cli/issues/2120" }
Issue https://github.com/quarto-dev/quarto-cli/issues/2113 is a problem that I caused by not considering that symlinks to the quarto binary may be relative. Our dev configuration makes absolute path symlinks, and we don't otherwise have a check for this use case. It seems like we should add something to the CI process to test this behavior.
{ "assignee": null, "comments": 0, "created_at": "2022-08-25T00:54:18Z", "creator": "msarahan", "is_pull_request": false, "labels": [], "locked": false, "milestone": "Future", "number": 2114, "state": "open", "title": "Need test for relative symlinks to Quarto", "url": "https://github.com/quarto-dev/quarto-cli/issues/2114" }
### Bug description I am currently maintaining a set of homebrew formulae (for MacOS) for both quarto and quarto-dev, a user just reported (rundel/homebrew-quarto-cli#37) that as of v1.1.113 they are getting an error when running quarto installed using this formula. Specifically, ``` > quarto preview usage: basename string [suffix] basename [-a] [-s suffix] string [...] ERROR: Cannot determine the Quarto source path. This script must be run from the bin or common folder. ``` this is still occurring with the latest pre-release (v1.1.119). These formulae are installing the files from the `quarto-1.1.119-macos.tar.gz` assest into a homebrew cellar which are then symlinked into `/opt/homebrew`. The issue appears to be with how the primary quarto shell script is handling the construction of [`SCRIPT_PATH`](https://github.com/quarto-dev/quarto-cli/blob/1fbd4124cc00101f19601adbccd3ccc3474f6e1e/package/scripts/common/quarto#L4-L13) when the symlink is a relative path. ``` > ls -la /opt/homebrew/bin/quarto lrwxr-xr-x 1 rundel admin 39 Aug 24 17:54 /opt/homebrew/bin/quarto -> ../Cellar/quarto-dev/1.1.119/bin/quarto ``` For this case it appears that https://github.com/quarto-dev/quarto-cli/blob/1fbd4124cc00101f19601adbccd3ccc3474f6e1e/package/scripts/common/quarto#L8 does not work as a relative path is not handled properly by `cd` since this is relative to where the script was invoked and not where the script lives. The breaking changes seem to be part of #2015. ### Checklist - [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)? - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
{ "assignee": null, "comments": 6, "created_at": "2022-08-25T00:03:55Z", "creator": "rundel", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2113, "state": "closed", "title": "SCRIPT_PATH discovery is broken for relative symlinks ", "url": "https://github.com/quarto-dev/quarto-cli/issues/2113" }
### Bug description This bug is essentially #1141 but applied to citations in captions when using footnote citation styles. This Markdown doesn't work: ```md --- csl: oxford-university-press-note.csl --- ![A schematic diagram of known types of viroid-like agents. This figure was published in [@Lee2021a].](figures/viroid-like-schematic.png) ``` The error message also parallels #1141: ``` compilation failed- error Argument of \caption@ydblarg has an extra }. <inserted text> \par l.324 ...1093/nar/gkab974}{10.1093/nar/gkab974}.}} ``` ### Checklist - [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)? - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
{ "assignee": "dragonstyle", "comments": 1, "created_at": "2022-08-24T22:54:16Z", "creator": "Benjamin-Lee", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2112, "state": "closed", "title": "Footnote-style citation in figure caption crashed PDF render", "url": "https://github.com/quarto-dev/quarto-cli/issues/2112" }
Per previous conversations @cscheid -- Quarto websites are fantastic for individual websites, but features are lacking for group or organization websites. The Hugo Academic framework enabled a taxonomy across the site for aggregating publications by author in a seamless manner. Quarto Listings are a start to this but need some ability to flag authors on publication entries and then aggregate each respective authors' publications on their individual page within the site.
{ "assignee": "cscheid", "comments": 6, "created_at": "2022-08-24T20:56:34Z", "creator": "kmasiello", "is_pull_request": false, "labels": [], "locked": false, "milestone": "v1.4", "number": 2110, "state": "open", "title": "Better frameworks for organization-centric websites ", "url": "https://github.com/quarto-dev/quarto-cli/issues/2110" }
### Bug description Code: ````md --- title: "test webpage" format: html: code-fold: true execute: cache: true jupyter: python3 --- ```{python} #| label: fig-demo #| fig-cap: "This is a demo figure for debug" from bokeh.io import output_notebook output_notebook(hide_banner=True) from bokeh.palettes import Spectral5 from bokeh.plotting import figure, show from bokeh.sampledata.autompg import autompg as df from bokeh.transform import factor_cmap df.cyl = df.cyl.astype(str) group = df.groupby('cyl') cyl_cmap = factor_cmap('cyl', palette=Spectral5, factors=sorted(df.cyl.unique())) p = figure(height=350, x_range=group, title="MPG by # Cylinders", toolbar_location=None, tools="") p.vbar(x='cyl', top='mpg_mean', width=1, source=group, line_color=cyl_cmap, fill_color=cyl_cmap) show(p) ``` ```` Output: ![image](https://user-images.githubusercontent.com/5415510/186504610-7b9a4437-45b5-461d-b2bc-570ee8a45dd0.png) The subfigure 1b and 1c is empty and should be exist. ### Checklist - [x] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)? - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
{ "assignee": "cscheid", "comments": 9, "created_at": "2022-08-24T19:19:42Z", "creator": "y9c", "is_pull_request": false, "labels": [ "bug", "needs-discussion" ], "locked": false, "milestone": "v1.3", "number": 2107, "state": "closed", "title": "A single bokeh plot will be wrongly identified as several subfigures. ", "url": "https://github.com/quarto-dev/quarto-cli/issues/2107" }
### Bug description The ipynb may be there from keep-ipynb or just not cleaned up from a previous render error ### Checklist - [ ] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)? - [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
{ "assignee": "jjallaire", "comments": 1, "created_at": "2022-08-24T17:02:21Z", "creator": "jjallaire", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2101, "state": "closed", "title": "index.qmd and index.ipynb causes rendering error in website", "url": "https://github.com/quarto-dev/quarto-cli/issues/2101" }
### Bug description Hi, thank you for your amazing work. I'm trying to add an audio file to my blog, and I get a Babushka-like bug: The audio is being rendered but every time a get another copy of "_site" inside the previous "_site" file. I made a reprex of the problem: ### Rendered Blog (everything is working well here): https://reproduce-bug-audio.netlify.app/about.html ### Github Links: - Reprex of the blog: https://github.com/uriahf/reproduce_bug_audio - YMAL call for resources: https://github.com/uriahf/reproduce_bug_audio/blob/a262d13fced8ab6010b33bdb1c6527d434db35f5/about.qmd#L16-L19 - Babushka-like _site files https://github.com/uriahf/reproduce_bug_audio/tree/main/_site/_site/_site/_site/_site/_site/_site/_site - Commits (one for each time I rendered the quarto file): https://github.com/uriahf/reproduce_bug_audio/commits/main ### My Rstudio IDE version: RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36 My OS is windows. ![](https://images.rawpixel.com/image_800/cHJpdmF0ZS9zdGF0aWMvaW1hZ2Uvd2Vic2l0ZS8yMDIyLTA0L2xyL2ZybWF0cmlvc2hrYV93b29kZW5fY3VsdHVyZV9zeW1ib2xfMC1pbWFnZS1reWJiMHRrdi5qcGc.jpg) ### Checklist - [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)? - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
{ "assignee": "dragonstyle", "comments": 0, "created_at": "2022-08-24T14:03:38Z", "creator": "uriahf", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2097, "state": "closed", "title": "Adding audio file to quarto-blog creates \"_site\" new nested file each time that the site is being rendered.", "url": "https://github.com/quarto-dev/quarto-cli/issues/2097" }
I've seen many users put document level YAML options in the `project` and `website` keys. This does not get reported as an error b/c those schemas aren't closed. I think we need to close up schemas that can be right away as the longer we wait the more projects/documents will be broken when we do (or at the limit we can never close them).
