From 77bc7492ffd1ab7f90142ee5b3104e95fb63812b Mon Sep 17 00:00:00 2001 From: Maya Gans Date: Thu, 20 Aug 2026 17:50:31 -0700 Subject: [PATCH 1/4] Fix renv restore in CI by pinning a dated PPM snapshot CI has failed at "Set up renv" on every branch since ~24 July 2026, including pushes straight to main. The trigger was GitHub migrating ubuntu-latest to a new image: setup-renv keys its package cache on sessionInfo()$running, so the migration invalidated every cache at once. That exposed a latent problem. renv.lock pointed at packagemanager.posit.co/cran/latest, which only ever serves the *current* version of each package, and 154 of the 374 pinned versions were no longer current. With no binary available, renv fell back to compiling old source tarballs from the CRAN archive, which fails on the new runner. A warm cache had hidden this for months. Changes: - Pin the repository to a dated snapshot (cran/2026-08-14) and re-snapshot so every recorded version matches that date. Verified that all 365 repository-sourced records resolve on macOS arm64, Windows and Linux, and that all 170 compiled packages are served as prebuilt binaries for both noble and resolute. CI now compiles nothing. - Stop recording the 15 packages that ship with R (mgcv, Matrix, survival, lattice, ...). Their versions track the R build rather than CRAN, so no snapshot date can ever satisfy them; this is also what broke local installs on macOS. utils/quarto_check_pkg_dependencies.R already handles these having no hash. - Add survRM2 1.0-4 and its dependency muhaz, to unblock #598. - Drop survMisc: CRAN archived it on 17 March 2026, it is no longer a survminer dependency, and it is only mentioned in prose. km.ci, KMsurv, plyr, reshape2 and rgl go with it as transitive dependencies that current versions no longer need. - Pin runs-on to ubuntu-24.04 in both workflows so a future image migration cannot silently invalidate the caches again. Note: 138 package versions change, so the Quarto freeze cache will be largely invalidated and most pages will re-execute on the first run. --- .github/workflows/action.yml | 5 +- .github/workflows/pull_request_action.yml | 5 +- renv.lock | 1054 ++++++++++----------- renv/settings.json | 18 +- 4 files changed, 500 insertions(+), 582 deletions(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 66d73232c..154ccc666 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -6,7 +6,10 @@ name: Render and Publish jobs: build-deploy: - runs-on: ubuntu-latest + # Pinned deliberately: setup-renv keys its package cache on the OS string, + # so a floating ubuntu-latest silently invalidates every cache when GitHub + # migrates the image (this is what broke CI in July 2026). + runs-on: ubuntu-24.04 env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes diff --git a/.github/workflows/pull_request_action.yml b/.github/workflows/pull_request_action.yml index 077eea22e..0111e55a4 100644 --- a/.github/workflows/pull_request_action.yml +++ b/.github/workflows/pull_request_action.yml @@ -11,7 +11,10 @@ name: Test Rendering jobs: build-deploy: - runs-on: ubuntu-latest + # Pinned deliberately: setup-renv keys its package cache on the OS string, + # so a floating ubuntu-latest silently invalidates every cache when GitHub + # migrates the image (this is what broke CI in July 2026). + runs-on: ubuntu-24.04 env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes diff --git a/renv.lock b/renv.lock index f1b12a0a5..e598b1a3d 100644 --- a/renv.lock +++ b/renv.lock @@ -1,10 +1,10 @@ { "R": { - "Version": "4.5.2", + "Version": "4.5.3", "Repositories": [ { "Name": "CRAN", - "URL": "https://packagemanager.posit.co/cran/latest" + "URL": "https://packagemanager.posit.co/cran/2026-08-14" } ] }, @@ -14,6 +14,13 @@ "Name": "./renv/python/virtualenvs/renv-python-3.12" }, "Packages": { + "AsioHeaders": { + "Package": "AsioHeaders", + "Version": "1.30.2-1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "a6d3ad7ba83bd5dc4b9c13b685b2b4a4" + }, "BH": { "Package": "BH", "Version": "1.90.0-1", @@ -37,14 +44,27 @@ }, "DBI": { "Package": "DBI", - "Version": "1.2.3", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "065ae649b05f1ff66bb0c793107508f5" + "Hash": "dbfa2adb83f8063640982459e153f650" + }, + "DFBA": { + "Package": "DFBA", + "Version": "0.1.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "graphics", + "methods", + "stats" + ], + "Hash": "8dda5e864eeb9fe227bcac7db8a0d7df" }, "DOS2": { "Package": "DOS2", @@ -81,13 +101,14 @@ }, "Deriv": { "Package": "Deriv", - "Version": "4.2.0", + "Version": "4.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "Rcpp", "methods" ], - "Hash": "3c3130705944f882654c991829c0b5bc" + "Hash": "70e217897316149c9c655ad78b379fa1" }, "DescTools": { "Package": "DescTools", @@ -137,7 +158,7 @@ }, "FactoMineR": { "Package": "FactoMineR", - "Version": "2.13", + "Version": "2.16", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -151,27 +172,32 @@ "flashClust", "ggplot2", "ggrepel", + "ggtext", "grDevices", "graphics", + "irlba", "lattice", "leaps", "multcompView", + "scales", "scatterplot3d", + "showtext", "stats", + "sysfonts", "utils" ], - "Hash": "7712f6d5b2d91bf4ead51ba97d7a5c9a" + "Hash": "2f9baeca11e74364b6dc171f76a17aa6" }, "Formula": { "Package": "Formula", - "Version": "1.2-5", + "Version": "1.2-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "stats" ], - "Hash": "7a29697b75e027767a53fde6c903eca7" + "Hash": "a2fceb52bfbc3be9df984e98755f9ae1" }, "GLMMadaptive": { "Package": "GLMMadaptive", @@ -199,7 +225,7 @@ }, "Hmisc": { "Package": "Hmisc", - "Version": "5.2-5", + "Version": "5.2-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -223,40 +249,7 @@ "rpart", "viridisLite" ], - "Hash": "883b941aee155e7d7d6cdf35b17080d1" - }, - "KMsurv": { - "Package": "KMsurv", - "Version": "0.1-6", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "9b4949ea5c24451e7b3c7e1c1647801b" - }, - "KernSmooth": { - "Package": "KernSmooth", - "Version": "2.23-26", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats" - ], - "Hash": "2fb39782c07b5ad422b0448ae83f64c4" - }, - "MASS": { - "Package": "MASS", - "Version": "7.3-65", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "methods", - "stats", - "utils" - ], - "Hash": "a41d0fc833ea756a1136b60a437efe26" + "Hash": "30eba6d0597b6af63edeb31056fdbab1" }, "MatchIt": { "Package": "MatchIt", @@ -277,23 +270,6 @@ ], "Hash": "4605e6e151faa5275ee1eaae441c5f24" }, - "Matrix": { - "Package": "Matrix", - "Version": "1.7-4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "grid", - "lattice", - "methods", - "stats", - "utils" - ], - "Hash": "7dbe8933065523bfc227027091bf2b1f" - }, "MatrixModels": { "Package": "MatrixModels", "Version": "0.5-4", @@ -331,10 +307,10 @@ }, "QuickJSR": { "Package": "QuickJSR", - "Version": "1.9.0", + "Version": "1.10.