From 2d1e8ba37b6e14f1db0b60ee4b323054a3311ca4 Mon Sep 17 00:00:00 2001 From: Jay Hesselberth Date: Sun, 23 Jun 2024 08:40:26 -0600 Subject: [PATCH] Update to R 4.4. and bioc 3.19 (#22) --- .github/workflows/quarto.yaml | 2 +- .../final-projects/execute-results/html.json | 5 +- .../fonts/league-gothic/league-gothic.eot | Bin .../fonts/league-gothic/league-gothic.ttf | Bin .../fonts/league-gothic/league-gothic.woff | Bin .../source-sans-pro-italic.eot | Bin .../source-sans-pro-italic.woff | Bin .../source-sans-pro-regular.eot | Bin .../source-sans-pro-regular.woff | Bin .../source-sans-pro-semibold.eot | Bin .../source-sans-pro-semibold.woff | Bin .../source-sans-pro-semibolditalic.eot | Bin .../source-sans-pro-semibolditalic.woff | Bin .../revealjs/plugin/markdown/plugin.js | 0 .../site_libs/revealjs/plugin/math/katex.js | 0 .../quarto-line-highlight/line-highlight.js | 8 +- .../revealjs/plugin/quarto-support/support.js | 34 +- course-info/final-projects.qmd | 2 +- index.qmd | 19 +- renv.lock | 1328 ++++++++--------- renv/activate.R | 45 +- renv/settings.json | 2 +- 22 files changed, 692 insertions(+), 753 deletions(-) mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.eot mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.ttf mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.woff mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.eot mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.woff mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.eot mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.woff mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.eot mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.woff mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot mode change 100644 => 100755 _freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff mode change 100644 => 100755 _freeze/site_libs/revealjs/plugin/markdown/plugin.js mode change 100644 => 100755 _freeze/site_libs/revealjs/plugin/math/katex.js diff --git a/.github/workflows/quarto.yaml b/.github/workflows/quarto.yaml index 3bd6b1ae..c50d90dd 100644 --- a/.github/workflows/quarto.yaml +++ b/.github/workflows/quarto.yaml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: ✅ Check out repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: 🆀 Set up Quarto uses: quarto-dev/quarto-actions/setup@v2 diff --git a/_freeze/course-info/final-projects/execute-results/html.json b/_freeze/course-info/final-projects/execute-results/html.json index 95b6bf68..b3d8611c 100644 --- a/_freeze/course-info/final-projects/execute-results/html.json +++ b/_freeze/course-info/final-projects/execute-results/html.json @@ -1,7 +1,8 @@ { - "hash": "43fe8b6d7bb6a8f25c6b170f5a0dfae2", + "hash": "2a3e207e8951f963c66aaea78321e3cb", "result": { - "markdown": "---\ntitle: \"MOLB 7950 -- Final Projects\"\neditor: \n markdown: \n wrap: 72\n---\n\n\n## Short proposal\n\nPlease submit a short proposal for your final projects with the\nfollowing information.\n\n- the names of people you are working with\n\n- a description of the data set you will be working worth. This can\n refer to a publication and/or contain a link to public data\n available at NCBI GEO.\n\n- a hypothesis (tentative) you will be testing\n\n- a few bullets on your planned analysis approach.\n\nPlease include this information in a quarto document in a new Posit\ncloud project.\n\n## Overview\n\n- Final projects can involve groups of 1-3 people.\n\n- Projects are choose your own adventure:\n\n 1. The [resource documents](resources/block-dna-resources.qmd)\n contain data sets in from human S. cerevisiae. For example,\n sub-nucleosomal fragments provide a DNA-based signal to\n understand chromatin transactions that lead to transcription.\n\n 2. You could find a data set on [NCBI\n GEO](https://www.ncbi.nlm.nih.gov/geo/) of interest (e.g.,\n relevant to your thesis work), and work it up with salmon,\n DEseq, and exploratory analysis. We are happy to help you work\n through the pseudo-alignment steps.\n\n 3. You can start with your own sequencing data (bulk/single-cell\n RNA seq, DNA sequencing).\n\n## Deliverables\n\n- A Quarto document with code, plots, interpretations, and next steps.\n\n- If you work in a group, list the members of the group at the top of\n the document, and make it clear which parts are your work by adding\n your initials to code chunks.\n\n- Short presentations (5-8 minutes) by the groups the week of Nov 1.\n Presentations should include 1-2 slides of background, a hypothesis\n for the approach, code output (table or graph) that addresses the\n hypothesis, and one or more tests of the statistical significance of\n the observation.\n\n## Grading and rubric\n\nThe final project will be worth 20% of your grade and we will use the\ngrading scheme outlined in the [grading\nrubric](syllabus.qmd#problem-set-rubric).\n\nEach individual in a group will be evaluated separately, so\ncontributions must be clearly marked in the document, using e.g. using\nchunk labels:\n\n\n::: {.cell}\n\n````{.cell-code}\n```{{r}}\n#| label: plotting-code-by-jay-h\n#| eval: false\nggplot(mtcars, aes(hp, mpg)) + geom_point()\n```\n````\n:::\n", + "engine": "knitr", + "markdown": "---\ntitle: \"MOLB 7950 -- Final Projects\"\neditor: \n markdown: \n wrap: 72\n---\n\n\n## Short proposal\n\nPlease submit a short proposal for your final projects with the\nfollowing information.\n\n- the names of people you are working with\n\n- a description of the data set you will be working worth. This can\n refer to a publication and/or contain a link to public data\n available at NCBI GEO.\n\n- a hypothesis (tentative) you will be testing\n\n- a few bullets on your planned analysis approach.\n\nPlease include this information in a quarto document in a new Posit\ncloud project.\n\n## Overview\n\n- Final projects can involve groups of 1-3 people.\n\n- Projects are choose your own adventure:\n\n 1. The [resource documents](/resources/block-dna-resources.qmd)\n contain data sets in from human S. cerevisiae. For example,\n sub-nucleosomal fragments provide a DNA-based signal to\n understand chromatin transactions that lead to transcription.