{ "assignee": "cscheid", "comments": 2, "created_at": "2022-08-24T13:53:16Z", "creator": "jjallaire", "is_pull_request": false, "labels": [ "yaml-validation" ], "locked": false, "milestone": "v1.1", "number": 2096, "state": "closed", "title": "close yaml schemas that can be closed", "url": "https://github.com/quarto-dev/quarto-cli/issues/2096" }
I've created a new Quarto book project. When I render the provided example in HTML format (without having made any changes), the search index appears to be incomplete. Example: The file `intro.qmd` begins like this: ``` # Introduction This is a book created from markdown and executable code. See @knuth84 for additional discussion of literate programming. ``` The corresponding part in `search.json` however looks like this: ``` { "objectID": "intro.html", "href": "intro.html", "title": "1  Introduction", "section": "", "text": "See Knuth (1984) for additional discussion of literate programming." } ``` The same issue occurs with `summary.qmd`. ``` R version 4.2.1 (2022-06-23) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Big Sur 11.6.8 RStudio version: 2022.07.1 Build 554 Quarto version: 1.1.113 ```
{ "assignee": "dragonstyle", "comments": 0, "created_at": "2022-08-24T13:22:07Z", "creator": "jderrfuss", "is_pull_request": false, "labels": [], "locked": false, "milestone": "v1.2", "number": 2095, "state": "closed", "title": "search.json appears to be incomplete", "url": "https://github.com/quarto-dev/quarto-cli/issues/2095" }
### Bug description Take this example where we have a very wide code chunk `````markdown --- title: "Untitled" format: revealjs execute: echo: true --- ## Slides 1 ```{r} #| output-location: column library(ggplot2) ggplot(airquality, aes(Temp, Ozone)) + geom_point() + geom_smooth(method = "loess") ``` ````` This is what we get with stable quarto ![image](https://user-images.githubusercontent.com/6791940/186413711-3f269b45-da48-459f-8c44-adf240d7e58c.png) This is what we get with pre-release ![image](https://user-images.githubusercontent.com/6791940/186413399-f17f574a-7668-49a9-90d0-16b782be1b1b.png) The second column is outside the slide ![image](https://user-images.githubusercontent.com/6791940/186413522-c76a638d-0441-4259-bf5a-e25f3b7051bc.png) Possibly related to this change: https://github.com/quarto-dev/quarto-cli/commit/a43090353c454860dca50164f06896dec5a48968 to try fixing https://github.com/quarto-dev/quarto-cli/issues/1940 as `flex` is replacing `width` ![image](https://user-images.githubusercontent.com/6791940/186413851-d41ded98-4296-4dda-9c25-d854aff5bc58.png) This came up from a discussion in https://github.com/quarto-dev/quarto-cli/discussions/2088#discussioncomment-3464422
{ "assignee": "jjallaire", "comments": 1, "created_at": "2022-08-24T12:05:30Z", "creator": "cderv", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.1", "number": 2093, "state": "closed", "title": "output-location to column does not work anymore for revealjs", "url": "https://github.com/quarto-dev/quarto-cli/issues/2093" }
### Bug description I don't know what `xfun::session_info()` is, hopefully the GH issue works without that?? (from the link with instructions to follow...) I am following this tutorial: https://quarto.org/docs/get-started/authoring/jupyter.html and am using `nb_conda_kernel` to manage my Jupyter kernels from different environments. This leads to notebook metadata having different kernelspec metadata than what are available. However, this should not matter, as the YAML doc options should precede those kind of findings, but I find that that is not the case. Here's my whole notebook: ```json { "cells": [ { "cell_type": "raw", "id": "563ca2fc-b9a0-4e94-ab33-a511b79debe4", "metadata": {}, "source": [ "---\n", "title: \"Quarto Document\"\n", "author: \"Michael Aye\"\n", "toc: true\n", "number-sections: true\n", "highlight-style: pygments\n", "format:\n", " html:\n", " code-fold: false\n", " html-math-method: katex\n", " pdf:\n", " geometry:\n", " - top=30mm\n", " - left=20mm\n", " docx: default \n", "jupyter: python3\n", "---" ] }, { "cell_type": "markdown", "id": "86065445-3aab-4e52-ad26-2edf63ff1670", "metadata": {}, "source": [ "# Test\n", "\n", "This is a test." ] }, { "cell_type": "code", "execution_count": null, "id": "a5fa2a9c-093f-4558-a4b9-686e684c6d59", "metadata": {}, "outputs": [], "source": [ "2+2" ] } ], "metadata": { "kernelspec": { "display_name": "Python [conda env:py310] *", "language": "python", "name": "conda-env-py310-py" } }, "nbformat": 4, "nbformat_minor": 5 } ``` Here are the available kernels, note the matching `python3` kernel name, fitting the doc options. ```bash /Dropbox/src/quarto_hello ❯ jupyter kernelspec list [ListKernelSpecs] WARNING | Config option `kernel_spec_manager_class` not recognized by `ListKernelSpecs`. Available kernels: python3 /home/ayek72/mambaforge/envs/py310/share/jupyter/kernels/python3 xonsh /usr/share/jupyter/kernels/xonsh ``` and here's what `quarto` says: ``` ~/Dropbox/src/quarto_hello ❯ quarto render formats.ipynb --to html --execute ERROR: No such kernel named conda-env-py310-py ``` For reference, here's my output of `quarto check`: ```bash ~/Dropbox/src/quarto_hello ❯ quarto check [✓] Checking Quarto installation......OK Version: 1.0.37 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.5 (Conda) Path: /home/ayek72/mambaforge/envs/py310/bin/python Jupyter: 4.11.1 Kernels: python3, xonsh [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` I don't know what a QMD file is, but with above notebook json and the commands, it should be easily reproducible. It simply seems to be the case that `quarto` looks at the notebook metadata first instead of looking at the YAML docoptions first. ## OS ``` ~/Dropbox/src/quarto_hello ❯ uname -a Linux apollo.planet.fu-berlin.de 5.15.0-46-generic #49~20.04.1-Ubuntu SMP Thu Aug 4 19:15:44 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux ``` Running a KDE Neon : ![image](https://user-images.githubusercontent.com/69774/186401244-b94bbd27-83eb-40d3-af9d-050bfd04aa3b.png) ### Checklist - [ ] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)? - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
{ "assignee": "jjallaire", "comments": 1, "created_at": "2022-08-24T10:55:16Z", "creator": "michaelaye", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2091, "state": "closed", "title": "quarto --execute ignores jupyter kernel name in yaml doc options", "url": "https://github.com/quarto-dev/quarto-cli/issues/2091" }
At https://quarto.org/docs/presentations/revealjs/presenting.html, there is a section on the Navigation Menu. It gives an example of the `side`, `width` and `number` options: ``` format: revealjs: side: right width: wide ``` However, this does not seem to work. Autocompletion in the yaml header also doesn't mention these options. Well, it does mention the `width` option, but that's for the overall presentation, not the nav menu. Borrowing from the documentation for revealjs in RMarkdown (https://github.com/rstudio/revealjs), this does seem to work: ``` format: revealjs: menu: side: right width: wide ``` However, this implementation seems to obliviate the option to not show the hamburger, which is done as follows: ``` format: revealjs: menu: false ``` because you can either give `menu: false` OR `menu: <<options on following lines>>` in the yaml section. There is no option for not showing the hamburger thingy AND having options for the case where you do want to open the menu (hitting the `M` key). So, two things: * There's an error in the documentation * A suboption in the `menu` option list (besides `side`, `width`, `numbers` and `use-text-content-for-missing-titles`) for not showing the hamburger would be nice (e.g., `show-hamburger: true/false`). To be clear, the second bullet refers to something like this: ``` format: revealjs: menu: side: right width: wide show-hamburger: false ```