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "3026f0119ebb60c5c12028f857f83291" + "Hash": "08b7b1ee36f1ad560fe72b1588a6f5d2" }, "R6": { "Package": "R6", @@ -358,7 +334,7 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.1.1", + "Version": "1.1.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -366,11 +342,11 @@ "methods", "utils" ], - "Hash": "60df6f11cbeffbf9d50ad0852867f6b6" + "Hash": "f481f89daa906a34eab8ef8658c8a89c" }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "15.2.3-1", + "Version": "15.4.2-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -380,7 +356,7 @@ "stats", "utils" ], - "Hash": "180d6ae1fc15b124e1ea2ea95555d385" + "Hash": "f7694f9bd161314b273073279998a69b" }, "RcppEigen": { "Package": "RcppEigen", @@ -397,13 +373,13 @@ }, "RcppParallel": { "Package": "RcppParallel", - "Version": "5.1.11-1", + "Version": "6.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "07d228a359f31d8aebe6d2f643c1f012" + "Hash": "ae97343f2392836689f02881879ff787" }, "RcppProgress": { "Package": "RcppProgress", @@ -439,14 +415,14 @@ }, "S7": { "Package": "S7", - "Version": "0.2.1", + "Version": "0.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "9da85950949574264f92f91f0e23de26" + "Hash": "6a72e94a8c9be4ef719af3aa3628f2dc" }, "SampleSize4ClinicalTrials": { "Package": "SampleSize4ClinicalTrials", @@ -495,7 +471,7 @@ }, "TMB": { "Package": "TMB", - "Version": "1.9.19", + "Version": "1.9.23", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -507,7 +483,7 @@ "stats", "utils" ], - "Hash": "17093525d3c647976a5da3538f9f12d7" + "Hash": "298f827b699d7d905260516b1c7b3544" }, "TrialSize": { "Package": "TrialSize", @@ -518,7 +494,7 @@ }, "V8": { "Package": "V8", - "Version": "8.0.1", + "Version": "8.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -527,7 +503,7 @@ "jsonlite", "utils" ], - "Hash": "f0301ca7b867eeb5c9b586a9e400729a" + "Hash": "9fcf4128ded76196cf5f9e731d5e14ef" }, "VGAM": { "Package": "VGAM", @@ -593,13 +569,13 @@ }, "backports": { "Package": "backports", - "Version": "1.5.0", + "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "e1e1b9d75c37401117b636b7ae50827a" + "Hash": "e3e65442a2749b59692220f368f46c46" }, "base64enc": { "Package": "base64enc", @@ -613,7 +589,7 @@ }, "bayestestR": { "Package": "bayestestR", - "Version": "0.17.0", + "Version": "0.18.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -625,7 +601,7 @@ "stats", "utils" ], - "Hash": "06396210f1414b47a2702eb5d574934c" + "Hash": "ca4a1cadca567b46156e073e6deab1dc" }, "bdsmatrix": { "Package": "bdsmatrix", @@ -674,7 +650,7 @@ }, "bit64": { "Package": "bit64", - "Version": "4.6.0-1", + "Version": "4.8.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -685,14 +661,14 @@ "stats", "utils" ], - "Hash": "4f572fbc586294afff277db583b9060f" + "Hash": "71778c0b60bbf439ac64e6a8be695917" }, "bitops": { "Package": "bitops", - "Version": "1.0-9", + "Version": "1.1-0", "Source": "Repository", "Repository": "CRAN", - "Hash": "d972ef991d58c19e6efa71b21f5e144b" + "Hash": "baf391dcfdfee22a934bdc688a4c0adf" }, "blob": { "Package": "blob", @@ -706,21 +682,9 @@ ], "Hash": "1e0ae40898be928695fd90a80e816253" }, - "boot": { - "Package": "boot", - "Version": "1.3-32", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "graphics", - "stats" - ], - "Hash": "d39b147eb7fe9df64a1a55f72346360c" - }, "bpcp": { "Package": "bpcp", - "Version": "1.4.2", + "Version": "1.5.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -729,7 +693,7 @@ "stats", "survival" ], - "Hash": "31fa7c29be33fb72d3338e0cabf31174" + "Hash": "4ca2b7f6ebfd6f7e86210415574644c7" }, "brio": { "Package": "brio", @@ -743,7 +707,7 @@ }, "broom": { "Package": "broom", - "Version": "1.0.12", + "Version": "1.0.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -760,11 +724,11 @@ "tibble", "tidyr" ], - "Hash": "6cf2f6757591ea712c57c5d7bedc3c27" + "Hash": "b91eb25282a25d746f84dbd340ace9db" }, "bslib": { "Package": "bslib", - "Version": "0.10.0", + "Version": "0.12.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -782,7 +746,7 @@ "rlang", "sass" ], - "Hash": "d6072fb96c4868d8cb40d4071cdc472b" + "Hash": "b2d0b0a17142ed4858f252d88eb56223" }, "ca": { "Package": "ca", @@ -807,16 +771,17 @@ }, "callr": { "Package": "callr", - "Version": "3.7.6", + "Version": "3.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "R6", + "otel", "processx", "utils" ], - "Hash": "d7e13f49c19103ece9e58ad2d83a7354" + "Hash": "cb2799e0a02c2ac4d0395b0e29bb6799" }, "car": { "Package": "car", @@ -855,7 +820,7 @@ }, "cards": { "Package": "cards", - "Version": "0.7.1", + "Version": "0.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -868,11 +833,11 @@ "tidyr", "tidyselect" ], - "Hash": "78b4b998c31ef49c1e75b96f5e498bf2" + "Hash": "0f49ff3fb56262a47ba4f582c4cecc1c" }, "cardx": { "Package": "cardx", - "Version": "0.3.2", + "Version": "0.3.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -885,7 +850,7 @@ "rlang", "tidyr" ], - "Hash": "f5c603963977f502b06f4931d9a763ee" + "Hash": "6eed70361109b605cc66b3ba340e44a5" }, "cellranger": { "Package": "cellranger", @@ -941,18 +906,28 @@ ], "Hash": "155015404e9e9b55339384dec942fc7d" }, - "class": { - "Package": "class", - "Version": "7.3-23", + "chromote": { + "Package": "chromote", + "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "MASS", - "R", - "stats", - "utils" + "R6", + "cli", + "curl", + "fastmap", + "jsonlite", + "later", + "magrittr", + "processx", + "promises", + "rlang", + "utils", + "websocket", + "withr", + "zip" ], - "Hash": "d0cb9cc838c3b43560bd958fc4317fdc" + "Hash": "645cd21d708d14c2732a34b2ccba87b8" }, "classInt": { "Package": "classInt", @@ -972,28 +947,28 @@ }, "cli": { "Package": "cli", - "Version": "3.6.5", + "Version": "3.6.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "16850760556401a2eeb27d39bd11c9cb" + "Hash": "a73d822b669d443ff8de6928f9c49850" }, "clipr": { "Package": "clipr", - "Version": "0.8.0", + "Version": "0.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" + "Hash": "cc6e507cf89f11ffc44b32519e0198da" }, "clubSandwich": { "Package": "clubSandwich", - "Version": "0.6.2", + "Version": "0.7.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1002,21 +977,7 @@ "sandwich", "stats" ], - "Hash": "45c2e9af8484812eb3cb70c16fd84ae2" - }, - "cluster": { - "Package": "cluster", - "Version": "2.1.8.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "stats", - "utils" - ], - "Hash": "e16d49a008e1a22ee863fb9a51de9bde" + "Hash": "aa6ac2da8a6bb076549ea51c02cc13b2" }, "cmprsk": { "Package": "cmprsk", @@ -1029,19 +990,9 @@ ], "Hash": "c733af3a77ab8bde9b6a632197342cb9" }, - "codetools": { - "Package": "codetools", - "Version": "0.2-20", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "61e097f35917d342622f21cdc79c256e" - }, "coin": { "Package": "coin", - "Version": "1.4-3", + "Version": "1.4-5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1058,22 +1009,22 @@ "survival", "utils" ], - "Hash": "4084b5070a40ad99dad581ed3b67bd55" + "Hash": "4bf75823ffa387ea2630231cb397fb8c" }, "collapse": { "Package": "collapse", - "Version": "2.1.6", + "Version": "2.1.