\n\n 2. You could find a data set on [NCBI\n GEO](https://www.ncbi.nlm.nih.gov/geo/) of interest (e.g.,\n relevant to your thesis work), and work it up with salmon,\n DEseq, and exploratory analysis. We are happy to help you work\n through the pseudo-alignment steps.\n\n 3. You can start with your own sequencing data (bulk/single-cell\n RNA seq, DNA sequencing).\n\n## Deliverables\n\n- A Quarto document with code, plots, interpretations, and next steps.\n\n- If you work in a group, list the members of the group at the top of\n the document, and make it clear which parts are your work by adding\n your initials to code chunks.\n\n- Short presentations (5-8 minutes) by the groups the week of Nov 1.\n Presentations should include 1-2 slides of background, a hypothesis\n for the approach, code output (table or graph) that addresses the\n hypothesis, and one or more tests of the statistical significance of\n the observation.\n\n## Grading and rubric\n\nThe final project will be worth 20% of your grade and we will use the\ngrading scheme outlined in the [grading\nrubric](syllabus.qmd#problem-set-rubric).\n\nEach individual in a group will be evaluated separately, so\ncontributions must be clearly marked in the document, using e.g. using\nchunk labels:\n\n\n::: {.cell}\n\n````{.cell-code}\n```{{r}}\n#| label: plotting-code-by-jay-h\n#| eval: false\nggplot(mtcars, aes(hp, mpg)) + geom_point()\n```\n````\n:::\n", "supporting": [ "final-projects_files" ], diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.eot b/_freeze/site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.eot old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.ttf b/_freeze/site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.ttf old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.woff b/_freeze/site_libs/revealjs/dist/theme/fonts/league-gothic/league-gothic.woff old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.eot b/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.eot old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.woff b/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.woff old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.eot b/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.eot old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.woff b/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.woff old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.eot b/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.eot old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.woff b/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.woff old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot b/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff b/_freeze/site_libs/revealjs/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/plugin/markdown/plugin.js b/_freeze/site_libs/revealjs/plugin/markdown/plugin.js old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/plugin/math/katex.js b/_freeze/site_libs/revealjs/plugin/math/katex.js old mode 100644 new mode 100755 diff --git a/_freeze/site_libs/revealjs/plugin/quarto-line-highlight/line-highlight.js b/_freeze/site_libs/revealjs/plugin/quarto-line-highlight/line-highlight.js index 5bffdc77..a69ca1df 100644 --- a/_freeze/site_libs/revealjs/plugin/quarto-line-highlight/line-highlight.js +++ b/_freeze/site_libs/revealjs/plugin/quarto-line-highlight/line-highlight.js @@ -38,7 +38,7 @@ window.QuartoLineHighlight = function () { divSourceCode.forEach((el) => { if (el.hasAttribute(kCodeLineNumbersAttr)) { const codeLineAttr = el.getAttribute(kCodeLineNumbersAttr); - el.removeAttribute("data-code-line-numbers"); + el.removeAttribute(kCodeLineNumbersAttr); if (handleLinesSelector(deck, codeLineAttr)) { // Only process if attr is a string to select lines to highlights // e.g "1|3,6|8-11" @@ -165,9 +165,9 @@ window.QuartoLineHighlight = function () { if (typeof highlight.last === "number") { spanToHighlight = [].slice.call( codeBlock.querySelectorAll( - ":scope > span:nth-child(n+" + + ":scope > span:nth-of-type(n+" + highlight.first + - "):nth-child(-n+" + + "):nth-of-type(-n+" + highlight.last + ")" ) @@ -175,7 +175,7 @@ window.QuartoLineHighlight = function () { } else if (typeof highlight.first === "number") { spanToHighlight = [].slice.call( codeBlock.querySelectorAll( - ":scope > span:nth-child(" + highlight.first + ")" + ":scope > span:nth-of-type(" + highlight.first + ")" ) ); } diff --git a/_freeze/site_libs/revealjs/plugin/quarto-support/support.js b/_freeze/site_libs/revealjs/plugin/quarto-support/support.js index 9adc9213..b0262ee6 100644 --- a/_freeze/site_libs/revealjs/plugin/quarto-support/support.js +++ b/_freeze/site_libs/revealjs/plugin/quarto-support/support.js @@ -4,6 +4,20 @@ window.QuartoSupport = function () { return /print-pdf/gi.test(window.location.search); } + // helper for theme toggling + function toggleBackgroundTheme(el, onDarkBackground, onLightBackground) { + if (onDarkBackground) { + el.classList.add('has-dark-background') + } else { + el.classList.remove('has-dark-background') + } + if (onLightBackground) { + el.classList.add('has-light-background') + } else { + el.classList.remove('has-light-background') + } + } + // implement controlsAudo function controlsAuto(deck) { const config = deck.getConfig(); @@ -111,8 +125,19 @@ window.QuartoSupport = function () { } } - // add footer text - function addFooter(deck) { + // tweak slide-number element + function tweakSlideNumber(deck) { + deck.on("slidechanged", function (ev) { + const revealParent = deck.getRevealElement(); + const slideNumberEl = revealParent.querySelector(".slide-number"); + const onDarkBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-dark-background'); + const onLightBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-light-background'); + toggleBackgroundTheme(slideNumberEl, onDarkBackground, onLightBackground); + }) + } + + // add footer text + function addFooter(deck) { const revealParent = deck.getRevealElement(); const defaultFooterDiv = document.querySelector(".footer-default"); if (defaultFooterDiv) { @@ -127,13 +152,17 @@ window.QuartoSupport = function () { prevSlideFooter.remove(); } const currentSlideFooter = ev.currentSlide.querySelector(".footer"); + const onDarkBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-dark-background') + const onLightBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-light-background') if (currentSlideFooter) { defaultFooterDiv.style.display = "none"; const slideFooter = currentSlideFooter.cloneNode(true); handleLinkClickEvents(deck, slideFooter); deck.getRevealElement().appendChild(slideFooter); + toggleBackgroundTheme(slideFooter, onDarkBackground, onLightBackground) } else { defaultFooterDiv.style.display = "block"; + toggleBackgroundTheme(defaultFooterDiv, onDarkBackground, onLightBackground) } }); } @@ -280,6 +309,7 @@ window.QuartoSupport = function () { fixupForPrint(deck); applyGlobalStyles(deck); addLogoImage(deck); + tweakSlideNumber(deck); addFooter(deck); addChalkboardButtons(deck); handleTabbyClicks(); diff --git a/course-info/final-projects.qmd b/course-info/final-projects.qmd index 878f21aa..da2e75a8 100644 --- a/course-info/final-projects.qmd +++ b/course-info/final-projects.qmd @@ -29,7 +29,7 @@ cloud project. - Projects are choose your own adventure: - 1. The [resource documents](resources/block-dna-resources.qmd) + 1. The [resource documents](/resources/block-dna-resources.qmd) contain data sets in from human S. cerevisiae. For example, sub-nucleosomal fragments provide a DNA-based signal to understand chromatin transactions that lead to transcription. diff --git a/index.qmd b/index.qmd index 462ab93f..c1226dbf 100644 --- a/index.qmd +++ b/index.qmd @@ -18,7 +18,6 @@ This page contains an outline of the topics, content, and assignments for the se #| echo: false #| message: false #| warning: false -#| column: screen-inset-right library(tidyverse) library(fs) library(glue) @@ -67,34 +66,39 @@ sched_tbl <- read_tsv(here("data/syllabus.tsv")) |> # set up links prepare_link = case_when( qmd_exists(prepare_html) == TRUE ~ glue('[{emo::ji("book")}]({prepare_html})'), - .default = '' + .default = '.' ), prepare_link = map(prepare_link, gt::md), slides_link = case_when( qmd_exists(slides_html) == TRUE ~ glue('[{emo::ji("page")}]({slides_html})'), - .default = '' + .default = '.' ), slides_link = map(slides_link, gt::md), # exercises links ex_link = case_when( qmd_exists(ex_html) == TRUE ~ glue('[{emo::ji("biceps")}]({ex_html})'), - .default = '' + .default = '.' ), ex_link = map(ex_link, gt::md), # problem sets links hw_link = case_when( qmd_exists(hw_html) == TRUE ~ glue('[{emo::ji("brain")}]({hw_html})'), - .default = '' + .default = '.' ), hw_link = map(hw_link, gt::md), # problem set keys links hw_key_link = case_when( qmd_exists(hw_key_html) == TRUE ~ glue('[{emo::ji("key")}]({hw_key_html})'), - .default = '' + .default = '.' ), hw_key_link = map(hw_key_link, gt::md) ) +``` +```{r} +#| label: render-table +#| echo: false +#| column: screen-inset-right gt( sched_tbl, groupname_col = "week", @@ -151,6 +155,5 @@ gt( opt_row_striping() |> cols_align( align = "center" - ) - + ) ``` diff --git a/renv.lock b/renv.lock index ef72cf59..5b63b33f 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.3.2", + "Version": "4.4.0", "Repositories": [ { "Name": "CRAN", @@ -9,14 +9,14 @@ ] }, "Bioconductor": { - "Version": "3.18" + "Version": "3.19" }, "Packages": { "AnnotationDbi": { "Package": "AnnotationDbi", - "Version": "1.64.1", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.66.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "Biobase", "BiocGenerics", @@ -30,13 +30,13 @@ "stats", "stats4" ], - "Hash": "27587689922e22f60ec9ad0182a0a825" + "Hash": "b7df9c597fb5533fc8248d73b8c703ac" }, "AnnotationFilter": { "Package": "AnnotationFilter", - "Version": "1.26.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.28.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "GenomicRanges", "R", @@ -44,13 +44,13 @@ "methods", "utils" ], - "Hash": "759acec0b1522c1a85c6ba703d4c0ec5" + "Hash": "24e809470aef6d81b25003d775b2fb56" }, "AnnotationHub": { "Package": "AnnotationHub", - "Version": "3.10.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "3.12.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "AnnotationDbi", "BiocFileCache", @@ -63,13 +63,12 @@ "dplyr", "grDevices", "httr", - "interactiveDisplayBase", "methods", "rappdirs", "utils", "yaml" ], - "Hash": "a25fbabd5d4c7bf62d7149443b21a35d" + "Hash": "346ca347b61989d1da5f655d7bac6a8c" }, "BH": { "Package": "BH", @@ -80,9 +79,9 @@ }, "BSgenome": { "Package": "BSgenome", - "Version": "1.70.2", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.72.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BiocGenerics", "BiocIO", @@ -100,13 +99,12 @@ "stats", "utils" ], - "Hash": "41a60ca70f713322ca31026f6b9e052b" + "Hash": "9e00bf24b78d10f32cb8e1dceb5f87ff" }, "BSgenome.Hsapiens.UCSC.hg19": { "Package": "BSgenome.Hsapiens.UCSC.hg19", "Version": "1.4.3", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/data/annotation", + "Source": "Bioconductor", "Requirements": [ "BSgenome" ], @@ -115,8 +113,7 @@ "BSgenome.Scerevisiae.UCSC.sacCer3": { "Package": "BSgenome.Scerevisiae.UCSC.sacCer3", "Version": "1.4.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/data/annotation", + "Source": "Bioconductor", "Requirements": [ "BSgenome" ], @@ -124,22 +121,22 @@ }, "Biobase": { "Package": "Biobase", - "Version": "2.62.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "2.64.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BiocGenerics", "R", "methods", "utils" ], - "Hash": "38252a34e82d3ff6bb46b4e2252d2dce" + "Hash": "9bc4cabd3bfda461409172213d932813" }, "BiocFileCache": { "Package": "BiocFileCache", - "Version": "2.10.1", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "2.12.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "DBI", "R", @@ -153,13 +150,13 @@ "stats", "utils" ], - "Hash": "ac2a12468b948654220ed90ae94e9d08" + "Hash": "9c3414bcfae204d56080dd0f0a220136" }, "BiocGenerics": { "Package": "BiocGenerics", - "Version": "0.48.1", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "0.50.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "R", "graphics", @@ -167,13 +164,13 @@ "stats", "utils" ], - "Hash": "e34278c65d7dffcc08f737bf0944ca9a" + "Hash": "ef32d07aafdd12f24c5827374ae3590d" }, "BiocIO": { "Package": "BiocIO", - "Version": "1.12.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.14.