To install core packages, type the following in an R command window:
-+if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") @@ -12,7 +12,7 @@Install Bioconductor Packages
To install core packages, type the following in an R command window:
-+BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))@@ -38,7 +38,7 @@Find Bioconductor Packages
To search through available packages programmatically, use the following: -+BiocManager::available()@@ -59,7 +59,7 @@version of Bioconductor, start a new session of R and enter: -
+BiocManager::install()@@ -78,7 +78,7 @@Updgrading Installed Bioconductor Packages
for your version of R, enter: -+if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") @@ -113,7 +113,7 @@Recompiling Installed Bioconductor Packages
to address this might be to start a new R session and enter: -+if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") @@ -136,7 +136,7 @@
Use the commands:
-+BiocManager::valid() ## R version 3.5 or later@@ -212,7 +212,7 @@Why use BiocManager::install()?
R in use regardless of the R and Bioconductor release cycles. -+> library(BiocManager) Bioconductor version 3.9 (BiocManager 1.30.4), ?BiocManager::install @@ -233,7 +233,7 @@Why use BiocManager::install()?
would like to update. -+> BiocManager::install() Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 Patched @@ -250,7 +250,7 @@Why use BiocManager::install()?
version of Bioconductor. -+> BiocManager::install(version = "devel") Upgrade 89 packages to Bioconductor version '3.10'? [y/n]: y @@ -286,7 +286,7 @@Why use BiocManager::install()?
a repository; regular users would seldom have these). -+> BiocManager::valid() diff --git a/layouts/_bioc_views_package_detail.html b/layouts/_bioc_views_package_detail.html index 4575078e6..b8f977f37 100644 --- a/layouts/_bioc_views_package_detail.html +++ b/layouts/_bioc_views_package_detail.html @@ -35,7 +35,17 @@<%= @package[:Title]%>
Maintainer: <%= filter_emails(@package[:Maintainer])%>- Citation (from within R, enter@@ -47,4 +57,3 @@citation("<%=@package[:Package]%>")): ++ Citation (from within R, entercitation("<%=@package[:Package]%>")): + +<%= @package[:Title]%>
<%= render("/components/packages/details/", :package => @package) %> <%= render("/components/packages/archives/", :package => @package) %> - diff --git a/layouts/components/packages/installation.html b/layouts/components/packages/installation.html index efe4469bb..d14e355bb 100644 --- a/layouts/components/packages/installation.html +++ b/layouts/components/packages/installation.html @@ -4,7 +4,7 @@Installation
To install this package, start R (version "<%= r_ver_for_bioc_ver(@package[:bioc_version_num]) %>") and enter: -+if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") <% if (@package[:bioc_version_str] == "Development") %> From 18bb54aa2f218e849f5a9ab1f14b1c7bf96cc180 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 17 Jul 2026 14:54:28 +0000 Subject: [PATCH 3/6] Handle copy button success and error states --- assets/js/code_blocks.js | 24 ++++++++++++++++-------- assets/style/components/code.css | 5 +++++ 2 files changed, 21 insertions(+), 8 deletions(-) diff --git a/assets/js/code_blocks.js b/assets/js/code_blocks.js index 8bf2678af..b4869b4d3 100644 --- a/assets/js/code_blocks.js +++ b/assets/js/code_blocks.js @@ -30,12 +30,19 @@ const getCopyText = (button) => { return ""; }; -const setCopyButtonState = (button, copied) => { +const setCopyButtonState = (button, state = "default") => { const defaultLabel = button.dataset.copyLabel || "Copy"; const successLabel = button.dataset.copySuccessLabel || "Copied"; - const label = copied ? successLabel : defaultLabel; - - button.classList.toggle("copied", copied); + const errorLabel = button.dataset.copyErrorLabel || "Copy failed"; + const label = + state === "copied" + ? successLabel + : state === "error" + ? errorLabel + : defaultLabel; + + button.classList.toggle("copied", state === "copied"); + button.classList.toggle("copy-error", state === "error"); button.setAttribute("aria-label", label); button.setAttribute("title", label); @@ -72,10 +79,11 @@ const handleCopyClick = async (event) => { fallbackCopyText(text); } - setCopyButtonState(button, true); - window.setTimeout(() => setCopyButtonState(button, false), 2000); - } catch (error) { - setCopyButtonState(button, false); + setCopyButtonState(button, "copied"); + window.setTimeout(() => setCopyButtonState(button), 2000); + } catch { + setCopyButtonState(button, "error"); + window.setTimeout(() => setCopyButtonState(button), 2000); } }; diff --git a/assets/style/components/code.css b/assets/style/components/code.css index 8c65c0dd6..2a65a32dc 100644 --- a/assets/style/components/code.css +++ b/assets/style/components/code.css @@ -140,6 +140,11 @@ pre code.light .hljs-title { border-color: var(--primary-p400); } +.copy-button.copy-error { + background: var(--error-e500); + border-color: var(--error-e500); +} + .copy-button svg { fill: currentcolor; height: 0.9rem; From 75eb6973e1c911b28f10f4667c99b8d27661a1d2 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 17 Jul 2026 14:55:39 +0000 Subject: [PATCH 4/6] Tighten copy fallback handling --- assets/js/code_blocks.js | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/assets/js/code_blocks.js b/assets/js/code_blocks.js index b4869b4d3..42f7152e2 100644 --- a/assets/js/code_blocks.js +++ b/assets/js/code_blocks.js @@ -60,8 +60,12 @@ const fallbackCopyText = (text) => { textArea.className = "sr-only"; document.body.appendChild(textArea); textArea.select(); - document.execCommand("copy"); + const copied = document.execCommand("copy"); document.body.removeChild(textArea); + + if (!copied) { + throw new Error("Copy command failed"); + } }; const handleCopyClick = async (event) => { @@ -99,7 +103,7 @@ const initializeCopyButton = (button) => { button.innerHTML = `${copyButtonIcon}`; } - setCopyButtonState(button, false); + setCopyButtonState(button); button.addEventListener("click", handleCopyClick); button.dataset.copyButtonReady = "true"; }; From 5d8656de052448363ecc0b666fd66e0e42af4234 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 17 Jul 2026 14:56:44 +0000 Subject: [PATCH 5/6] Polish copy button state logic --- assets/js/code_blocks.js | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/assets/js/code_blocks.js b/assets/js/code_blocks.js index 42f7152e2..1fba1ae3c 100644 --- a/assets/js/code_blocks.js +++ b/assets/js/code_blocks.js @@ -3,6 +3,7 @@ const copyButtonIcon = ``; +const defaultCopyLabel = "Copy"; const trimCodeBlocks = () => { Array.from(document.getElementsByTagName("code")).forEach((block) => { @@ -31,15 +32,16 @@ const getCopyText = (button) => { }; const setCopyButtonState = (button, state = "default") => { - const defaultLabel = button.dataset.copyLabel || "Copy"; + const defaultLabel = button.dataset.copyLabel || defaultCopyLabel; const successLabel = button.dataset.copySuccessLabel || "Copied"; const errorLabel = button.dataset.copyErrorLabel || "Copy failed"; - const label = - state === "copied" - ? successLabel - : state === "error" - ? errorLabel - : defaultLabel; + let label = defaultLabel; + + if (state === "copied") { + label = successLabel; + } else if (state === "error") { + label = errorLabel; + } button.classList.toggle("copied", state === "copied"); button.classList.toggle("copy-error", state === "error"); @@ -100,7 +102,7 @@ const initializeCopyButton = (button) => { button.classList.add("copy-button"); if (!button.querySelector(".copy-button-label")) { - button.innerHTML = `${copyButtonIcon}`; + button.innerHTML = `${copyButtonIcon}`; } setCopyButtonState(button); @@ -115,7 +117,7 @@ const addCodeCopyButton = (pre) => { const button = document.createElement("button"); button.className = "copy-button code-copy-button"; - button.dataset.copyLabel = "Copy"; + button.dataset.copyLabel = defaultCopyLabel; button.dataset.copySuccessLabel = "Copied"; pre.appendChild(button); initializeCopyButton(button); From 5c194ea86cd99db0155956d5fb9ba4833b9322d4 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 17 Jul 2026 14:57:58 +0000 Subject: [PATCH 6/6] Harden copy button fallback behavior --- assets/js/code_blocks.js | 9 ++++++++- assets/style/components/code.css | 5 +++++ 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/assets/js/code_blocks.js b/assets/js/code_blocks.js index 1fba1ae3c..64265c6f0 100644 --- a/assets/js/code_blocks.js +++ b/assets/js/code_blocks.js @@ -4,6 +4,7 @@ const copyButtonIcon = ` `; const defaultCopyLabel = "Copy"; +let copyFallbackWarningShown = false; const trimCodeBlocks = () => { Array.from(document.getElementsByTagName("code")).forEach((block) => { @@ -59,9 +60,15 @@ const fallbackCopyText = (text) => { const textArea = document.createElement("textarea"); textArea.value = text; textArea.setAttribute("readonly", ""); - textArea.className = "sr-only"; + textArea.style.position = "fixed"; + textArea.style.left = "-9999px"; + textArea.style.top = "0"; document.body.appendChild(textArea); textArea.select(); + if (!copyFallbackWarningShown) { + console.warn("Falling back to document.execCommand('copy')."); + copyFallbackWarningShown = true; + } const copied = document.execCommand("copy"); document.body.removeChild(textArea); diff --git a/assets/style/components/code.css b/assets/style/components/code.css index 2a65a32dc..06ac75785 100644 --- a/assets/style/components/code.css +++ b/assets/style/components/code.css @@ -23,6 +23,11 @@ pre code.hljs { font-family: Courier, monospace; } +pre[data-copyable] code, +pre[data-copyable] code.hljs { + padding-top: 3rem; +} + pre code, pre code.hljs, .hljs-punctuation {