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "Rcpp" ], - "Hash": "158158a0aad21d43154cf68f72d31fdc" + "Hash": "9c35542dc0acb8ff66128047585a7fef" }, "colorspace": { "Package": "colorspace", - "Version": "2.1-2", + "Version": "2.1-3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1083,18 +1034,18 @@ "methods", "stats" ], - "Hash": "2c14b873da71cacec1284f3f6d112ddc" + "Hash": "acb51c45a64447d9deb5e4d5c9e0de9e" }, "common": { "Package": "common", - "Version": "1.1.4", + "Version": "1.1.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "8358b227f4a0026a4fe08471339013d6" + "Hash": "20bb061342078956abce7bcb010d0f0c" }, "commonmark": { "Package": "commonmark", @@ -1178,13 +1129,13 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.5.3", + "Version": "0.5.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "af5958631ca49510aff96d0f5c0bbb76" + "Hash": "20ecb9105a3fb48a8390919abc3b7e90" }, "crayon": { "Package": "crayon", @@ -1223,28 +1174,28 @@ }, "curl": { "Package": "curl", - "Version": "7.0.0", + "Version": "7.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "aa27e963d3deccf4bade44d06b976977" + "Hash": "2e004ed19964915a8faf48a574439be9" }, "data.table": { "Package": "data.table", - "Version": "1.18.2.1", + "Version": "1.18.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "df99cd4333ce592df5173d6ad39b5c14" + "Hash": "da9ddede68a6f6e5d3098c0ab81b6e1f" }, "datawizard": { "Package": "datawizard", - "Version": "1.3.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1253,11 +1204,11 @@ "stats", "utils" ], - "Hash": "6acfecf3792005ee2e2e1eb7ede6c1c1" + "Hash": "82c29732e404f45c41314eab720e52d3" }, "dbplyr": { "Package": "dbplyr", - "Version": "2.5.2", + "Version": "2.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1281,7 +1232,7 @@ "vctrs", "withr" ], - "Hash": "751a4c05422caab7c7f74f10a94961fa" + "Hash": "ddbed6865865c509ea0b516faf83042b" }, "dendextend": { "Package": "dendextend", @@ -1335,7 +1286,7 @@ }, "diffobj": { "Package": "diffobj", - "Version": "0.3.6", + "Version": "0.3.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1346,7 +1297,7 @@ "tools", "utils" ], - "Hash": "e036ce354ab60e705ac5f40bac87e8cb" + "Hash": "fc69a29e9a851af8d0d07b3d4ed1dea4" }, "digest": { "Package": "digest", @@ -1361,7 +1312,7 @@ }, "distributional": { "Package": "distributional", - "Version": "0.6.0", + "Version": "0.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1375,11 +1326,11 @@ "utils", "vctrs" ], - "Hash": "e39534d5c70549298cbe7dc2f1fda65b" + "Hash": "72f50cd7f9ae374a323c832ab6c25171" }, "doBy": { "Package": "doBy", - "Version": "4.7.1", + "Version": "4.7.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1394,18 +1345,17 @@ "forecast", "ggplot2", "methods", - "microbenchmark", "modelr", "purrr", "rlang", "tibble", "tidyr" ], - "Hash": "5f2c39d5a7cac55afb304e3a70c77554" + "Hash": "da344b4511e1b22d30dc39e62e9c9bbc" }, "dplyr": { "Package": "dplyr", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1424,7 +1374,7 @@ "utils", "vctrs" ], - "Hash": "71a469a5d5f9fdbf7de6c0dbeece0e22" + "Hash": "d71f190466b9496cf8543c76641be5cf" }, "dtplyr": { "Package": "dtplyr", @@ -1475,7 +1425,7 @@ }, "emmeans": { "Package": "emmeans", - "Version": "2.0.1", + "Version": "2.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1489,15 +1439,16 @@ "stats", "utils" ], - "Hash": "a080e7cd7ab0cede46c10b6fd5aaad7e" + "Hash": "4b1a9deaadc921992795563ef658ca19" }, "epiR": { "Package": "epiR", - "Version": "2.0.90", + "Version": "2.0.96", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "BiasedUrn", + "DFBA", "R", "flextable", "lubridate", @@ -1509,18 +1460,18 @@ "survival", "zoo" ], - "Hash": "8e7a32486485bcc4d6913936ad042421" + "Hash": "76bd40b89fdaab589b7cc050807aac94" }, "estimability": { "Package": "estimability", - "Version": "1.5.1", + "Version": "2.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "stats" ], - "Hash": "21ec52af13afbcab1cb317567b639b0a" + "Hash": "0a032de8b3ae5b5695c8319112607bda" }, "evaluate": { "Package": "evaluate", @@ -1547,7 +1498,7 @@ }, "exactRankTests": { "Package": "exactRankTests", - "Version": "0.8-35", + "Version": "0.8-37", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1555,7 +1506,7 @@ "stats", "utils" ], - "Hash": "790c46974d99ff51442f4d134b2d70eb" + "Hash": "0aa957b0217c8f42e1b36d907a730c47" }, "exactci": { "Package": "exactci", @@ -1582,24 +1533,22 @@ }, "factoextra": { "Package": "factoextra", - "Version": "1.0.7", + "Version": "2.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "FactoMineR", "R", - "abind", "cluster", "dendextend", "ggplot2", "ggpubr", "ggrepel", "grid", - "reshape2", - "stats", - "tidyr" + "rlang", + "stats" ], - "Hash": "e95f1aed34b3f0a15a0c308175ee4c80" + "Hash": "d80190c5c2e2b6256a33f1f94dd3e408" }, "farver": { "Package": "farver", @@ -1627,7 +1576,7 @@ }, "flextable": { "Package": "flextable", - "Version": "0.9.11", + "Version": "0.10.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1647,11 +1596,11 @@ "uuid", "xml2" ], - "Hash": "016c4b282f7dbb621fa30560924a4085" + "Hash": "4b9095bab25f9ff8387974c5ecd63a17" }, "fmtr": { "Package": "fmtr", - 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"Version": "2.5.0", + "Version": "2.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2379,11 +2316,11 @@ "tidyr", "vctrs" ], - "Hash": "ef592ba4c689a6867e9f571697fa2ecb" + "Hash": "55d23d7b05dbb99ec5653d7f68ef5ca9" }, "hardhat": { "Package": "hardhat", - "Version": "1.4.2", + "Version": "1.4.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2395,7 +2332,7 @@ "tibble", "vctrs" ], - "Hash": "3925b503926399e7f9ae563faf11da4d" + "Hash": "d7610d4cd0047f81634ebc1faecacbf1" }, "haven": { "Package": "haven", @@ -2430,14 +2367,14 @@ }, "highr": { "Package": "highr", - "Version": "0.11", + "Version": "0.12", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "xfun" ], - "Hash": "d65ba49117ca223614f71b60d85b8ab7" + "Hash": "2a2f862ade01a56dcbcd60944de11255" }, "hms": { "Package": "hms", @@ -2456,7 +2393,7 @@ }, "htmlTable": { "Package": "htmlTable", - "Version": "2.4.3", + "Version": "2.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2470,7 +2407,7 @@ "rstudioapi", "stringr" ], - 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"km.ci": { - "Package": "km.ci", - "Version": "0.5-6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats", - "survival" - ], - "Hash": "41d857f78edf8f5db59608b6a42b6005" - }, "knitr": { "Package": "knitr", "Version": "1.51", @@ -2728,7 +2689,7 @@ }, "later": { "Package": "later", - "Version": "1.4.6", + "Version": "1.4.