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BiocGenerics", "R", @@ -181,23 +178,23 @@ "methods", "tools" ], - "Hash": "aa543468283543c9a8dad23a4897be96" + "Hash": "f97a7ef01d364cf20d1946d43a3d526f" }, "BiocManager": { "Package": "BiocManager", - "Version": "1.30.22", + "Version": "1.30.23", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "d57e43105a1aa9cb54fdb4629725acb1" + "Hash": "47e968dfe563c1b22c2e20a067ec21d5" }, "BiocNeighbors": { "Package": "BiocNeighbors", - "Version": "1.20.2", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.22.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BiocParallel", "Matrix", @@ -207,13 +204,13 @@ "methods", "stats" ], - "Hash": "c5c8ade5852fd3b25c66ec28873d00f1" + "Hash": "da9f332c88453734623406dcca13ee03" }, "BiocParallel": { "Package": "BiocParallel", - "Version": "1.36.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.38.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BH", "R", @@ -226,13 +223,13 @@ "stats", "utils" ], - "Hash": "6d1689ee8b65614ba6ef4012a67b663a" + "Hash": "7b6e79f86e3d1c23f62c5e2052e848d4" }, "BiocSingular": { "Package": "BiocSingular", - "Version": "1.18.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.20.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BiocGenerics", "BiocParallel", @@ -247,23 +244,23 @@ "rsvd", "utils" ], - 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"rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" + "Hash": "ab19d02b3418e44d6f32ffb8060427d2" }, "emo": { "Package": "emo", "Version": "0.0.0.9000", - "Source": "GitHub", - "RemoteType": "github", + "Source": "git", + "RemoteType": "git", + "RemoteUrl": "https://github.com/hadley/emo", "RemoteHost": "api.github.com", - "RemoteRepo": "emo", "RemoteUsername": "hadley", - "RemoteRef": "HEAD", + "RemoteRepo": "emo", + "RemoteRef": "master", "RemoteSha": "3f03b11491ce3d6fc5601e210927eff73bf8e350", "Requirements": [ "R", @@ -2518,13 +2495,13 @@ "stringr", "utils" ], - "Hash": "10f2391a926b0087a671ed9965ea30a3" + "Hash": "eb32b8f0bb50621ad498f5d836b546a4" }, "enrichplot": { "Package": "enrichplot", - "Version": "1.22.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.24.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "DOSE", "GOSemSim", @@ -2551,13 +2528,13 @@ "utils", "yulab.utils" ], - "Hash": "92d736b111bdefed6b7a073f0978e7b7" + "Hash": "19039e8a7075c61615d6f1459fb13ec6" }, "ensembldb": { "Package": "ensembldb", - "Version": "2.26.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "2.28.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "AnnotationDbi", "AnnotationFilter", @@ -2578,7 +2555,7 @@ "methods", "rtracklayer" ], - "Hash": "6be48b1a96556976a4e9ee6836f88b97" + "Hash": "f9a5e52468ec832a839c012e15c41c15" }, "entropy": { "Package": "entropy", @@ -2592,14 +2569,14 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.23", + "Version": "0.24.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" + "Hash": "a1066cbc05caee9a4bf6d90f194ff4da" }, "fansi": { "Package": "fansi", @@ -2615,10 +2592,10 @@ }, "farver": { "Package": "farver", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "8106d78941f34855c440ddb946b8f7a5" + "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastDummies": { "Package": "fastDummies", @@ -2635,10 +2612,10 @@ }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "fastmatch": { "Package": "fastmatch", @@ -2652,9 +2629,9 @@ }, "fgsea": { "Package": "fgsea", - "Version": "1.28.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.30.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BH", "BiocParallel", @@ -2670,7 +2647,7 @@ "stats", "utils" ], - "Hash": "b2de43d04c504b819feec692e2b94523" + "Hash": "ead409e5a973cd285681c3bb0ade49a7" }, "filelock": { "Package": "filelock", @@ -2686,7 +2663,7 @@ "Package": "fitdistrplus", "Version": "1.1-11", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "MASS", "R", @@ -2742,7 +2719,7 @@ "Package": "foreign", "Version": "0.8-86", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods", @@ -2763,14 +2740,14 @@ }, "fs": { "Package": "fs", - "Version": "1.6.3", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "47b5f30c720c23999b913a1a635cf0bb" + "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a" }, "futile.logger": { "Package": "futile.logger", @@ -2797,7 +2774,7 @@ }, "future": { "Package": "future", - "Version": "1.33.1", + "Version": "1.33.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2808,11 +2785,11 @@ "parallelly", "utils" ], - "Hash": "e57e292737f7a4efa9d8a91c5908222c" + "Hash": "fd7b1d69d16d0d114e4fa82db68f184c" }, "future.apply": { "Package": "future.apply", - "Version": "1.11.1", + "Version": "1.11.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2822,7 +2799,7 @@ "parallel", "utils" ], - "Hash": "455e00c16ec193c8edcf1b2b522b3288" + "Hash": "afe1507511629f44572e6c53b9baeb7c" }, "gargle": { "Package": "gargle", @@ -2861,7 +2838,7 @@ "Package": "ggbeeswarm", "Version": "0.7.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "beeswarm", @@ -2903,18 +2880,19 @@ }, "ggfun": { "Package": "ggfun", - "Version": "0.1.4", + "Version": "0.1.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", + "dplyr", "ggplot2", "grid", "rlang", "utils" ], - "Hash": "91780e07f1d631a1152835b4e25c66b9" + "Hash": "4fca342cc17bb91af2a279146bc57fef" }, "ggnewscale": { "Package": "ggnewscale", @@ -2928,7 +2906,7 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.5.0", + "Version": "3.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2949,7 +2927,7 @@ "vctrs", "withr" ], - "Hash": "52ef83f93f74833007f193b2d4c159a2" + "Hash": "44c6a2f8202d5b7e878ea274b1092426" }, "ggplotify": { "Package": "ggplotify", @@ -2998,24 +2976,23 @@ }, "ggraph": { "Package": "ggraph", - "Version": "2.1.0", + "Version": "2.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "MASS", "R", - "Rcpp", "cli", - "digest", + "cpp11", "dplyr", "ggforce", "ggplot2", "ggrepel", "graphlayouts", "grid", - "gtable", "igraph", "lifecycle", + "memoise", "rlang", "scales", "stats", @@ -3025,13 +3002,13 @@ "viridis", "withr" ], - "Hash": "62672fd99df5df5814f442e9cd5ec29b" + "Hash": "1f5d21a9e1f84b4a81ddacb8f052ca61" }, "ggrastr": { "Package": "ggrastr", "Version": "1.0.