{ "assignee": "cscheid", "comments": 1, "created_at": "2022-08-24T07:48:45Z", "creator": "mathijsdeen", "is_pull_request": false, "labels": [ "enhancement", "revealjs" ], "locked": false, "milestone": "Future", "number": 3376, "state": "open", "title": "documentation error on navigation menu in revealjs", "url": "https://github.com/quarto-dev/quarto-cli/issues/3376" }
Really excited about quarto, but coming from blogdown/hugo world I'm struggling to understand how custom SASS themes work. In particular, I've read https://quarto.org/docs/output-formats/html-themes-more.html#bootswatch-sass-theme-files, which says: > We’ve merged Bootswatch themes for Bootstrap 5 into this single file theme format in our repo here: > https://github.com/twbs/bootstrap/blob/main/scss/_variables.scss err... is that the correct link? That appears to be the (unmerged?) official bootstrap-5 sources of the Bootstrap team, not a merged scss file in "our repo"? (trying to better understand this single-file format deal). More generally, it's not clear how I would go about bringing in external bootstrap-based SASS themes. For instance, I rather like the MIT-licensed bootstrap-5 themes from CreativeTim, like https://github.com/creativetimofficial/material-kit. It seems like to work with quarto, I need to refactor that whole sass stack into a single .scss file, ordered specifically as quarto expects, with the five decorations described in the above link? (e.g. ` /*-- scss:uses --*/`, `/*-- scss:functions --*/`). Is that correct? Or do I just need to convert my sass theme to a bootswatch theme (al al https://bootswatch.com/help/#customization) ? Maybe just my ignorance here in these things, but manually refactoring perfectly good SASS code seems like a significant and somewhat cumbersome and needless design -- e.g. compared to converting material-kit or other bootstrap-based SASS templates into hugo themes which was super straight-forward. Maybe the answer is that users who want lower-level customization should just stick with hugo and this is out of scope for quarto? All the same, I had hoped that quarto would lower rather than raise the barrier for user-contributed themes. Sorry if I'm just confused?
{ "assignee": null, "comments": 2, "created_at": "2022-08-24T00:35:56Z", "creator": "cboettig", "is_pull_request": false, "labels": [], "locked": false, "milestone": null, "number": 2086, "state": "closed", "title": "Questions/ need more advice on extending themes ?", "url": "https://github.com/quarto-dev/quarto-cli/issues/2086" }
This came up in https://github.com/quarto-ext/code-filename/issues/4 Quarto allows to install from a file (https://quarto.org/docs/extensions/distributing.html#archive-files) but expect a specific structure. When downloading from Github source, there is a parent folder to the repo folder. We could maybe check for that structure instead of just directly looking for the `_extensions` folder. See discussion in the issue link cc @dragonstyle
{ "assignee": "dragonstyle", "comments": 2, "created_at": "2022-08-23T19:11:17Z", "creator": "cderv", "is_pull_request": false, "labels": [ "bug", "extensions" ], "locked": false, "milestone": "v1.2", "number": 2081, "state": "closed", "title": "Installing extension from Git archive repo does not work", "url": "https://github.com/quarto-dev/quarto-cli/issues/2081" }
Tag @dragonstyle per discussion, here are the pre-release references. It might be helpful to formalize the strategy of if y'all do or do not want to indicate a minimum version when introducing new features that aren't backported. Reference to 0.9: [Mermaid Diagrams](https://github.com/quarto-dev/quarto-web/blob/5a79cba1d466d55da139cd447c9f3fe1fc812d4d/docs/authoring/diagrams.qmd#L22) Reference to 1.0.15: [Shortcodes](https://github.com/quarto-dev/quarto-web/blob/5a79cba1d466d55da139cd447c9f3fe1fc812d4d/docs/extensions/shortcodes.qmd#L105) Reference to 0.9: [YAML Intelligence](https://github.com/quarto-dev/quarto-web/blob/5a79cba1d466d55da139cd447c9f3fe1fc812d4d/docs/tools/vscode.qmd#L124)
{ "assignee": null, "comments": 5, "created_at": "2022-08-23T18:44:20Z", "creator": "jthomasmock", "is_pull_request": false, "labels": [ "documentation", "needs-discussion" ], "locked": false, "milestone": "v1.3", "number": 4463, "state": "closed", "title": "Reference to old or pre-release RStudio/Quarto versions", "url": "https://github.com/quarto-dev/quarto-cli/issues/4463" }
Allowing variable overrides in batch scripts is hairy because of the need for complicated `startlocal enabledelayedexpansion` stuff. It makes our scripts fragile and limits the number of people who are willing to work on them. I propose that we cut `configure.cmd` completely, and run configure.sh on all platforms. What this requires is the use of msys2 or git for windows. WSL is not useful here, it behaves like a linux system for the sake of our scripts instead of a bash-on-windows thing. We clearly can't require this on end user systems for our quarto.cmd script. This proposal is only for development. The quarto.cmd script doesn't present the same override headaches anyway, so it's not a big deal there. I will put up a PR showing that configure.sh can run fine on windows. If that is satisfactory, then maybe we can consider removing configure.cmd.
{ "assignee": null, "comments": 3, "created_at": "2022-08-23T13:47:26Z", "creator": "msarahan", "is_pull_request": false, "labels": [], "locked": false, "milestone": "Future", "number": 2071, "state": "open", "title": "Proposal: use bash on windows for configure", "url": "https://github.com/quarto-dev/quarto-cli/issues/2071" }
### Bug description I'm unable to schedule a cron job to automatically render/publish a quarto website. The command get executed but the log just shows an empty line (like the output you get when you just execute quarto without any parameter). This is the entry in my cron schedule file (linux/debian). The exact same command works when executed in the terminal. `*/10 * * * * /usr/local/bin/quarto publish --no-prompt --no-browser quarto-pub '/home/rstudio/mine_2022/' >> '/home/rstudio/mine_2022/siteupdate.log' 2>&1` I was not able to find documentation on how to schedule such a command. Thank you in advance for your help. Best, Fabio ### Checklist - [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)? - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
{ "assignee": "jjallaire", "comments": 2, "created_at": "2022-08-23T09:42:54Z", "creator": "fabiogiglietto", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2066, "state": "closed", "title": "Schedule quarto publish with cron", "url": "https://github.com/quarto-dev/quarto-cli/issues/2066" }
When using `quarto` to build websites, some static site generators, for instance `mkdocs`, create sites with "pretty" URLs by default. It would be great if Quarto also did this. For instance, in a project containing the file `science.md`, `quarto render` will generate that as `science.html`, resulting in a URL like, `https://example.com/science.html`. In contrast, `mkdocs build` would generate it as `science/index.html`, meaning that, when published, it could be accessed at `https://example.com/science/`. The current workaround would be to create the original file at `science/index.md`, in which case, both `quarto` and `mkdocs` would generate the same HTML in the same places. This is important for sites that might be considering migrating to `quarto` that are not currently structured along the lines of the workaround.