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2736,26 +2697,11 @@ "Rcpp", "rlang" ], - "Hash": "a651844fe479e1cc9c2355f74a722ae6" - }, - "lattice": { - "Package": "lattice", - "Version": "0.22-7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "grid", - "stats", - "utils" - ], - "Hash": "934f30aea6442867f57a610034ab06d3" + "Hash": "824c180e69b9be79ab96a985e233c470" }, "lavaan": { "Package": "lavaan", - "Version": "0.6-21", + "Version": "0.7-2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2771,17 +2717,18 @@ "stats4", "utils" ], - "Hash": "bbe0a613f6b8d6db76a37a1924d0c4f1" + "Hash": "c5a930ce6cf452dc272a2caefa614ed1" }, "lazyeval": { "Package": "lazyeval", - "Version": "0.2.2", + "Version": "0.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "R" + "R", + "rlang" ], - "Hash": "d908914ae53b04d4c0c0fd72ecc35370" + "Hash": "2757e46c2633dd5854f62615df70d0d7" }, "leaps": { "Package": "leaps", @@ -2792,7 +2739,7 @@ }, "libcoin": { "Package": "libcoin", - "Version": "1.0-11", + "Version": "1.0-13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2800,7 +2747,7 @@ "mvtnorm", "stats" ], - "Hash": "93f4a49f798031107629653b0fbbd0c4" + "Hash": "68d41be2b6dddf01880400e0c4ad1fa3" }, "lifecycle": { "Package": "lifecycle", @@ -2816,17 +2763,17 @@ }, "listenv": { "Package": "listenv", - "Version": "0.10.0", + "Version": "1.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "6debfba65f9df176bbb98bc63f934272" + "Hash": "c5a4adae4290385ff5819e02ff9b9931" }, "litedown": { "Package": "litedown", - "Version": "0.9", + "Version": "0.10", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2835,11 +2782,11 @@ "utils", "xfun" ], - "Hash": "6b9435273e6506fbafa5909adf4abb88" + "Hash": "0bb78ad1932aa147c433f16183382219" }, "lme4": { "Package": "lme4", - "Version": "1.1-38", + "Version": "2.0-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2859,16 +2806,15 @@ "nloptr", "parallel", "reformulas", - "rlang", "splines", "stats", "utils" ], - "Hash": "0a0abf28da4a31382cf6d523f2e1e3d1" + "Hash": "dbedab779d23065e0f4905b79429fa68" }, "lmom": { "Package": "lmom", - "Version": "3.2", + "Version": "3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2876,7 +2822,7 @@ "graphics", "stats" ], - "Hash": "a75d2dd42af9b4cb291815889cdcff77" + "Hash": "ac4b8fed655d152553e8208b78078cda" }, "lmtest": { "Package": "lmtest", @@ -2907,7 +2853,7 @@ }, "loo": { "Package": "loo", - "Version": "2.9.0", + "Version": "2.10.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2918,7 +2864,7 @@ "posterior", "stats" ], - "Hash": "553d13a5e2b45cfd7ca2d782a7054f31" + "Hash": "557142a63f951e40db1af9f907365cfc" }, "lubridate": { "Package": "lubridate", @@ -2935,13 +2881,13 @@ }, "magrittr": { "Package": "magrittr", - "Version": "2.0.4", + "Version": "2.0.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "8b3b213aa0c54a0dec254288ccb545d1" + "Hash": "665e77ab6e5f37a7913226d40b324e37" }, "markdown": { "Package": "markdown", @@ -3007,7 +2953,7 @@ }, "merDeriv": { "Package": "merDeriv", - "Version": "0.2-5", + "Version": "0.2-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3022,24 +2968,7 @@ "stats", "utils" ], - "Hash": "12196168eeebfe7e6c73328812a680f4" - }, - "mgcv": { - "Package": "mgcv", - "Version": "1.9-3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Matrix", - "R", - "graphics", - "methods", - "nlme", - "splines", - "stats", - "utils" - ], - "Hash": "51fcbccd59569cdad6da6b8e49cdf4f2" + "Hash": "b958fe1bdcc871b3b35ac861f8e44e7e" }, "mice": { "Package": "mice", @@ -3139,7 +3068,7 @@ }, "mmrm": { "Package": "mmrm", - "Version": "0.3.17", + "Version": "0.3.18", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3162,7 +3091,7 @@ "tibble", "utils" ], - "Hash": "f16234e9c97b54463bb4c62314182046" + "Hash": "9e03ced755deb0f4983018780a73099e" }, "mnormt": { "Package": "mnormt", @@ -3211,9 +3140,20 @@ "Repository": "CRAN", "Hash": "bb94fd8ee5f7f127eae2bddbff26864d" }, + "muhaz": { + "Package": "muhaz", + "Version": "1.2.6.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "survival" + ], + "Hash": "5925fd639ecaa05db6e9777bc895e2e5" + }, "multcomp": { "Package": "multcomp", - "Version": "1.4-29", + "Version": "1.4-31", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3225,17 +3165,17 @@ "stats", "survival" ], - "Hash": "3350139bac9264546e523634ff6aa74b" + "Hash": "e6cf35bb9128e705a848363da2ca4bc3" }, "multcompView": { "Package": "multcompView", - "Version": "0.1-11", + "Version": "0.1-12", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "grid" ], - "Hash": "e043f633d898be14de143d5a32457a78" + "Hash": "9b4782acb7684558e63c0255331b9aed" }, "multgee": { "Package": "multgee", @@ -3267,28 +3207,15 @@ }, "mvtnorm": { "Package": "mvtnorm", - "Version": "1.3-3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats" - ], - "Hash": "c7241e6be9d6df551a2e539a50f5c875" - }, - "nlme": { - "Package": "nlme", - "Version": "3.1-168", + "Version": "1.4-2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "graphics", - "lattice", "stats", "utils" ], - "Hash": "b1d2ea08d5d392831fbc32c872362b06" + "Hash": "f12b9432ec251666c49e7d01f1aff3c7" }, "nloptr": { "Package": "nloptr", @@ -3297,21 +3224,9 @@ "Repository": "CRAN", "Hash": "dd6975473dd4c9b96e9be93b796b9c1a" }, - "nnet": { - "Package": "nnet", - "Version": "7.3-20", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats", - "utils" - ], - "Hash": "c955edf99ff24a32e96bd0a22645af60" - }, "nonnest2": { "Package": "nonnest2", - "Version": "0.5-8", + "Version": "0.5-9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3322,7 +3237,7 @@ "mvtnorm", "sandwich" ], - "Hash": "f76473d3210524e30c0ec2e5b91f8455" + "Hash": "9df8b8ecad5a549b79a28652f488b57f" }, "nph": { "Package": "nph", @@ -3338,8 +3253,8 @@ "mvtnorm", "stats", "survival" - ], - "Hash": "aef516378ec2181493aa2bdeb08f94d7" + ], + "Hash": "aef516378ec2181493aa2bdeb08f94d7" }, "nphRCT": { "Package": "nphRCT", @@ -3378,7 +3293,7 @@ }, "officer": { "Package": "officer", - "Version": "0.7.3", + "Version": "0.7.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3396,17 +3311,17 @@ "xml2", "zip" ], - "Hash": "6c1b10689d4e3a49a50a093c4bd263ef" + "Hash": "8ecbb62f412a5939760ea7eb565acc77" }, "openssl": { "Package": "openssl", - "Version": "2.3.4", + "Version": "2.