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "Cairo", "R", @@ -3075,7 +3052,7 @@ }, "ggsci": { "Package": "ggsci", - "Version": "3.0.0", + "Version": "3.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3084,7 +3061,7 @@ "grDevices", "scales" ], - "Hash": "93664e03010c3f4b570c890dda99ade5" + "Hash": "0c3268cddf4d3a3ce4e7e6330f8e92c8" }, "ggsignif": { "Package": "ggsignif", @@ -3098,7 +3075,7 @@ }, "ggstats": { "Package": "ggstats", - "Version": "0.5.1", + "Version": "0.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3117,13 +3094,13 @@ "stringr", "tidyr" ], - "Hash": "006a64911e79a7dc7cbf839a57baaff4" + "Hash": "02cdab34154e9e70dac279afbb20d34b" }, "ggtext": { "Package": "ggtext", "Version": "0.1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "ggplot2", @@ -3155,15 +3132,9 @@ }, "ggtree": { "Package": "ggtree", - "Version": "3.11.1", - "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "YuLab-SMU", - "RemoteRepo": "ggtree", - "RemoteRef": "devel", - "RemoteSha": "38016ab1e3fde1ff88ec131e2e6e89aa4a234d9d", - "Remotes": "YuLab-SMU/treeio", + "Version": "3.12.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "R", "ape", @@ -3185,18 +3156,18 @@ "utils", "yulab.utils" ], - "Hash": "41a59e03e60c200ca7b4d6e1e2e7d1cf" + "Hash": "6c4748308cbe296a022cba26e118075a" }, "globals": { "Package": "globals", - "Version": "0.16.2", + "Version": "0.16.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "codetools" ], - "Hash": "baa9585ab4ce47a9f4618e671778cc6f" + "Hash": "2580567908cafd4f187c1e5a91e98b7f" }, "glue": { "Package": "glue", @@ -3213,7 +3184,7 @@ "Package": "goftest", "Version": "1.2-3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "stats" @@ -3290,7 +3261,7 @@ }, "graphlayouts": { "Package": "graphlayouts", - "Version": "1.1.0", + "Version": "1.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3299,7 +3270,7 @@ "RcppArmadillo", "igraph" ], - "Hash": "5e9e4cd284ff8abba3cfc43268e3ddd5" + "Hash": "d329345a6a37666ca3f18f3b3c1347b7" }, "gridExtra": { "Package": "gridExtra", @@ -3331,7 +3302,7 @@ "Package": "gridtext", "Version": "0.1.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "Rcpp", @@ -3394,7 +3365,7 @@ }, "gtable": { "Package": "gtable", - "Version": "0.3.4", + "Version": "0.3.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3405,7 +3376,7 @@ "lifecycle", "rlang" ], - "Hash": "b29cf3031f49b04ab9c852c912547eef" + "Hash": "e18861963cbc65a27736e02b3cd3c4a0" }, "gtools": { "Package": "gtools", @@ -3469,14 +3440,14 @@ }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.11", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "xfun" ], - "Hash": "06230136b2d2b9ba5805e1963fa6e890" + "Hash": "d65ba49117ca223614f71b60d85b8ab7" }, "hms": { "Package": "hms", @@ -3512,20 +3483,19 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.7", + "Version": "0.5.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "digest", - "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" + "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" }, "htmlwidgets": { "Package": "htmlwidgets", @@ -3544,7 +3514,7 @@ }, "httpuv": { "Package": "httpuv", - "Version": "1.6.14", + "Version": "1.6.15", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3555,7 +3525,7 @@ "promises", "utils" ], - "Hash": "16abeb167dbf511f8cc0552efaf05bab" + "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0" }, "httr": { "Package": "httr", @@ -3572,11 +3542,32 @@ ], "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" }, + "httr2": { + "Package": "httr2", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "cli", + "curl", + "glue", + "lifecycle", + "magrittr", + "openssl", + "rappdirs", + "rlang", + "vctrs", + "withr" + ], + "Hash": "03d741c92fda96d98c3a3f22494e3b4a" + }, "ica": { "Package": "ica", "Version": "1.0-3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "d9b52ced14e24a0e69e228c20eb5eb27" }, "ids": { @@ -3592,7 +3583,7 @@ }, "igraph": { "Package": "igraph", - "Version": "2.0.2", + "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3611,21 +3602,7 @@ "utils", "vctrs" ], - "Hash": "e3baa015afa83d9f1b748db5a2aedb5a" - }, - "interactiveDisplayBase": { - "Package": "interactiveDisplayBase", - "Version": "1.40.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", - "Requirements": [ - "BiocGenerics", - "DT", - "R", - "methods", - "shiny" - ], - "Hash": "776b86cd30211a590997dc15d02c8eff" + "Hash": "c3b7d801d722e26e4cd888e042bf9af5" }, "interp": { "Package": "interp", @@ -3644,7 +3621,7 @@ "Package": "irlba", "Version": "2.3.5.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "Matrix", "R", @@ -3739,7 +3716,7 @@ }, "knitr": { "Package": "knitr", - "Version": "1.45", + "Version": "1.47", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3751,7 +3728,7 @@ "xfun", "yaml" ], - "Hash": "1ec462871063897135c1bcbe0fc8f07d" + "Hash": "7c99b2d55584b982717fcc0950378612" }, "labeling": { "Package": "labeling", @@ -3766,7 +3743,7 @@ }, "labelled": { "Package": "labelled", - "Version": "2.12.0", + "Version": "2.13.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3777,9 +3754,10 @@ "rlang", "stringr", "tidyr", + "tidyselect", "vctrs" ], - "Hash": "1ec27c624ece6c20431e9249bd232797" + "Hash": "ad4b6d757624221aec6220b8c78defeb" }, "lambda.r": { "Package": "lambda.r", @@ -3805,9 +3783,9 @@ }, "lattice": { "Package": "lattice", - "Version": "0.22-5", + "Version": "0.22-6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", @@ -3816,7 +3794,7 @@ "stats", "utils" ], - "Hash": "7c5e89f04e72d6611c77451f6331a091" + "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2" }, "latticeExtra": { "Package": "latticeExtra", @@ -3876,9 +3854,9 @@ }, "limma": { "Package": "limma", - "Version": "3.58.1", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "3.60.3", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "R", "grDevices", @@ -3888,7 +3866,7 @@ "stats", "utils" ], - "Hash": "74c3b64358e0be7edc3ecd130816dd3f" + "Hash": "229b85fef79976cc42c4fbcaf25eb44a" }, "listenv": { "Package": "listenv", @@ -3902,7 +3880,7 @@ }, "lme4": { "Package": "lme4", - "Version": "1.1-35.1", + "Version": "1.1-35.