{ "assignee": null, "comments": 1, "created_at": "2022-08-23T09:02:29Z", "creator": "sellorm", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": "Future", "number": 2065, "state": "open", "title": "Quarto should output websites with \"pretty\" URLs", "url": "https://github.com/quarto-dev/quarto-cli/issues/2065" }
I find the ability to insert tikz pictures by simply calling `![caption](tikz_code.tex){#label}` when rendering to PDF to be extremely elegant and practical, unfortunately the pictures do not seem to render for HTML outputs. Trying to find a workaround I found the [TikZJax](https://github.com/kisonecat/tikzjax) library. It looks like it could be helpfu for this.
{ "assignee": null, "comments": 0, "created_at": "2022-08-23T07:41:08Z", "creator": "Matrsz", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": "Future", "number": 2064, "state": "open", "title": "Feature Request: Rendering TikZ pictures for HTML output", "url": "https://github.com/quarto-dev/quarto-cli/issues/2064" }
Currently the callout blocks visible text stays the same if the block is collapsed or expanded, like here: Collapsed: <img width="773" alt="image" src="https://user-images.githubusercontent.com/32404415/186082810-09ec1c12-fe70-4704-850f-d0e34c7d2410.png"> Expanded: <img width="770" alt="image" src="https://user-images.githubusercontent.com/32404415/186082849-91ad430e-399a-4c70-b99f-75bfdac4459f.png"> Would it make sense to have different text for when be block is collapsed: "Expand to see me" and different when it's expanded: "Collapse to hide me"?
{ "assignee": null, "comments": 0, "created_at": "2022-08-23T06:10:17Z", "creator": "miwojc", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": "Future", "number": 2063, "state": "open", "title": "[feature request] change visible text for callout blocks when collapsed/expanded", "url": "https://github.com/quarto-dev/quarto-cli/issues/2063" }
### Bug description When I choose `revealjs` as a `format` for a `qmd` document, it does not render `width` variable from `ojs` properly. ````{qmd} --- format: revealjs --- ## DEMO ```{ojs} md`${width}` ``` ```` ![image](https://user-images.githubusercontent.com/10469752/186004708-b1e97dbf-8c70-4f34-8035-35b9c0de83e2.png) When I render it as `html`, it works well. ![image](https://user-images.githubusercontent.com/10469752/186004760-8875e7bd-91be-424c-bcf8-f6d1a42ad4ff.png) OS: mac air m1 Venture 13.0 Beta 22A5321d ### Checklist - [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)? - [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
{ "assignee": "cscheid", "comments": 3, "created_at": "2022-08-22T19:45:45Z", "creator": "kwangkim", "is_pull_request": false, "labels": [ "bug", "ojs-engine" ], "locked": false, "milestone": "v1.2", "number": 2058, "state": "closed", "title": "[revealjs] ojs runtime error: Cannot read properties of null (reading 'clientWidth') from width", "url": "https://github.com/quarto-dev/quarto-cli/issues/2058" }
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2056 <div type='discussions-op-text'> <sup>Originally posted by **Hedonical** August 22, 2022</sup> Hi everyone, I am trying to make it so only the header of a section is centered and center text as seen in the live editor view: ![Screenshot from 2022-08-22 11-11-08](https://user-images.githubusercontent.com/91704211/185992668-ea435ec6-3cce-40d4-b481-c867d3f87091.png) But when I render the HTML document, it applys the centering and color to the entire section: ![Screenshot from 2022-08-22 14-24-18](https://user-images.githubusercontent.com/91704211/185992753-fd422d6e-5a8d-4162-947e-9a3ce3b2e9e4.png) Is there an easy way to make it so the css elements only apply to the header and not all of the text under? </div>
{ "assignee": null, "comments": 7, "created_at": "2022-08-22T18:51:32Z", "creator": "cscheid", "is_pull_request": false, "labels": [], "locked": false, "milestone": null, "number": 2057, "state": "closed", "title": "How to stop CSS styling of a header applying to entire section?", "url": "https://github.com/quarto-dev/quarto-cli/issues/2057" }
I have created a Blog and I use Github Pages to deploy it. However, my blog struggles to get updated on the web when I have modified something in an old post. What I do, is that I push the changes to the main repo and then I go to the terminal and just type the usual command: `quarto publish ` I have tried to delete my cache in the browser, but the blog fails to update. I honestly cannot understand what is the process to update a blog manually, i.e. without GithubActions, when one is using Github Pages for deployment.
{ "assignee": null, "comments": 9, "created_at": "2022-08-22T17:35:24Z", "creator": "ghost", "is_pull_request": false, "labels": [ "bug", "needs-repro" ], "locked": false, "milestone": null, "number": 2055, "state": "closed", "title": "Deployment with Github Pages ", "url": "https://github.com/quarto-dev/quarto-cli/issues/2055" }
Fixes `colorlinks` issue in pdf output
{ "assignee": "dragonstyle", "comments": 0, "created_at": "2022-08-22T17:08:11Z", "creator": "dragonstyle", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.1", "number": 2054, "state": "closed", "title": "Update pandoc template to 2.19.1", "url": "https://github.com/quarto-dev/quarto-cli/issues/2054" }
### Bug description It is [documented](https://quarto.org/docs/computations/r.html#chunk-options) that `!expr` works with `fig-cap`, but it doesn't work with `fig-subcap`. ````md ```{r} #| label: fig-charts #| fig-cap: Charts #| fig-subcap: !expr c("First", "Second") plot(cars) plot(pressure) ``` ```` I get the following error when running `quarto render` on the file: ``` ERROR: Validation of YAML cell metadata failed. In file subfig-eval-yaml.qmd (line 4, columns 16--42) Key fig-subcap has value !expr c("First", "Second"), which must be 'true' 3: #| fig-cap: Charts 4: #| fig-subcap: !expr c("First", "Second") ~~~~~~~~~~~~~~~~~~~~~~~~~~ ERROR: Render failed due to invalid YAML. ``` ### `quarto check` Output ``` [>] Checking Quarto installation......OK Version: 1.0.38 Path: C:\scoop\apps\quarto\current\bin\ CodePage: 1250 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.6 Path: C:/msys64/mingw64/bin/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with python -m pip install jupyter [>] Checking R installation...........OK Version: 4.2.1 Path: C:/scoop/apps/r-release/current LibPaths: - C:/scoop/apps/r-release/4.2.1/library rmarkdown: 2.15 [>] Checking Knitr engine render......OK ``` ### `quarto tools check` Output ``` [>] Inspecting tools Tool Status Installed Latest chromium Not installed --- 869685 tinytex External Installation --- v2022.08 ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area? - [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?