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "d5811dade9cd3a34a9038a45f1a59bae" + "Hash": "6994d1c3ea954f29de6aeca5da95c99d" }, "operator.tools": { "Package": "operator.tools", @@ -3437,7 +3352,7 @@ }, "ordinal": { "Package": "ordinal", - "Version": "2025.12-29", + "Version": "2026.7-26", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3450,7 +3365,7 @@ "stats", "ucminf" ], - "Hash": "e4f565f2e23677b4245ee511e2b291c9" + "Hash": "41d4647ceb1cce9aab3937fe25348a39" }, "otel": { "Package": "otel", @@ -3464,13 +3379,10 @@ }, "pan": { "Package": "pan", - "Version": "1.9", + "Version": "2.0", "Source": "Repository", "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "aefe2753a8e7277e0fdd6d1d08d1692e" + "Hash": "9abc4f798150b318a13afcc277e9d636" }, "pander": { "Package": "pander", @@ -3492,7 +3404,7 @@ }, "parallelly": { "Package": "parallelly", - "Version": "1.46.1", + "Version": "1.48.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3500,11 +3412,11 @@ "tools", "utils" ], - "Hash": "f4d2d1926bcb9a9384193bd7fea39fe3" + "Hash": "a21defc75d66882933d80b7ae824a7b1" }, "parameters": { "Package": "parameters", - "Version": "0.28.3", + "Version": "0.29.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3517,11 +3429,11 @@ "stats", "utils" ], - "Hash": "5c812a68308c47fa9cafbfebccc3e356" + "Hash": "b574f87f7b4ba68770acb837cfd3fe2c" }, "parsnip": { "Package": "parsnip", - "Version": "1.4.1", + "Version": "1.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3544,10 +3456,9 @@ "tibble", "tidyr", "utils", - "vctrs", - "withr" + "vctrs" ], - "Hash": "01b65f5a5d1397b31f62defa71cce5b2" + "Hash": "2097696035afde4836f54ea4a0bb524c" }, "patchwork": { "Package": "patchwork", @@ -3647,7 +3558,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.5.0", + "Version": "1.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3664,7 +3575,7 @@ "rprojroot", "utils" ], - "Hash": "91a99cbfcb01c854584e7d1b69035c2c" + "Hash": "912acb56e1e3362766b63278d8b60a61" }, "plm": { "Package": "plm", @@ -3690,7 +3601,7 @@ }, "plotly": { "Package": "plotly", - "Version": "4.12.0", + "Version": "4.12.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3706,7 +3617,6 @@ "htmlwidgets", "httr", "jsonlite", - "lazyeval", "magrittr", "promises", "purrr", @@ -3718,28 +3628,17 @@ "vctrs", "viridisLite" ], - "Hash": "282f8b208bc767c67a370b47bff6ada7" - }, - "plyr": { - "Package": "plyr", - "Version": "1.8.9", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp" - ], - "Hash": "6b8177fd19982f0020743fadbfdbd933" + "Hash": "3609e47f0d9713dfd7f68bd6e731e27b" }, "png": { "Package": "png", - "Version": "0.1-8", + "Version": "0.1-9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "bd54ba8a0a5faded999a7aab6e46b374" + "Hash": "961c433971606243a724eb19b1075e60" }, "polspline": { "Package": "polspline", @@ -3765,7 +3664,7 @@ }, "posterior": { "Package": "posterior", - "Version": "1.6.1", + "Version": "1.7.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3783,7 +3682,7 @@ "tibble", "vctrs" ], - "Hash": "6ce9d5bf852882c96029dfc35b46da2b" + "Hash": "5c78a3f8f08513ca28a3df5211f016db" }, "praise": { "Package": "praise", @@ -3804,7 +3703,7 @@ }, "processx": { "Package": "processx", - "Version": "3.8.6", + "Version": "3.9.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3813,24 +3712,26 @@ "ps", "utils" ], - "Hash": "720161b280b0a35f4d1490ead2fe81d0" + "Hash": "188d6caf38e81bf15b5e918726a6fd3d" }, "procs": { "Package": "procs", - "Version": "1.0.7", + "Version": "1.0.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "common", "fmtr", + "graphics", "reporter", "sasLM", "stats", "tibble", - "utils" + "utils", + "withr" ], - "Hash": "7b941743d6101b315e73c6652c3246db" + "Hash": "001f28a451da3ab559c0f1849e4d95a2" }, "progress": { "Package": "progress", @@ -3877,18 +3778,18 @@ }, "ps": { "Package": "ps", - "Version": "1.9.1", + "Version": "1.9.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "093688087b0bacce6ba2f661f36328e2" + "Hash": "83e7e486c434e7acc71766dfc20adf2b" }, "purrr": { "Package": "purrr", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3899,7 +3800,7 @@ "rlang", "vctrs" ], - "Hash": "0154ac5b9ef4df1a7be3a54602e781cf" + "Hash": "0a35605539b085a4828ec55ad973fe60" }, "pwr": { "Package": "pwr", @@ -3949,7 +3850,7 @@ }, "r2rtf": { "Package": "r2rtf", - "Version": "1.3.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3957,18 +3858,18 @@ "grDevices", "tools" ], - "Hash": "036ba1ef84d42329c59a07958b290027" + "Hash": "6646b92ae9296ff667622eac1231bbbe" }, "ragg": { "Package": "ragg", - "Version": "1.5.0", + "Version": "1.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "cdb40b21711a8870f305b24226698f9f" + "Hash": "c06b460d55dd27458977e417e8ff02c7" }, "rappdirs": { "Package": "rappdirs", @@ -3986,14 +3887,14 @@ "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", - "RemoteRepo": "ratesci", "RemoteUsername": "petelaud", - "RemotePkgRef": "petelaud/ratesci", + "RemoteRepo": "ratesci", + "RemoteRef": "e1cd177c0f1fac61e8837d798f87a97c3c56a161", "RemoteSha": "e1cd177c0f1fac61e8837d798f87a97c3c56a161", "Requirements": [ "R" ], - "Hash": "ba42cacf19fe2f8c3c08faa17d7c93cc" + "Hash": "b59285780b3f393c521abd8a63812121" }, "rbibutils": { "Package": "rbibutils", @@ -4009,7 +3910,7 @@ }, "rbmi": { "Package": "rbmi", - "Version": "1.6.0", + "Version": "1.6.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4019,13 +3920,14 @@ "assertthat", "fs", "jinjar", + "lifecycle", "methods", "mmrm", "pkgload", "stringr", "tools" ], - "Hash": "5ed5f819dbf63b81fcaa0593f554ea3f" + "Hash": "7375406ade6cdd7c429716cc4a0f7c4f" }, "reactR": { "Package": "reactR", @@ -4054,7 +3956,7 @@ }, "readr": { "Package": "readr", - "Version": "2.1.6", + "Version": "2.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4064,6 +3966,7 @@ "clipr", "cpp11", "crayon", + "glue", "hms", "lifecycle", "methods", @@ -4071,13 +3974,14 @@ "tibble", "tzdb", "utils", - "vroom" + "vroom", + "withr" ], - "Hash": "141ebcec1bf55707751c7956a34d93db" + "Hash": "4425ad9e28b8e3351184ca2739995b87" }, "readxl": { "Package": "readxl", - "Version": "1.4.5", + "Version": "1.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4088,7 +3992,7 @@ "tibble", "utils" ], - "Hash": "18948de59f05d38a44d3e5065a76b4b6" + "Hash": "db51be8ae666e3d16195395b9058a91a" }, "reformulas": { "Package": "reformulas", @@ -4144,7 +4048,7 @@ }, "reporter": { "Package": "reporter", - "Version": "1.4.6", + "Version": "1.4.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4160,7 +4064,7 @@ "withr", "zip" ], - "Hash": "a033d4c973ec27ec29b15270b414a2ef" + "Hash": "492792a9e5c8277d503e84e8219f5b1c" }, "reprex": { "Package": "reprex", @@ -4184,22 +4088,9 @@ ], "Hash": "97b1d5361a24d9fb588db7afe3e5bcbf" }, - "reshape2": { - "Package": "reshape2", - "Version": "1.4.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "plyr", - "stringr" - ], - "Hash": "2677962d949a7a879537a2364d56be84" - }, "reticulate": { "Package": "reticulate", - "Version": "1.45.0", + "Version": "1.46.