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3924,13 +3902,13 @@ "stats", "utils" ], - "Hash": "07fb0c5b727b15b0ce40feb641498e4e" + "Hash": "a6f5390caceaa1b23b68f57d663b2061" }, "lmtest": { "Package": "lmtest", "Version": "0.9-40", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "graphics", @@ -3941,14 +3919,14 @@ }, "locfit": { "Package": "locfit", - "Version": "1.5-9.8", + "Version": "1.5-9.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "lattice" ], - "Hash": "3434988413fbabfdb0fcd6067d7e1aa4" + "Hash": "3885127e04b35dafded049075057ad83" }, "lubridate": { "Package": "lubridate", @@ -3987,7 +3965,7 @@ }, "markdown": { "Package": "markdown", - "Version": "1.12", + "Version": "1.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3996,17 +3974,17 @@ "utils", "xfun" ], - "Hash": "765cf53992401b3b6c297b69e1edb8bd" + "Hash": "074efab766a9d6360865ad39512f2a7e" }, "matrixStats": { "Package": "matrixStats", - "Version": "1.2.0", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "33a3ca9e732b57244d14f5d732ffc9eb" + "Hash": "4b3ea27a19d669c0405b38134d89a9d1" }, "memoise": { "Package": "memoise", @@ -4021,19 +3999,19 @@ }, "metapod": { "Package": "metapod", - "Version": "1.10.1", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.12.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "Rcpp" ], - "Hash": "64e76c256313f40ff540e371e58b5503" + "Hash": "026552a86c3aa0d92d4d8b12d80010cc" }, "mgcv": { "Package": "mgcv", "Version": "1.9-1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "Matrix", "R", @@ -4070,13 +4048,13 @@ }, "minqa": { "Package": "minqa", - "Version": "1.2.6", + "Version": "1.2.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "Rcpp" ], - "Hash": "f48238f8d4740426ca12f53f27d004dd" + "Hash": "aba060ef3c097b26a4d304ea39d87f32" }, "modelr": { "Package": "modelr", @@ -4114,20 +4092,20 @@ }, "munsell": { "Package": "munsell", - "Version": "0.5.0", + "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "colorspace", "methods" ], - "Hash": "6dfe8bf774944bd5595785e3229d8771" + "Hash": "4fd8900853b746af55b81fda99da7695" }, "nlme": { "Package": "nlme", - "Version": "3.1-164", + "Version": "3.1-165", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "graphics", @@ -4135,17 +4113,14 @@ "stats", "utils" ], - "Hash": "a623a2239e642806158bc4dc3f51565d" + "Hash": "2769a88be217841b1f33ed469675c3cc" }, "nloptr": { "Package": "nloptr", - "Version": "2.0.3", + "Version": "2.1.0", "Source": "Repository", "Repository": "CRAN", - "Requirements": [ - "testthat" - ], - "Hash": "277c67a08f358f42b6a77826e4492f79" + "Hash": "2f436f0a4e224ae7542c68f1896a00d9" }, "nnet": { "Package": "nnet", @@ -4171,25 +4146,24 @@ }, "openssl": { "Package": "openssl", - "Version": "2.1.1", + "Version": "2.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" + "Hash": "2bcca3848e4734eb3b16103bc9aa4b8e" }, "org.Hs.eg.db": { "Package": "org.Hs.eg.db", - "Version": "3.18.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/data/annotation", + "Version": "3.19.1", + "Source": "Bioconductor", "Requirements": [ "AnnotationDbi", "R", "methods" ], - "Hash": "120d734b7c6eaed99d8f5f61e6c125ed" + "Hash": "1ac8a004ad2e4f6489dadf3a2ffeb638" }, "palmerpenguins": { "Package": "palmerpenguins", @@ -4203,7 +4177,7 @@ }, "parallelly": { "Package": "parallelly", - "Version": "1.37.0", + "Version": "1.37.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4211,7 +4185,7 @@ "tools", "utils" ], - "Hash": "8da17de8b15c89b574269fc414ff4e20" + "Hash": "5410df8d22bd36e616f2a2343dbb328c" }, "patchwork": { "Package": "patchwork", @@ -4235,7 +4209,7 @@ "Package": "pbapply", "Version": "1.7-2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "parallel" @@ -4294,21 +4268,6 @@ ], "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, - "pkgbuild": { - "Package": "pkgbuild", - "Version": "1.4.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "callr", - "cli", - "desc", - "processx" - ], - "Hash": "c0143443203205e6a2760ce553dafc24" - }, "pkgconfig": { "Package": "pkgconfig", "Version": "2.0.3", @@ -4319,27 +4278,6 @@ ], "Hash": "01f28d4278f15c76cddbea05899c5d6f" }, - "pkgload": { - "Package": "pkgload", - "Version": "1.3.4", - "Source": "Repository", - "Repository": "CRAN", - 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"Repository": "https://packagemanager.posit.co/cran/latest", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -4479,7 +4410,7 @@ }, "promises": { "Package": "promises", - "Version": "1.2.1", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4491,7 +4422,7 @@ "rlang", "stats" ], - "Hash": "0d8a15c9d000970ada1ab21405387dee" + "Hash": "434cd5388a3979e74be5c219bcd6e77d" }, "proxy": { "Package": "proxy", @@ -4533,7 +4464,7 @@ }, "quantreg": { "Package": "quantreg", - "Version": "5.97", + "Version": "5.98", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4547,13 +4478,13 @@ "stats", "survival" ], - "Hash": "1bbc97f7d637ab3917c514a69047b2c1" + "Hash": "017561f17632c065388b7062da030952" }, "qvalue": { "Package": "qvalue", - "Version": "2.34.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "2.36.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "R", "ggplot2", @@ -4561,13 +4492,13 @@ "reshape2", "splines" ], - 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"Version": "2.25", + "Version": "2.27", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4847,20 +4783,19 @@ "jsonlite", "knitr", "methods", - "stringr", "tinytex", "tools", "utils", "xfun", "yaml" ], - "Hash": "d65e35823c817f09f4de424fcdfa812a" + "Hash": "27f9502e1cdbfa195f94e03b0f517484" }, "rpart": { "Package": "rpart", "Version": "4.1.23", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", @@ -4904,16 +4839,16 @@ }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.15.0", + "Version": "0.16.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "5564500e25cffad9e22244ced1379887" + "Hash": "96710351d642b70e8f02ddeb237c46a7" }, "rsvd": { "Package": "rsvd", "Version": "1.0.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "Matrix", "R" @@ -4922,9 +4857,9 @@ }, "rtracklayer": { "Package": "rtracklayer", - "Version": "1.62.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.64.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BiocGenerics", "BiocIO", @@ -4934,17 +4869,18 @@ "GenomicRanges", "IRanges", "R", - "RCurl", "Rsamtools", "S4Vectors", "XML", "XVector", + "curl", + "httr", "methods", "restfulr", "tools", "zlibbioc" ], - "Hash": "e940c622725a16a0069505876051b077" + "Hash": "3d6f004fce582bd7d68e2e18d44abbc1" }, "rvest": { "Package": "rvest", @@ -4967,7 +4903,7 @@ }, "sass": { "Package": "sass", - "Version": "0.4.8", + "Version": "0.4.