{ "assignee": null, "comments": 6, "created_at": "2022-08-22T15:25:06Z", "creator": "svraka", "is_pull_request": false, "labels": [ "bug", "yaml-validation" ], "locked": false, "milestone": "Future", "number": 2047, "state": "open", "title": "Evaluating R code with `!expr` in `fig-subcap` doesn't work", "url": "https://github.com/quarto-dev/quarto-cli/issues/2047" }
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2043 <div type='discussions-op-text'> <sup>Originally posted by **maelle** August 22, 2022</sup> Say I have a chapter file called `abb-blurb.qmd`. How can I make the corresponding HTML file something else than `abb-blurb.HTML`? Do I need to use a YAML field in the file?</div>
{ "assignee": "dragonstyle", "comments": 2, "created_at": "2022-08-22T15:13:09Z", "creator": "jjallaire", "is_pull_request": false, "labels": [], "locked": false, "milestone": "v1.2", "number": 2045, "state": "closed", "title": "How to change the rendered file path in Quarto books", "url": "https://github.com/quarto-dev/quarto-cli/issues/2045" }
### Bug description This is a minimal sample project. [quarto_minimal.zip](https://github.com/quarto-dev/quarto-cli/files/9394347/quarto_minimal.zip) The post content is simply: ````qmd --- title: test --- ```{r} plot(1) ``` ```` The rendered site will not display the picture stated in post. ![image](https://user-images.githubusercontent.com/13306020/185921680-8b47fdce-27c0-496e-96de-dc0658b0cb6b.png) Error message from console is as follows: ```r #> GET: / #> /index_files/figure-html/unnamed-chunk-1-1.png (404: Not Found) #> /index_files/figure-html/unnamed-chunk-1-1.png (404: Not Found) ``` <sup>Created on 2022-08-22 with [reprex v2.0.2](https://reprex.tidyverse.org)</sup> <details style="margin-bottom:10px;"> <summary> Session info </summary> ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.1 (2022-06-23 ucrt) #> os Windows 10 x64 (build 22000) #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate Chinese (Simplified)_China.utf8 #> ctype Chinese (Simplified)_China.utf8 #> tz Asia/Taipei #> date 2022-08-22 #> pandoc 2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.1) #> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.1) #> evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.1) #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.1) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1) #> highr 0.9 2021-04-16 [1] CRAN (R 4.2.1) #> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1) #> knitr 1.39 2022-04-26 [1] CRAN (R 4.2.1) #> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.1) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1) #> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.1) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.1) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0) #> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.1) #> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1) #> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.1) #> rmarkdown 2.15 2022-08-16 [1] CRAN (R 4.2.1) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.1) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1) #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1) #> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.1) #> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.1) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1) #> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.1) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1) #> xfun 0.32 2022-08-10 [1] CRAN (R 4.2.1) #> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.1) #> #> [1] C:/Users/lenovo/AppData/Local/R/win-library/4.2 #> [2] C:/Program Files/R/R-4.2.1/library #> #> ────────────────────────────────────────────────────────────────────────────── ``` </details> ### `quarto check` Output ```bash [>] Checking Quarto installation......OK Version: 1.0.38 Path: C:\PROGRA~1\Quarto\bin\ CodePage: 936 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.5 (Conda) Path: C:/Users/lenovo/miniconda3/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with conda install jupyter (/) Checking R installation........... ``` ### `quarto tools check` Output ```bash [>] Inspecting tools Tool Status Installed Latest chromium Not installed --- 869685 tinytex Not installed --- v2022.08 ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area? - [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?
{ "assignee": "dragonstyle", "comments": 9, "created_at": "2022-08-22T12:40:13Z", "creator": "psychelzh", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.3", "number": 2042, "state": "closed", "title": "For website project, images generated by R code does not display normally in listing page", "url": "https://github.com/quarto-dev/quarto-cli/issues/2042" }
See discussion and example in https://github.com/quarto-dev/quarto-cli/issues/1581 In short, some **knitr** option could be useful with other computation engine and this require broader Quarto support This could maybe even be done using Lua filter in an extension (TBC)
{ "assignee": null, "comments": 0, "created_at": "2022-08-22T07:49:51Z", "creator": "cderv", "is_pull_request": false, "labels": [], "locked": false, "milestone": "Future", "number": 2040, "state": "open", "title": " Consider support for `class.source` `class.output` `attr.source` `attr.output` equivalent (not only available for knitr cells)", "url": "https://github.com/quarto-dev/quarto-cli/issues/2040" }
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2003 <div type='discussions-op-text'> <sup>Originally posted by **andrewcstewart** August 19, 2022</sup> Looking under the list of formats under https://quarto.org/docs/output-formats/all-formats.html, one format that would be nice to add is Confluence's. I think there are probably a few different options there, but one would be https://confluence.atlassian.com/doc/confluence-storage-format-790796544.html Just starting this conversation to see if there is similar interest out there.</div>
{ "assignee": "allenmanning", "comments": 3, "created_at": "2022-08-22T07:05:16Z", "creator": "allenmanning", "is_pull_request": false, "labels": [ "enhancement" ], "locked": false, "milestone": "v1.3", "number": 2038, "state": "closed", "title": "Publish to Confluence", "url": "https://github.com/quarto-dev/quarto-cli/issues/2038" }
### Bug description ````markdown --- title: "test" format: html: self-contained: true keep-md: true --- ```{r} plot(mtcars) ``` ```` This will produce with quarto 1.1.107 on the RStudio Viewer preview pane on Windows ![image](https://user-images.githubusercontent.com/6791940/185857724-7c6225f6-7960-4c3e-b9d2-e06938f6d060.png) This is due to a bug in Pandoc introduced in version 2.19.1 when base64 package was changed. See https://github.com/jgm/pandoc/issues/8239 We should probably wait for new Pandoc release before new Quarto release FWIW I check with R Markdown document that using Pandoc 2.19 works, and 2.19.1 does not.
{ "assignee": null, "comments": 2, "created_at": "2022-08-22T06:56:20Z", "creator": "cderv", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2037, "state": "closed", "title": "self-contained document have broken images", "url": "https://github.com/quarto-dev/quarto-cli/issues/2037" }
Hi, I was running a simple Quarto document that just takes the mean of `c(1,2,3)` and wanted to know how `code-link` and `code-line-numbers` work. The versions are Quarto 1.0.11, R 4.2.1 and RStudio 2022.07.1 Build 554. Hopefully the issue reported can be reproduced. I understand that both R packages `downlit` and `xml2` need to be installed. Below is the content of the Quarto document. ``` --- title: "CodeNumberVSCodeLink" format: html: code-link: true code-line-numbers: true --- ## Quarto Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>. ```{r} mean(c(1,2,3)) ``` If I set `code-link: true` and `code-line-numbers: false` and click render, the hyperlink works ![image](https://user-images.githubusercontent.com/9066508/185841447-780f55c9-9928-43e4-a8de-98a1ec7a0339.png) If I set `code-link: false` and `code-line-numbers: true` and click render, the code numbering works ![image](https://user-images.githubusercontent.com/9066508/185841533-b4f56945-578d-448d-82ba-0306f2ada545.png) However when I set both `code-link: true` and `code-line-numbers: true` and click render, **only** the the code numbering works. ![image](https://user-images.githubusercontent.com/9066508/185841667-cfa72099-7f39-4f26-8bc8-6e9e57876909.png) Is there a reason for this behaviour ?
{ "assignee": null, "comments": 2, "created_at": "2022-08-22T04:55:25Z", "creator": "JauntyJJS", "is_pull_request": false, "labels": [ "bug", "upstream" ], "locked": false, "milestone": "Future", "number": 2036, "state": "open", "title": "`code-link` and `code-line-numbers` does not work together when both set to true", "url": "https://github.com/quarto-dev/quarto-cli/issues/2036" }
### Bug description I keep getting the error "\Quarto\bin\ was unexpected at this time" when trying to use a fresh install of Quarto. The only command I have found so far that works is "quarto -- version" which outputs: "1.0.38" Windows 10 Version 10.0.19044 Build 19044 I have verified that quarto is in my path. ### `quarto check` Output \Quarto\bin\ was unexpected at this time. ### `quarto tools check` Output \Quarto\bin\ was unexpected at this time. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area? - [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?