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4217,40 +4108,18 @@ "utils", "withr" ], - 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"Hash": "4e664a5d610d58f27ec196e96cdb7f6f" + "Hash": "54b09824b3ac78eb4fa44f76c0616131" }, "samplesize": { "Package": "samplesize", @@ -4489,7 +4345,7 @@ }, "sandwich": { "Package": "sandwich", - "Version": "3.1-1", + "Version": "3.1-3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4498,19 +4354,24 @@ "utils", "zoo" ], - "Hash": "072bb2d27425f2a58fe71fe1080676ce" + "Hash": "b371412dbbf43cf39d0302556a0b7c39" }, "sasLM": { "Package": "sasLM", - "Version": "0.10.7", + "Version": "1.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", + "grDevices", + "graphics", "methods", - "mvtnorm" + "mvtnorm", + "stats", + "tools", + "utils" ], - "Hash": "2f8e8e88b3267f0d61319e77876eaf90" + "Hash": "98153af4af3af99fa0c2fc9a74f4e84e" }, "sass": { "Package": "sass", @@ -4547,7 +4408,7 @@ }, "scatterplot3d": { "Package": "scatterplot3d", - "Version": "0.3-44", + "Version": "0.3-45", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4556,20 +4417,18 @@ "graphics", "stats" ], - "Hash": "10ee4b91ec812690bd55d9bf51edccee" + "Hash": "e5723914ce450822d08213e2c0e92ca8" }, "selectr": { "Package": "selectr", - "Version": "0.5-1", + "Version": "0.6-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "R6", - "methods", - "stringr" + "R6" ], - "Hash": "fb6f4aacfcc16539458c66b698339e69" + "Hash": "c538f20abf5a9a4ab8fac8f1ee3f50e8" }, "sensitivity2x2xk": { "Package": "sensitivity2x2xk", @@ -4614,20 +4473,20 @@ }, "sessioninfo": { "Package": "sessioninfo", - "Version": "1.2.2", + "Version": "1.2.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "cli", "tools", "utils" ], - "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f" + "Hash": "0cffa1e2f8c8a67e000fc75db09892f1" }, "sf": { "Package": "sf", - "Version": "1.0-24", + "Version": "1.1-2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4638,7 +4497,6 @@ "grDevices", "graphics", "grid", - "magrittr", "methods", "s2", "stats", @@ -4646,7 +4504,7 @@ "units", "utils" ], - "Hash": "7a4756aedf70812aa33fba3d29529424" + "Hash": "02483c8ee4115581472646cd5d5984d9" }, "shape": { "Package": "shape", @@ -4661,6 +4519,29 @@ ], "Hash": "5c47e84dc0a3ca761ae1d307889e796d" }, + "showtext": { + "Package": "showtext", + "Version": "0.9-8", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "grDevices", + "showtextdb", + "sysfonts" + ], + "Hash": "599c73082d4a9f00fde3c7bc7eb669ff" + }, + "showtextdb": { + "Package": "showtextdb", + "Version": "3.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "sysfonts", + "utils" + ], + "Hash": "c12e756cf947e58b0f2c2a520521a5a8" + }, "slider": { "Package": "slider", "Version": "0.3.3", @@ -4719,12 +4600,12 @@ "Requirements": [ "R", "mvtnorm" - ], - "Hash": "8dd22e4fb2dfce04d0d4927771e61aba" + ], + "Hash": "8dd22e4fb2dfce04d0d4927771e61aba" }, "stringi": { "Package": "stringi", - "Version": "1.8.7", + "Version": "1.8.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4733,7 +4614,7 @@ "tools", "utils" ], - "Hash": "2b56088e23bdd58f89aebf43a0913457" + "Hash": "67f6c2a9e67d08e1e419ff89ad135444" }, "stringr": { "Package": "stringr", @@ -4752,32 +4633,19 @@ ], "Hash": "d47392652eedc68bf916657347ff2526" }, - "survMisc": { - "Package": "survMisc", - "Version": "0.5.6", + "survRM2": { + "Package": "survRM2", + "Version": "1.0-4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "KMsurv", - "data.table", - "ggplot2", - "grDevices", - "graphics", - "grid", - "gridExtra", - "km.ci", - "knitr", - "stats", - "survival", - "utils", - "xtable", - "zoo" + "survival" ], - "Hash": "2367feed5d6f99ee1e380da3eac55ab6" + "Hash": "6af75caf3bfa6dd6b0a6ef0fed599478" }, "survey": { "Package": "survey", - "Version": "4.4-8", + "Version": "4.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4796,27 +4664,11 @@ "stats", "survival" ], - "Hash": "b30e7e82e4bebedc3e509976c7dd7403" - }, - "survival": { - "Package": "survival", - "Version": "3.8-3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Matrix", - "R", - "graphics", - "methods", - "splines", - "stats", - "utils" - ], - "Hash": "fe42836742a4f065b3f3f5de81fccab9" + "Hash": "e8eab1ebe57968ce5e4f92c36348a518" }, "survminer": { "Package": "survminer", - "Version": "0.5.1", + "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4834,12 +4686,11 @@ "rlang", "scales", "stats", - "survMisc", "survival", "tibble", "tidyr" ], - "Hash": "d0e3855987f93df5f194b1240aaa30a5" + "Hash": "0b5b30ad970581d2bcbe106b24bef5ef" }, "sys": { "Package": "sys", @@ -4848,9 +4699,16 @@ "Repository": "CRAN", "Hash": "de342ebfebdbf40477d0758d05426646" }, + "sysfonts": { + "Package": "sysfonts", + "Version": "0.8.9", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "7dfca1e9c5c278300b5ca6a1772072f7" + }, "systemfonts": { "Package": "systemfonts", - "Version": "1.3.1", + "Version": "1.3.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4863,7 +4721,7 @@ "tools", "utils" ], - "Hash": "4fae513a3bb1a155943d1e9d1ae467ec" + "Hash": "1f930828d6590af5da47b3ab4fe161e6" }, "tensorA": { "Package": "tensorA", @@ -4906,7 +4764,7 @@ }, "textshaping": { "Package": "textshaping", - "Version": "1.0.4", + "Version": "1.0.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4918,7 +4776,7 @@ "systemfonts", "utils" ], - "Hash": "477d70e23914730aa7f5c5fd351f4721" + "Hash": "addb750a886a2ac415dea6f8068867de" }, "tibble": { "Package": "tibble", @@ -4941,7 +4799,7 @@ }, "tidycmprsk": { "Package": "tidycmprsk", - "Version": "1.1.1", + "Version": "1.1.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4960,7 +4818,7 @@ "tibble", "tidyr" ], - "Hash": "0003cdeb29c3ce3bb94fb05a13bc34b2" + "Hash": "95ea265245b8866cb59dce89eeefb854" }, "tidyr": { "Package": "tidyr", @@ -5068,13 +4926,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.58", + "Version": "0.60", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "03af3ad04817f3019de8ee5c73dab807" + "Hash": "263651b52279eaa7835e44aa32f9b754" }, "tzdb": { "Package": "tzdb", @@ -5089,24 +4947,24 @@ }, "ucminf": { "Package": "ucminf", - "Version": "1.2.2", + "Version": "1.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "e0750b911c01c3e5aaab143a86e9e478" + "Hash": "1a25002d0e84de7ccd0807c7d63ce9fc" }, "units": { "Package": "units", - "Version": "1.0-0", + "Version": "1.0-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "Rcpp" ], - "Hash": "3797c73fd3bde8b1601a4e1bf53557ac" + "Hash": "14743a941151a12449e8af67497c7b96" }, "urca": { "Package": "urca", @@ -5144,7 +5002,7 @@ }, "vcd": { "Package": "vcd", - "Version": "1.4-13", + "Version": "1.4-14", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5157,11 +5015,11 @@ "stats", "utils" ], - "Hash": "c371981692e15016fd45aa5cf8f9b42c" + "Hash": "48b5337cfd2e425ec77c56c60c69c373" }, "vcdExtra": { "Package": "vcdExtra", - "Version": "0.9.1", + "Version": "0.9.