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4977,7 +4913,7 @@ "rappdirs", "rlang" ], - "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035" + "Hash": "d53dbfddf695303ea4ad66f86e99b95d" }, "scales": { "Package": "scales", @@ -5001,9 +4937,9 @@ }, "scater": { "Package": "scater", - "Version": "1.30.1", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.32.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BiocGenerics", "BiocNeighbors", @@ -5032,13 +4968,13 @@ "uwot", "viridis" ], - "Hash": "d92b4aa892e1f28148ce3ecad8e63cfb" + "Hash": "4a6eb8ab8a2b926fe67cf83aa731a3df" }, "scattermore": { "Package": "scattermore", "Version": "1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "ggplot2", "grDevices", @@ -5050,7 +4986,7 @@ }, "scatterpie": { "Package": "scatterpie", - "Version": "0.2.1", + "Version": "0.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5064,13 +5000,13 @@ "tidyr", "utils" ], - "Hash": "a272b0f2f06b3aa01fa4f5a033f0cf4a" + "Hash": "197ec6df5b165beb6c737ce40a8923e6" }, "scran": { "Package": "scran", - "Version": "1.30.2", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.32.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BH", "BiocGenerics", @@ -5096,7 +5032,7 @@ "stats", "utils" ], - "Hash": "147b3753ca3cb0a1a24a7f2a35f05222" + "Hash": "5b11173a6b49f06dda0db31e80caa561" }, "sctransform": { "Package": "sctransform", @@ -5124,9 +5060,9 @@ }, "scuttle": { "Package": "scuttle", - "Version": "1.12.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.14.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "BiocGenerics", "BiocParallel", @@ -5143,7 +5079,7 @@ "stats", "utils" ], - "Hash": "1412c4b6dfd8de528e1101e493e66a02" + "Hash": "6d94b72071aefd6e8b041c34ee83ebd0" }, "selectr": { "Package": "selectr", @@ -5160,9 +5096,9 @@ }, "seqLogo": { "Package": "seqLogo", - "Version": "1.68.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.70.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "R", "grDevices", @@ -5170,7 +5106,7 @@ "methods", "stats4" ], - "Hash": "422323877fb63ab24ae09cc429a8a4b1" + "Hash": "8d3102283e7ba083042118b22d805510" }, "shadowtext": { "Package": "shadowtext", @@ -5200,7 +5136,7 @@ }, "shiny": { "Package": "shiny", - "Version": "1.8.0", + "Version": "1.8.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5210,7 +5146,6 @@ "cachem", "commonmark", "crayon", - "ellipsis", "fastmap", "fontawesome", "glue", @@ -5230,13 +5165,13 @@ "withr", "xtable" ], - "Hash": "3a1f41807d648a908e3c7f0334bf85e6" + "Hash": "54b26646816af9960a4c64d8ceec75d6" }, "shinydashboard": { "Package": "shinydashboard", "Version": "0.7.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "htmltools", @@ -5292,7 +5227,7 @@ }, "sp": { "Package": "sp", - "Version": "2.1-3", + "Version": "2.1-4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5305,7 +5240,7 @@ "stats", "utils" ], - "Hash": "1a0cc0cec2915700e63fd0921085cf6a" + "Hash": "75940133cca2e339afce15a586f85b11" }, "spam": { "Package": "spam", @@ -5323,9 +5258,9 @@ }, "sparseMatrixStats": { "Package": "sparseMatrixStats", - "Version": "1.14.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.16.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "Matrix", "MatrixGenerics", @@ -5333,11 +5268,11 @@ "matrixStats", "methods" ], - "Hash": "49383d0f6c6152ff7cb594f254c23cc8" + "Hash": "7e500a5a527460ca0406473bdcade286" }, "spatstat.data": { "Package": "spatstat.data", - "Version": "3.0-4", + "Version": "3.1-2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5345,11 +5280,11 @@ "R", "spatstat.utils" ], - "Hash": "114a35341cb4955e1b8d30e28ec356c6" + "Hash": "69781a4d1dd8d1575d24b8b133e1e09f" }, "spatstat.explore": { "Package": "spatstat.explore", - "Version": "3.2-6", + "Version": "3.2-7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5369,11 +5304,11 @@ "stats", "utils" ], - "Hash": "79f7cc7fdf4b818334483e8f2a159cf6" + "Hash": "b590c5d278d0606d53278afac666ad60" }, "spatstat.geom": { "Package": "spatstat.geom", - "Version": "3.2-8", + "Version": "3.2-9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5388,11 +5323,11 @@ "stats", "utils" ], - "Hash": "309fb3fbebc875c09c8b96c21cba61c1" + "Hash": "96b9f23da42d16660aa6d136ad99cf5f" }, "spatstat.random": { "Package": "spatstat.random", - "Version": "3.2-2", + "Version": "3.2-3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5405,11 +5340,11 @@ "stats", "utils" ], - "Hash": "d05f37e83177665a5eb466da953ffc0f" + "Hash": "01aff260c49550e820a47d97e566af6a" }, "spatstat.sparse": { "Package": "spatstat.sparse", - "Version": "3.0-3", + "Version": "3.1-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5422,11 +5357,11 @@ "tensor", "utils" ], - "Hash": "1daaecefd754bb259a5ad5ce95a2cdcc" + "Hash": "3a0f41a2a77847f2bc1a909160cace56" }, "spatstat.utils": { "Package": "spatstat.utils", - "Version": "3.0-4", + "Version": "3.0-5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5437,13 +5372,13 @@ "stats", "utils" ], - "Hash": "81d929f43f8532c1f8180a105449d414" + "Hash": "b7af29c1a4e649734ac1d9b423d762c9" }, "statmod": { "Package": "statmod", "Version": "1.5.