{ "assignee": null, "comments": 2, "created_at": "2022-08-22T04:37:27Z", "creator": "kpjmcg", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2035, "state": "closed", "title": "\"\\Quarto\\bin\\ was unexpected at this time\" error for all commands", "url": "https://github.com/quarto-dev/quarto-cli/issues/2035" }
### Bug description More a question than a bug but wondering if I have multiple Jupyter Notebooks in my project, each of those with different figures that I would like to reference from other notebook, how can I do that? In the "testing copy.ipynb" notebook I put two cross references: @fig-plot and @fig-plot-copy fig-plot belongs to testin.ipynb and as shown in the image below, not rendering. Also getting `WARNING: Unable to resolve crossref @fig-plot` Minimal Reproducible Example here: https://lgonzalezsa.github.io/hello_quarto/cross_copy.html https://github.com/lgonzalezsa/hello_quarto/blob/main/test/testing%20copy.ipynb ![image](https://user-images.githubusercontent.com/704686/185818466-69459ec2-5c8e-4b90-8178-ad9f7f5d63f4.png) ### `quarto check` Output _No response_ ### `quarto tools check` Output _No response_ ### Checklist - [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area? - [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?
{ "assignee": null, "comments": 1, "created_at": "2022-08-22T00:43:47Z", "creator": "lgonzalezsa", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2034, "state": "closed", "title": "How to cross reference figures from distinct Jupyter Notebooks ?", "url": "https://github.com/quarto-dev/quarto-cli/issues/2034" }
### Bug description Creating quarto website with a Jupyter Notebook using Python [Holoviz](https://holoviz.org/) plot but getting `Unable to display output for mime type(s):` I also tested seaborn package and the plots render properly. Do I need to configure a property for Holoviz plots to render properly with Quarto? Please check my minimal reproducible example here: https://lgonzalezsa.github.io/hello_quarto/testing.html#fig-plot https://github.com/lgonzalezsa/hello_quarto/blob/main/test/testing.ipynb ### `quarto check` Output ```bash [✓] Checking Quarto installation......OK Version: 1.0.38 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.12 (Conda) Path: /home/gonluisr/miniconda3/envs/conda_dev/bin/python Jupyter: 4.10.0 Kernels: julia-(8-threads)-1.7, julia-1.7, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### `quarto tools check` Output ```bash [✓] Inspecting tools Tool Status Installed Latest chromium Not installed --- 869685 tinytex Not installed --- v2022.08 ``` Linux OS: ```bash OS: Pop!_OS 22.04 LTS x86_64 Kernel: 5.19.0-76051900-generic ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area? - [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?
{ "assignee": null, "comments": 2, "created_at": "2022-08-22T00:07:04Z", "creator": "lgonzalezsa", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2033, "state": "closed", "title": "Quarto not rendering Holoviz plots | Unable to display output for mime type(s):", "url": "https://github.com/quarto-dev/quarto-cli/issues/2033" }
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2030 <div type='discussions-op-text'> <sup>Originally posted by **lukefullard** August 21, 2022</sup> Hi, I'm trying to add a table to my quarto document using the [Panel Tabulator widget](https://panel.holoviz.org/reference/widgets/Tabulator.html). While the table displays nicely and is interactive, I get a warning printed into my pdf: _Unable to display output for mime type(s)_ I googled and found [another document with a similar warning](https://nasa-openscapes.github.io/2021-Cloud-Hackathon/tutorials/05_Data_Access_Direct_S3.html#plot-the-hls-s3-object). I tried adding #| warning: false #| error: false to my Python block, bit the warning text still appeared. Could anyone tell me how to suppress this warning? Thanks. </div>
{ "assignee": "jjallaire", "comments": 3, "created_at": "2022-08-21T21:09:33Z", "creator": "jjallaire", "is_pull_request": false, "labels": [], "locked": false, "milestone": "v1.1", "number": 2031, "state": "closed", "title": "Warning: \"Unable to display output for mime type(s)\"", "url": "https://github.com/quarto-dev/quarto-cli/issues/2031" }
### Bug description ````markdown --- title: "test" format: docx --- :::{.callout-caution} ## Running Code ```{r} 1 + 1 ``` ::: ```` This causes this issue : ````bash An error occurred Found a nested callout in the document. Please fix this issue and try again. ```` This does not happen in PDF and HTML. This error is thrown from https://github.com/quarto-dev/quarto-cli/blob/852c9bb99e54e0163575ceecf7dde372b4b73321/src/resources/filters/quarto-pre/callout.lua#L533-L538 where we check for nested Divs. The Markdown generated by Quarto before Pandoc rendering is the following ````markdown :::{.callout-caution} ## Running Code ::: {.cell} ```{.r .cell-code} 1 + 1 ``` ::: {.cell-output .cell-output-stdout} ``` [1] 2 ``` ::: ::: ::: ```` Hence the error thrown. I believe this should be fixed - not sure about the context of nested Divs not allowed in Docx @dragonstyle (https://github.com/quarto-dev/quarto-cli/commit/688fd1c070739e3d629d65773da6760ad1d74e41) but it does seem something we should allow for our own expected div right ? Initially reported in https://community.rstudio.com/t/quarto-render-to-docx-word-fails-if-callout-has-a-code-chunk/145189 ### `quarto check` Output ```` quarto check [>] Checking Quarto installation......OK Version: 1.1.80 Path: C:\Users\chris\scoop\apps\quarto-prerelease\current\bin\ CodePage: unknown [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.13 Path: C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.13/python3.exe Jupyter: 4.11.1 Kernels: bash, julia-1.7, python3 [>] Checking Jupyter engine render....OK (-) Checking R installation...........++ Activating rlang global_entrace ++ Setting QUARTO_PYTHON [>] Checking R installation...........OK Version: 4.2.0 Path: C:/PROGRA~1/R/R-42~1.0 LibPaths: - C:/Users/chris/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.0/library rmarkdown: 2.14.3 [>] Checking Knitr engine render......OK ````
{ "assignee": "dragonstyle", "comments": 0, "created_at": "2022-08-21T15:38:13Z", "creator": "cderv", "is_pull_request": false, "labels": [ "bug", "verify-fixed" ], "locked": false, "milestone": null, "number": 2027, "state": "closed", "title": "Nested callout error in Docx when include code chunk in callout block", "url": "https://github.com/quarto-dev/quarto-cli/issues/2027" }
Tracking issue for this PR: https://github.com/quarto-dev/quarto-cli/pull/2015
{ "assignee": "jjallaire", "comments": 1, "created_at": "2022-08-21T13:12:42Z", "creator": "jjallaire", "is_pull_request": false, "labels": [], "locked": false, "milestone": "v1.1", "number": 2025, "state": "closed", "title": "merge conda PR", "url": "https://github.com/quarto-dev/quarto-cli/issues/2025" }
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2009 @dragonstyle You should read to the bottom of the discussion to see the clearest explanation of what the bug is. <div type='discussions-op-text'> <sup>Originally posted by **sammo3182** August 19, 2022</sup> Recently I asked a question about varying the reference allocation with Quarto in #1728. Then I find the problem that made the old rmarkdown tricks not work was because I used the [`article-format-template`](https://github.com/quarto-journals/article-format-template). The reference was in the right place I want when rendering the plain pdf but then moved to the very end of the document when rendering the `aft`. A replicable example: ```qmd --- format: pdf: number-sections: true aft-pdf: keep-tex: true aft-html: default bibliography: bio.bib title: A test --- content @Hu2020 # Reference ::: {#refs} ::: # Online Supplementary Materials ``` [bio.zip](https://github.com/quarto-dev/quarto-cli/files/9386033/bio.zip) See the difference of the reference when choosing the following options respectively: ![image](https://user-images.githubusercontent.com/6463211/185724871-cd89a2f3-24d7-4787-8515-d2aba80475e6.png) How could I allow the `aft` to recognize my reference setting? Any suggestion will be very helpful. Moreover, a more detailed instruction and examples about how to customize the template than the current [brief version](https://github.com/quarto-journals/article-format-template/blob/main/README.md) under aft repo and Quarto.org will be super welcomed---details like how to arrange the author area, showing the corresponding author, adding the key words and acknowledge, etc.</div>
{ "assignee": "dragonstyle", "comments": 5, "created_at": "2022-08-21T13:04:30Z", "creator": "jjallaire", "is_pull_request": false, "labels": [], "locked": false, "milestone": "v1.4", "number": 2024, "state": "open", "title": "Varying the reference position in `quarto-journals` template", "url": "https://github.com/quarto-dev/quarto-cli/issues/2024" }
### Bug description Would be great if collapsed sections would be accessible for follow hints, for example in qutebrowser or vimium/vimium-FF In this screenshot the collapsed section doesn't get it's own follow hint, making it not possible to navigate to it without mose. This website was generated by quarto from markdown files using github workflow actions from this repo: https://github.com/miwojc/mlq Website is built to `gh-pages` branch as per quarto instructions. <img width="1440" alt="image" src="https://user-images.githubusercontent.com/32404415/185790106-1041929f-8c94-4fce-bc5e-5d171b26c24e.png"> ### `quarto check` Output ```bash quarto check [✓] Checking Quarto installation......OK Version: 0.9.476 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 (Conda) Path: /Users/username/mambaforge/bin/python Jupyter: 4.10.0 Kernels: python3, dyalog-kernel [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### `quarto tools check` Output ```bash quarto tools check (\) Reading Tool DataDownload https://deno.land/x/[email protected]/directories.ts (|) Reading Tool DataDownload https://deno.land/x/[email protected]/deps.ts [✓] Reading Tool Data Tool Status Installed Latest tinytex Not installed ---- v2022.08 chromium Not installed ---- 869685 ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area? - [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?