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5170,21 +5028,27 @@ "ca", "colorspace", "dplyr", + "forcats", "gnm", "grDevices", "grid", "gt", - "rgl", + "htmlwidgets", + "igraph", + "knitr", + "methods", + "rlang", "scales", "stats", "utils", - "vcd" + "vcd", + "webshot2" ], - "Hash": "4ac959f853d8588bc2b841eeace108ae" + "Hash": "24d69862b7c6b584dd37bc14857fc2e8" }, "vctrs": { "Package": "vctrs", - "Version": "0.7.1", + "Version": "0.7.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5194,7 +5058,7 @@ "lifecycle", "rlang" ], - "Hash": "c64e64d93489bb62bb8747bbb9e06c09" + "Hash": "2dcde2d30d3ad67bf1d3a37177457b87" }, "viridis": { "Package": "viridis", @@ -5221,7 +5085,7 @@ }, "vroom": { "Package": "vroom", - "Version": "1.7.0", + "Version": "1.7.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5243,7 +5107,7 @@ "vctrs", "withr" ], - "Hash": "255cb6f090718455ff89cbc28cb5eea7" + "Hash": "1e9494eda38f3418f71474363293da2a" }, "waldo": { "Package": "waldo", @@ -5270,9 +5134,37 @@ ], "Hash": "8010fb39b9d16c928d924c2f310c0f6c" }, + "webshot2": { + "Package": "webshot2", + "Version": "0.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "callr", + "chromote", + "later", + "magrittr", + "promises" + ], + "Hash": "eebb1681cf21e47cf55e882f19c75648" + }, + "websocket": { + "Package": "websocket", + "Version": "1.4.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "AsioHeaders", + "R6", + "cpp11", + "later" + ], + "Hash": "1c674e92da114a65ce2b5a1ab59997ed" + }, "withr": { "Package": "withr", - "Version": "3.0.2", + "Version": "3.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5280,7 +5172,7 @@ "grDevices", "graphics" ], - "Hash": "cc2d62c76458d425210d1eb1478b30b4" + "Hash": "d979712ec72df779bc2d30bcc5d0d541" }, "wk": { "Package": "wk", @@ -5294,7 +5186,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.56", + "Version": "0.60", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5303,11 +5195,11 @@ "stats", "tools" ], - "Hash": "f1f18d352a39c6252932da4faa029cdd" + "Hash": "8304c2894061f6ae062996f09dd1528e" }, "xgboost": { "Package": "xgboost", - "Version": "3.2.0.1", + "Version": "3.2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5317,11 +5209,11 @@ "jsonlite", "methods" ], - "Hash": "6b1cd6c890fb985627c9d7529318ca83" + "Hash": "fd89e5cf669b6291404b3e3b38737c6f" }, "xml2": { "Package": "xml2", - "Version": "1.5.2", + "Version": "1.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5330,19 +5222,20 @@ "methods", "rlang" ], - "Hash": "d8e98d08a4a4d03f5052acc6e6204b99" + "Hash": "568fe669c645b2007e4e8fcf5cde40e7" }, "xtable": { "Package": "xtable", - "Version": "1.8-4", + "Version": "1.8-8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", + "methods", "stats", "utils" ], - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" + "Hash": "93b19c064862d315a828c7170d806453" }, "yaml": { "Package": "yaml", @@ -5353,14 +5246,17 @@ }, "zip": { "Package": "zip", - "Version": "2.3.3", + "Version": "3.0.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "6ebe4b1dc74c3e50e74e316323629583" + "Requirements": [ + "cli" + ], + "Hash": "5807bea03035bfdd7535c1d3eb258cb0" }, "zoo": { "Package": "zoo", - "Version": "1.8-15", + "Version": "1.9-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5371,7 +5267,7 @@ "stats", "utils" ], - "Hash": "3f85ec88dadbaa3301917cea59727329" + "Hash": "246123b6990acc8dfc4969d3e7225e2d" } } } diff --git a/renv/settings.json b/renv/settings.json index ffdbb3200..d686f6c84 100644 --- a/renv/settings.json +++ b/renv/settings.json @@ -1,7 +1,23 @@ { "bioconductor.version": null, "external.libraries": [], - "ignored.packages": [], + "ignored.packages": [ + "boot", + "class", + "cluster", + "codetools", + "foreign", + "KernSmooth", + "lattice", + "MASS", + "Matrix", + "mgcv", + "nlme", + "nnet", + "rpart", + "spatial", + "survival" + ], "package.dependency.fields": [ "Imports", "Depends", From 1060c6f935569769136dcdcbf92740dfbf14a66b Mon Sep 17 00:00:00 2001 From: Maya Gans Date: Thu, 20 Aug 2026 17:56:47 -0700 Subject: [PATCH 2/4] Document renv snapshot pitfalls in contributor guide Two notes in the "Setting up CAMIS with renv" section: - Check the `renv::snapshot()` diff before committing. Snapshot records the local environment, so it rewrites requirements.txt and the Python block of renv.lock from whichever Python environment is active, and sets the recorded R version to whatever R the contributor is running. An empty local venv has previously cut requirements.txt from 124 packages to one. - The package repository is pinned to a dated PPM snapshot, so installs get that date's version and packages published after it are unavailable until the date is moved forward. Explains why the pin exists (binaries on all three platforms) and why R-bundled packages are excluded via ignored.packages. --- contribution/get_started.qmd | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/contribution/get_started.qmd b/contribution/get_started.qmd index b778a9e8c..adf80f59f 100644 --- a/contribution/get_started.qmd +++ b/contribution/get_started.qmd @@ -106,6 +106,32 @@ renv::restore() These function calls help to record and update the `renv.lock` file with the package and associated dependencies in a reproducible manner. +::: {.callout-warning} +## Check your `renv::snapshot()` diff before committing + +`renv::snapshot()` records your *local* environment, not just the package you added, so it can quietly sweep unrelated changes into the lockfile. Before committing, run `git diff renv.lock requirements.txt` and confirm the only changes are the ones you meant to make. Two in particular catch people out: + +- **`requirements.txt` and the `Python` block of `renv.lock`.** `renv` rewrites both from whichever Python environment is active. If that is not the project's Python 3.12 virtualenv, `requirements.txt` is replaced by whatever your interpreter happens to have installed — on one occasion this cut it from 124 packages down to one. Unless you deliberately intended to change the Python environment, undo those with `git checkout -- requirements.txt` and restore the original `Python` block. +- **The recorded R version.