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "graphics", @@ -5453,7 +5388,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5462,7 +5397,7 @@ "tools", "utils" ], - "Hash": "058aebddea264f4c99401515182e656a" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", @@ -5483,9 +5418,9 @@ }, "survival": { "Package": "survival", - "Version": "3.5-8", + "Version": "3.7-0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "Matrix", "R", @@ -5495,7 +5430,7 @@ "stats", "utils" ], - "Hash": "184d7799bca4ba8c3be72ea396f4b9a3" + "Hash": "5aaa9cbaf4aba20f8e06fdea1850a398" }, "sys": { "Package": "sys", @@ -5506,62 +5441,35 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.5", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "cpp11" + "cpp11", + "lifecycle" ], - "Hash": "15b594369e70b975ba9f064295983499" + "Hash": "213b6b8ed5afbf934843e6c3b090d418" }, "tensor": { "Package": "tensor", "Version": "1.5", "Source": "Repository", - "Repository": "RSPM", - "Hash": "25cfab6cf405c15bccf7e69ec39df090" - }, - "testthat": { - "Package": "testthat", - "Version": "3.2.1", - "Source": "Repository", "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "brio", - "callr", - "cli", - "desc", - "digest", - "evaluate", - "jsonlite", - "lifecycle", - "magrittr", - "methods", - "pkgload", - "praise", - "processx", - "ps", - "rlang", - "utils", - "waldo", - "withr" - ], - "Hash": "4767a686ebe986e6cb01d075b3f09729" + "Hash": "25cfab6cf405c15bccf7e69ec39df090" }, "textshaping": { "Package": "textshaping", - "Version": "0.3.7", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11", + "lifecycle", "systemfonts" ], - "Hash": "997aac9ad649e0ef3b97f96cddd5622b" + "Hash": "5142f8bc78ed3d819d26461b641627ce" }, "tibble": { "Package": "tibble", @@ -5630,7 +5538,7 @@ }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5642,7 +5550,7 @@ "vctrs", "withr" ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" + "Hash": "829f27b9c4919c16b593794a6344d6c0" }, "tidytree": { "Package": "tidytree", @@ -5719,24 +5627,19 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.49", + "Version": "0.51", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "5ac22900ae0f386e54f1c307eca7d843" + "Hash": "d44e2fcd2e4e076f0aac540208559d1d" }, "treeio": { "Package": "treeio", - "Version": "1.27.0.002", - "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "YuLab-SMU", - "RemoteRepo": "treeio", - "RemoteRef": "devel", - "RemoteSha": "f6686330e437867add5dc80ef2e5db85c866c6c3", + "Version": "1.28.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "R", "ape", @@ -5751,11 +5654,11 @@ "utils", "yulab.utils" ], - "Hash": "f396e494d4ef9bf893639d78b9f453eb" + "Hash": "9e0a0b700763836cd36cb3a49be5a15d" }, "tweenr": { "Package": "tweenr", - "Version": "2.0.2", + "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5766,19 +5669,19 @@ "rlang", "vctrs" ], - "Hash": "c16efcef4c72d3bff5e65031f3f1f841" + "Hash": "82fac2b73e6a1f3874fc000aaf96d8bc" }, "tximport": { "Package": "tximport", - "Version": "1.30.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", + "Version": "1.32.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", "Requirements": [ "methods", "stats", "utils" ], - "Hash": "6e9621b0f1bf9398255f32c7000a7e16" + "Hash": "de83dfc887cf6205591b70500c987e43" }, "tzdb": { "Package": "tzdb", @@ -5813,12 +5716,13 @@ }, "uwot": { "Package": "uwot", - "Version": "0.1.16", + "Version": "0.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "FNN", "Matrix", + "RSpectra", "Rcpp", "RcppAnnoy", "RcppProgress", @@ -5826,13 +5730,13 @@ "irlba", "methods" ], - "Hash": "252deaa1c1d6d3da6946694243781ea3" + "Hash": "f693a0ca6d34b02eb432326388021805" }, "valr": { "Package": "valr", - "Version": "0.7.0", - "Source": "Repository", - "Repository": "RSPM", + "Version": "0.8.1", + "Source": "Bioconductor", + "Repository": "CRAN", "Requirements": [ "R", "Rcpp", @@ -5847,7 +5751,7 @@ "stringr", "tibble" ], - "Hash": "1e4f9c7b401073d4e562fb7989a4ab5c" + "Hash": "10a84b222f274cbc96947fce0596fae6" }, "vctrs": { "Package": "vctrs", @@ -5902,7 +5806,7 @@ "Package": "visNetwork", "Version": "2.1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", @@ -5942,24 +5846,6 @@ ], "Hash": "390f9315bc0025be03012054103d227c" }, - "waldo": { - "Package": "waldo", - "Version": "0.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "diffobj", - "fansi", - "glue", - "methods", - "rematch2", - "rlang", - "tibble" - ], - "Hash": "c7d3fd6d29ab077cbac8f0e2751449e6" - }, "withr": { "Package": "withr", "Version": "3.0.0", @@ -5974,7 +5860,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.42", + "Version": "0.45", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5982,7 +5868,7 @@ "stats", "tools" ], - "Hash": "fd1349170df31f7a10bd98b0189e85af" + "Hash": "ca59c87fe305b16a9141a5874c3a7889" }, "xml2": { "Package": "xml2", @@ -6035,16 +5921,16 @@ }, "zlibbioc": { "Package": "zlibbioc", - "Version": "1.48.0", - "Source": "Repository", - "Repository": "https://bioconductor.org/packages/3.18/bioc", - "Hash": "50ad6f7b0baaaccf1a387d2f1ecce911" + "Version": "1.50.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Hash": "3db02e3c460e1c852365df117a2b441b" }, "zoo": { "Package": "zoo", "Version": "1.8-12", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", diff --git a/renv/activate.R b/renv/activate.R index d98ed734..c4fe82ea 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,11 +2,13 @@ local({ # the requested version of renv - version <- "1.0.4" - attr(version, "sha") <- NULL + version <- "1.0.7.9000" + attr(version, "sha") <- "1f99d7d8ce7829fa67f3295f5a447e3df09c7a38" # the project directory - project <- getwd() + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() # use start-up diagnostics if enabled diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") @@ -129,6 +131,21 @@ local({ } + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + startswith <- function(string, prefix) { substring(string, 1, nchar(prefix)) == prefix } @@ -631,6 +648,9 @@ local({ # if the user has requested an automatic prefix, generate it auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) @@ -822,24 +842,23 @@ local({ # the loaded version of renv doesn't match the requested version; # give the user instructions on how to proceed - remote <- if (!is.null(description[["RemoteSha"]])) { + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) paste("rstudio/renv", description[["RemoteSha"]], sep = "@") - } else { + else paste("renv", description[["Version"]], sep = "@") - } # display both loaded version + sha if available friendly <- renv_bootstrap_version_friendly( version = description[["Version"]], - sha = description[["RemoteSha"]] + sha = if (dev) description[["RemoteSha"]] ) - fmt <- paste( - "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", - sep = "\n" - ) + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) FALSE diff --git a/renv/settings.json b/renv/settings.json index 45ee56fb..9dceb943 100644 --- a/renv/settings.json +++ b/renv/settings.json @@ -1,5 +1,5 @@ { - "bioconductor.version": "3.18", + "bioconductor.version": "3.19", "external.libraries": [], "ignored.packages": [], "package.dependency.fields": [