{ "assignee": "jooyoungseo", "comments": 0, "created_at": "2022-08-21T12:10:32Z", "creator": "miwojc", "is_pull_request": false, "labels": [ "bug", "accessibility" ], "locked": false, "milestone": "v1.4", "number": 2023, "state": "open", "title": "Add follow hint to collapsed section", "url": "https://github.com/quarto-dev/quarto-cli/issues/2023" }
It's fairly common for data scientists to produce reports which end up in Google Slides and it would be great if there were a pattern which let them use quarto to generate these slides. I know that people have asked for this in the Rmarkdown world and it was tricky to implement, but I was wondering if it would be possible to implement it in quarto. The only project that I'm aware of that kind of helps is this [md2googleslides](https://github.com/googleworkspace/md2googleslides) project.
{ "assignee": null, "comments": 6, "created_at": "2022-08-20T23:13:26Z", "creator": "GShotwell", "is_pull_request": false, "labels": [], "locked": false, "milestone": "Future", "number": 2022, "state": "open", "title": "Feature request: Google slides output", "url": "https://github.com/quarto-dev/quarto-cli/issues/2022" }
Hi, just getting started with quarto (thanks), and not sure I've got the jupyter side of things sorted out. I think I've installed the irkernel for R okay. but am struggling to convert a .qmd file to .ipynb. Running 'quarto check' in the folder I see the error (at bottom): ``` stephen@blur estimateq % quarto check [✓] Checking Quarto installation......OK Version: 1.0.38 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /opt/homebrew/opt/[email protected]/bin/python3.10 Jupyter: 4.11.1 Kernels: ir [✓] Checking Jupyter engine render....OK ERROR: Invalid jupyter YAML metadata found in file (must be string or object) ``` where might I find the invalid YAML? If the check script knows the location (file/line number) of the error, is there any chance it could report that? As far as I can tell, the only yaml file I've got in the folder is the following ``` --- title: "Example quarto document: estimating PI" author: "Stephen J Eglen" date: "2022-08-20" bibliography: refs.bib format: html: code-fold: false --- ``` (what I'd like to do is specify the ir kernel). (As a minor aside, when I saw the rstudioconf talk that quarto was 'batteries included', I had falsely assumed that it would include all the python/jupyter machinery. but I don't think it did, so I've done the following: ``` python3 -m pip install jupyter ``` and from the R side, installed the irkernel package and installed the kernel ``` install.packages('IRkernel') # Don’t forget step 2/3! IRkernel::installspec() ``` )
{ "assignee": null, "comments": 5, "created_at": "2022-08-20T22:28:04Z", "creator": "sje30", "is_pull_request": false, "labels": [], "locked": false, "milestone": null, "number": 2020, "state": "closed", "title": "ERROR: Invalid jupyter YAML metadata found in file (must be string or object)", "url": "https://github.com/quarto-dev/quarto-cli/issues/2020" }
### Bug description The "On this page" table of contents drop down menu sometimes glitches in and out when scrolling through a part of the page with margin elements. Here's an example from the Quarto website: [https://quarto.org/docs/authoring/article-layout.html]() with a screen recording of the behavior: https://user-images.githubusercontent.com/25734232/185762861-22533a12-ac99-4b67-9fdf-993ec86a120c.mov ### `quarto check` Output ``` [✓] Checking Quarto installation......OK Version: 1.0.38 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.12 Path: /usr/local/opt/[email protected]/bin/python3.9 Jupyter: 4.10.0 Kernels: ir, julia-1.6, juliapro_v1.5.0-1-1.5, julia-1.5, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.1.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.1/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### `quarto tools check` Output ``` [✓] Inspecting tools Tool Status Installed Latest chromium Not installed --- 869685 tinytex Not installed --- v2022.08 ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area? - [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?
{ "assignee": "dragonstyle", "comments": 2, "created_at": "2022-08-20T19:18:01Z", "creator": "maxdrohde", "is_pull_request": false, "labels": [ "bug", "duplicate", "verify-fixed" ], "locked": false, "milestone": "v1.1", "number": 2019, "state": "closed", "title": "\"On this page\" menu glitches when scrolling through margin elements on page", "url": "https://github.com/quarto-dev/quarto-cli/issues/2019" }
RStudio 2022.07.1 Build 554 OS Mac M1 Air ### Bug description What happens depends on the document class. Described below. If one passes in `hyperrefoptions: ` ``` pdf: documentclass: scrbook keep-tex: true hyperrefoptions: - "colorlinks=true" - "linkcolor=blue" - "urlcolor=cyan" ``` This is correctly passed to hyperref in the tex output. At top of generated tex: ``` \PassOptionsToPackage{unicode,colorlinks=true,linkcolor=blue,urlcolor=cyan}{hyperref} ``` But below that (after line 100 in the generated tex) is this `\hypersetup` command which overrides that. **`documentclass: scrbook` and `book`** No hyperlink color are seen because the `\hyperref` setup is not changed and includes `hidelinks`. ``` \hypersetup{ pdftitle={title}, pdfauthor={author}, hidelinks, pdfcreator={LaTeX via pandoc}} ``` **`documentclass: scrarticle`, `article`, `krantz`, `svmono`, `report`, `memoir`** Passing in any `hyperrefoptions: `, including `colorlinks=false`, triggers a change to `\hypersetup` to turn on colorlinks but none of the info in `hyperrefoptions` is used. The code the generated tex is this ``` \hypersetup{ pdftitle={title}, pdfauthor={the author}, colorlinks=true, linkcolor={blue}, filecolor={Maroon}, citecolor={Blue}, urlcolor={Blue}, pdfcreator={LaTeX via pandoc}} ``` whether one puts this ``` hyperrefoptions: - "colorlinks=false" ``` or this (or anything else) ``` hyperrefoptions: - "colorlinks=true" - "urlcolor=red" ``` in the format pdf YAML. Note in all cases the hyperref options are passed to hyperref at the top of the tex file, it's just that they are being overridden later by `\hypersetup` Personally as a LaTeX user, I find this preferable ``` hyperrefoptions: - "colorlinks=true" - "linkcolor=blue" - "urlcolor=cyan" ``` over this ``` colorlinks: true linkcolor: blue urlcolor: cyan ``` The former is what I use for `classoptions` and `geometry` and it is 100% clear what I am doing, i.e. I am setting the hyperref package options and I can look up all the possible options for that package. But the can co-exist just need the `\hyperrefoptions` commands to make it into `\hypersetup`. ### `quarto check` Output ``` [✓] Checking Quarto installation......OK Version: 1.0.38 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.12 Path: /opt/homebrew/opt/[email protected]/bin/python3.9 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.1.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/eli.holmes/Library/R/x86_64/4.1/library - /Library/Frameworks/R.framework/Versions/4.1/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### `quarto tools check` Output ``` [✓] Inspecting tools Tool Status Installed Latest chromium Not installed --- 869685 tinytex External Installation --- v2022.08 ``` MWE qmd ``` --- title: title author: - name: the author editor: source format: pdf: documentclass: scrbook keep-tex: true hyperrefoptions: - "colorlinks=true" - "linkcolor=blue" - "urlcolor=cyan" --- # Intro [Quarto](https://quarto.org/) is great. ``` ### Checklist - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area? - [x] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area? - [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?