** CI installs the R version named in `renv.lock`, and a snapshot sets it to whatever R *you* are running. + +Commit only the R package records unless a wider change is the point of your pull request. +::: + +::: {.callout-note} +## The package repository is pinned to a fixed date + +`renv.lock` points at a dated [Posit Package Manager](https://packagemanager.posit.co) snapshot rather than `latest`. This is deliberate: it means every recorded version still has a prebuilt binary available on Linux, macOS and Windows, so nobody needs a working compiler toolchain to run `renv::restore()`. Pointing at `latest` breaks this, because `latest` only ever serves the *current* version of each package, and anything pinned to an older version then has to be built from source. + +Two consequences when adding a package: + +- `renv::install("package_name")` installs the version that was current on the snapshot date, not today's version. +- A package published to CRAN *after* the snapshot date cannot be installed until the date is moved forward. + +Moving the date means re-snapshotting the whole lockfile, which shifts many package versions at once and invalidates most of the Quarto freeze cache. Please raise that as its own pull request rather than folding it into a content change. + +Packages that ship with R itself — `mgcv`, `Matrix`, `survival`, `lattice` and friends — are deliberately left out of the lockfile via `ignored.packages` in `renv/settings.json`. Their versions follow your R installation rather than CRAN, so they can never be pinned reliably, and recording them causes `renv::restore()` to fail. +::: + At this point, it is assumed that your system in RStudio is connected to Git and GitHub, and that the `renv` environment is successfully activated. Now every time you close RStudio and reopen the CAMIS project on your computer, you should see the option: ```{r} From 2888270c4dd8f00c03f45d66ceb2e83b08f3c02b Mon Sep 17 00:00:00 2001 From: Maya Gans Date: Thu, 20 Aug 2026 19:32:02 -0700 Subject: [PATCH 3/4] Install the system libraries the package set actually needs The first CI run on the new lockfile installed every package as a binary and compiled nothing, then failed loading igraph: libglpk.so.40: cannot open shared object file vcdExtra went 0.9.1 -> 0.9.7 in this update and the newer version imports igraph, which links against GLPK. GLPK is not on the runner image, and the workflows only installed libcurl, udunits2, GDAL, GLU and Xi. Because the restore aborts on the first failure, nothing after igraph had been attempted yet, so fixing GLPK alone would likely just surface the next missing library. Instead this asks Posit Package Manager's sysreqs API what the whole 366-package set requires on ubuntu-24.04 and installs that, which is 27 apt packages. The step now carries the URL to regenerate the list. libglu1-mesa and libxi-dev are kept even though rgl (the reason they were there) is no longer in the lockfile, since they cost nothing and nothing confirms they are unused. --- .github/workflows/action.yml | 17 +++++++++++++++-- .github/workflows/pull_request_action.yml | 17 +++++++++++++++-- 2 files changed, 30 insertions(+), 4 deletions(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 154ccc666..039a1c78c 100644 --- a/.github/workflows/action.yml +++ b/.github/workflows/action.yml @@ -26,10 +26,23 @@ jobs: cache: 'pip' # caching pip dependencies - run: pip install -r requirements.txt - - name: Install libcurl + - name: Install system dependencies + # Derived from Posit Package Manager's sysreqs API for the packages in + # renv.lock on ubuntu-24.04. Regenerate with: + # https://packagemanager.posit.co/__api__/repos/cran/sysreqs?all=false&distribution=ubuntu&release=24.04&pkgname=&... + # We install binaries, so these are needed as runtime shared libraries. run: | sudo apt-get update - sudo apt-get install -y libcurl4-openssl-dev libudunits2-dev gdal-bin libgdal-dev libglu1-mesa libxi-dev + sudo apt-get install -y \ + libcurl4-openssl-dev libssl-dev libxml2-dev libicu-dev zlib1g-dev \ + libglpk-dev \ + libudunits2-dev gdal-bin libgdal-dev libgeos-dev libproj-dev \ + libsqlite3-dev libabsl-dev \ + libcairo2-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev \ + libharfbuzz-dev \ + libjpeg-dev libpng-dev libtiff-dev libwebp-dev \ + libnode-dev libuv1-dev libx11-dev \ + libglu1-mesa libxi-dev - name: Put pandoc in PATH run: | mkdir -p ~/.local/bin diff --git a/.github/workflows/pull_request_action.yml b/.github/workflows/pull_request_action.yml index 0111e55a4..21050a458 100644 --- a/.github/workflows/pull_request_action.yml +++ b/.github/workflows/pull_request_action.yml @@ -32,10 +32,23 @@ jobs: - run: pip install -r requirements.txt - - name: Install libcurl + - name: Install system dependencies + # Derived from Posit Package Manager's sysreqs API for the packages in + # renv.lock on ubuntu-24.04. Regenerate with: + # https://packagemanager.posit.co/__api__/repos/cran/sysreqs?all=false&distribution=ubuntu&release=24.04&pkgname=&... + # We install binaries, so these are needed as runtime shared libraries. run: | sudo apt-get update - sudo apt-get install -y libcurl4-openssl-dev libudunits2-dev gdal-bin libgdal-dev libglu1-mesa libxi-dev + sudo apt-get install -y \ + libcurl4-openssl-dev libssl-dev libxml2-dev libicu-dev zlib1g-dev \ + libglpk-dev \ + libudunits2-dev gdal-bin libgdal-dev libgeos-dev libproj-dev \ + libsqlite3-dev libabsl-dev \ + libcairo2-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev \ + libharfbuzz-dev \ + libjpeg-dev libpng-dev libtiff-dev libwebp-dev \ + libnode-dev libuv1-dev libx11-dev \ + libglu1-mesa libxi-dev - name: Put pandoc in PATH run: | From a24c85935f024ad1c0be17ef38de634787b71bf1 Mon Sep 17 00:00:00 2001 From: Maya Gans Date: Thu, 20 Aug 2026 20:44:02 -0700 Subject: [PATCH 4/4] TEMPORARY: upload the regenerated freeze cache as an artifact The lockfile refresh changes rmarkdown 2.30 -> 2.31, which 180 of the 195 pages depend on, so the pre-render script invalidates nearly the whole freeze cache and the last run spent 55.6 minutes re-executing it. That cost repeats on every run, because the render happens in a throwaway checkout and nothing is committed back. Rather than reproduce the render environment locally, capture it from the run that already does it successfully: this uploads _freeze and data/quarto_pkg_dependencies.csv so they can be downloaded and committed. Once committed, the script finds no hash changes and builds return to ~12 minutes. Remove this step before merge. --- .github/workflows/pull_request_action.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/.github/workflows/pull_request_action.yml b/.github/workflows/pull_request_action.yml index 21050a458..35bc7539e 100644 --- a/.github/workflows/pull_request_action.yml +++ b/.github/workflows/pull_request_action.yml @@ -72,6 +72,19 @@ jobs: run: | quarto render + # TEMPORARY (remove before merge): the lockfile refresh invalidates most of + # the freeze cache, so this run regenerates it. Upload it so it can be + # committed, which returns build times to ~12 min instead of ~65. + - name: Upload regenerated freeze cache + uses: actions/upload-artifact@v4 + with: + name: freeze-cache + path: | + _freeze + data/quarto_pkg_dependencies.csv + retention-days: 5 + if-no-files-found: error + - name: Deploy preview 🔍 # Ensure this step only runs if we aren't on a fork, as otherwise it will fail with permissions errors if: ${{ github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name }}