{ "assignee": "dragonstyle", "comments": 10, "created_at": "2022-08-20T16:48:21Z", "creator": "eeholmes", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": "v1.2", "number": 2017, "state": "closed", "title": "For PDF, hyperrefoptions being overridden by \\hypersetup", "url": "https://github.com/quarto-dev/quarto-cli/issues/2017" }
I am trying to replicate the example shown here : https://quarto.org/docs/interactive/ojs/ but instead of using the csv file I am using the penguins data set and I am not able to get the plots showing up when I used the transpose function but it work when I use the csv file found [here](https://github.com/quarto-dev/quarto-web/blob/main/docs/interactive/ojs/palmer-penguins.csv) . ```` --- title: "test observ" format: html execute: echo: false --- ## Quarto ``` {r, include=FALSE} library("palmerpenguins") ojs_define(data = penguins) ``` ```{ojs} viewof bill_length_min = Inputs.range( [32, 50], {value: 35, step: 1, label: "Bill length (min):"} ) viewof islands = Inputs.checkbox( ["Torgersen", "Biscoe", "Dream"], { value: ["Torgersen", "Biscoe"], label: "Islands:" } ) ``` ```{ojs} filtered = transpose(data).filter(function(penguin) { return bill_length_min < penguin.bill_length && islands.includes(penguin.island); }) Plot.rectY(filtered, Plot.binX( {y: "count"}, {x: "body_mass", fill: "species", thresholds: 20} )) .plot({ facet: { data: filtered, x: "sex", y: "species", marginRight: 80 }, marks: [ Plot.frame(), ] } ) ``` ```` This is what I get the plots are not showing. When I use the csv the plots show up. ![image](https://user-images.githubusercontent.com/21668964/185757626-5390586d-64d4-4897-9968-9ef572be973c.png)
{ "assignee": "cscheid", "comments": 5, "created_at": "2022-08-20T16:45:34Z", "creator": "meldarionqeusse", "is_pull_request": false, "labels": [], "locked": false, "milestone": "v1.2", "number": 2018, "state": "closed", "title": "ObservableJS penguins exmaple does not work with transpose but works if you load csv file.", "url": "https://github.com/quarto-dev/quarto-cli/issues/2018" }
### Bug description Setting either `none-in` or `none-out` results in fading instead of nothing. Reprex: ````md --- format: revealjs --- ## slide 1 ## slide 2 {transition="none-in none-out"} ## slide 3 ```` results: ![Kapture 2022-08-20 at 18 22 37](https://user-images.githubusercontent.com/14034784/185756814-c45b403a-503d-4ba4-845f-674b80e402bc.gif) ## RStudio about Using MacOS <img width="299" alt="Screen Shot 2022-08-20 at 6 26 41 PM" src="https://user-images.githubusercontent.com/14034784/185756882-57d02ad1-b044-4c2f-b661-f4e947a67d0b.png"> ### `quarto check` Output ```bash [✓] Checking Quarto installation......OK Version: 1.0.38 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.9 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources LibPaths: - /Users/emilhvitfeldt/Library/R/arm64/4.2/library - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### `quarto tools check` Output ```bash [✓] Inspecting tools Tool Status Installed Latest chromium Not installed --- 869685 tinytex Update available v2021.12 v2022.08 ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area? - [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?
{ "assignee": null, "comments": 2, "created_at": "2022-08-20T16:27:23Z", "creator": "EmilHvitfeldt", "is_pull_request": false, "labels": [ "bug" ], "locked": false, "milestone": null, "number": 2016, "state": "closed", "title": "Setting transition=\"none-*\" turns on fading", "url": "https://github.com/quarto-dev/quarto-cli/issues/2016" }
### Bug description **distill** has also a `layout` option, and for now if the option is not correctly converted to Quarto supported one then there is an useful error * Content from distill without using YAML syntax ````markdown --- title: "A small example" format: html page-layout: article --- ```{r setup, layout="l-body-outset"} mtcars[,1:3] |> head() ``` ```` * After conversion using `knitr::convert_chunk_header()` ````markdown --- title: "A small example" format: html page-layout: article --- ```{r} #| layout: l-body-outset mtcars[,1:3] |> head() ``` ```` in both case, we'll have this issue ```` Error running filter C:/Users/chris/scoop/apps/quarto-prerelease/current/share/filters/layout/layout.lua: ...prerelease\current\bin\..\share\pandoc\datadir\_json.lua:167: bad 'for' initial value (number expected, got nil) stack traceback: ...prerelease\current\bin\..\share\pandoc\datadir\_json.lua:381: in function '_json.decode' ...uarto-prerelease/current/share/filters/layout/layout.lua:3641: in function 'parseLayoutWidths' ...uarto-prerelease/current/share/filters/layout/layout.lua:4274: in function 'layoutCells' ...uarto-prerelease/current/share/filters/layout/layout.lua:4098: in function <...uarto-prerelease/current/share/filters/layout/layout.lua:4091> ERROR: unexpected character 'l' at line 1 col 1 ````` Not so useful. And in the second case, YAML validation does not help to detect that. No error detected for the `layout` field in the chunk for me. Can we do better in the error or at least in the validation ? ### `quarto check` Output ```` $ quarto check [>] Checking Quarto installation......OK Version: 1.1.80 Path: C:\Users\chris\scoop\apps\quarto-prerelease\current\bin\ CodePage: unknown [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.13 Path: C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.13/python3.exe Jupyter: 4.11.1 Kernels: bash, julia-1.7, python3 [>] Checking Jupyter engine render....OK (\) Checking R installation...........++ Activating rlang global_entrace ++ Setting QUARTO_PYTHON [>] Checking R installation...........OK Version: 4.2.0 Path: C:/PROGRA~1/R/R-42~1.0 LibPaths: - C:/Users/chris/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.0/library rmarkdown: 2.14.3 [>] Checking Knitr engine render......OK ````
{ "assignee": "cscheid", "comments": 8, "created_at": "2022-08-20T13:21:25Z", "creator": "cderv", "is_pull_request": false, "labels": [ "enhancement", "yaml-validation" ], "locked": false, "milestone": "Future", "number": 2013, "state": "open", "title": "Improve validation for layout to help distill conversion ? ", "url": "https://github.com/quarto-dev/quarto-cli/issues/2013" }