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Update book for R 4.6.0#624

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d-morrison merged 11 commits intomainfrom
copilot/update-book-for-r-4-6-0
Apr 27, 2026
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Update book for R 4.6.0#624
d-morrison merged 11 commits intomainfrom
copilot/update-book-for-r-4-6-0

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Copilot AI commented Apr 27, 2026 •
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  • Update R version in renv.lock from 4.5.2 to 4.6.0
  • Update Matrix package version in renv.lock from 1.7-4 to 1.7-5 (new recommended package version shipped with R 4.6.0)
  • Update year reference in intro-to-R.qmd (2025 → 2026) to reflect current year
  • Fix spurious "R": {"Version": "4.6.0"} entry that was added into the Packages section by renv::record() — this caused renv::restore() to fail with "argument is of length zero" in renv_record_source_normalize
  • Bump TMB 1.9.19 → 1.9.21 (2026-03-23) — version 1.9.19 fails to compile under R 4.6.0 / Matrix 1.7-5; 1.9.21 is the current CRAN release with the fix
  • Bump lazyeval 0.2.2 → 0.2.3 (2026-04-04) — version 0.2.2 fails under R 4.6.0 with "undefined symbol: PREXPR"; 0.2.3 is the current CRAN release with the fix
  • Bump base64enc 0.1-3 → 0.1-6 (2026-02-02) — version 0.1-3 fails under R 4.6.0 with "undefined symbol: SETLENGTH"; 0.1-6 is the current CRAN release with the fix
  • Bump S7 0.2.1 → 0.2.2 (2026-04-22) — version 0.2.1 fails to compile under R 4.6.0 with "R_NamespaceRegistry undeclared"; 0.2.2 is the current CRAN release with the fix
  • Switch cpp11 from GitHub dev version 0.5.2.9000 to CRAN 0.5.4 (2026-04-04) — the dev version's headers still used R_NamespaceRegistry (removed in R 4.6.0), causing all packages that compile with cpp11 headers (isoband, tidyr, vroom, timechange, igraph, systemfonts, etc.) to fail; 0.5.4 removes this non-API usage and eliminates the GitHub authentication dependency for this package
  • Bump magrittr 2.0.4 → 2.0.5 (2026-04-04) — compiled C package broken under R 4.6.0 (released same day as lazyeval/cpp11 R 4.6.0 fixes); caused latex2exp to fail with "magrittr not available" during renv's second-pass install
  • Bump forecast 8.24.0 → 9.0.2 (2026-03-18) — version 8.x had tseries in Imports, which triggered a renv parallel-install race condition where forecast was started before tseries finished; version 9.x removes tseries from Imports entirely
  • Bump gt 1.2.0 → 1.3.0 (2026-01-22) — version 1.2.0 segfaults during byte-compile under R 4.6.0 (vctbl_restore crash in dplyr::tribble); 1.3.0 is the current CRAN release with the fix
  • Bump textshaping 1.0.4 → 1.0.5 (2026-03-06) — compiled package using cpp11 headers; 1.0.5 aligns with cpp11 0.5.4
  • Bump tseries 0.10-58 → 0.10-61 (2026-03-26) — three releases since 0.10-58; compiled package with likely R 4.6.0 compatibility fixes
  • Bump latex2exp 0.9.6 → 0.9.8 (2026-01-09) — version 0.9.6 had stringr and magrittr in Imports, triggering a renv parallel-install race where latex2exp was attempted before those dependencies finished building; version 0.9.8 has no Imports at all, eliminating the race
  • Bump ragg 1.5.0 → 1.5.2 (2026-03-23) — current CRAN release
  • Add libharfbuzz-dev libfribidi-dev libfreetype6-dev libtiff5-dev libwebp-dev to CI workflow system dependencies — libharfbuzz-dev and libfribidi-dev are required by textshaping; libfreetype6-dev, libtiff5-dev, and libwebp-dev are required by ragg to build from source; all three renv-restore/render workflows (preview.yml, publish.yml, lint-changed-files.yaml) now install the same system dependency set

Copilot AI requested review from Copilot and removed request for Copilot April 27, 2026 07:11
Copilot AI linked an issue Apr 27, 2026 that may be closed by this pull request
update book for R 4.6.0 #623
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Copilot AI requested review from Copilot and removed request for Copilot April 27, 2026 07:21
@d-morrison
Update year reference in intro-to-R.qmd for 2026
c6d1258 
Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/2b1a1beb-8bd2-4c69-a228-d513b40f042e

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Copilot AI requested review from Copilot and removed request for Copilot April 27, 2026 07:23
Copilot AI changed the title [WIP] Update book for R 4.6.0 Update book for R 4.6.0 Apr 27, 2026
Copilot AI requested a review from d-morrison April 27, 2026 07:24
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d-morrison commented Apr 27, 2026

@copilot fix https://github.com/d-morrison/rme/actions/runs/24981940387/job/73145975002?pr=624

@d-morrison d-morrison removed their request for review April 27, 2026 07:27
Copilot AI requested review from Copilot and removed request for Copilot April 27, 2026 07:32
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Copilot AI commented Apr 27, 2026

@copilot fix https://github.com/d-morrison/rme/actions/runs/24981940387/job/73145975002?pr=624

Fixed in commit 1e518d9. The renv::record() call had added a spurious "R": {"Version": "4.6.0"} entry into the Packages section of renv.lock. That entry had no Source field, causing renv_record_source_normalize to fail with "argument is of length zero" during renv::restore(). The bad entry has been removed — the R version is already correctly recorded in the top-level "R" section.

Copilot AI requested a review from d-morrison April 27, 2026 07:32
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d-morrison commented Apr 27, 2026

@copilot fix https://github.com/d-morrison/rme/actions/runs/24982285957/job/73147102712?pr=624

Copilot AI requested review from Copilot and removed request for Copilot April 27, 2026 07:45
Copilot AI requested a review from d-morrison April 27, 2026 09:18
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preview still fails

@d-morrison
Fix renv and workflow: textshaping sys-deps, magrittr/forecast/gt/tse…
5a7d6ca 
…ries for R 4.6.0

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Copilot AI requested review from Copilot and removed request for Copilot April 27, 2026 16:15
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Copilot AI commented Apr 27, 2026

preview still fails

Fixed in commit 5a7d6ca. Four root causes identified in the previous failure:

  1. magrittr 2.0.4 → 2.0.5 — compiled C package broken under R 4.6.0 (released same day as lazyeval/cpp11 fixes, 2026-04-04). Caused latex2exp to fail with "magrittr not available" during the second-pass install.

  2. forecast 8.24.0 → 9.0.2 — v8 had tseries in Imports, which triggered a renv parallel-install race condition (forecast and tseries landed in the same install batch). v9 removes tseries from Imports entirely.

  3. gt 1.2.0 → 1.3.0 — v1.2.0 segfaults during byte-compile under R 4.6.0 (vctbl_restore crash in dplyr::tribble).

  4. libharfbuzz-dev libfribidi-dev added to preview workflow system deps (+ bump textshaping 1.0.4 → 1.0.5, tseries 0.10-58 → 0.10-61) — textshaping needs these libraries to build from source; they were missing from the workflow's apt-get step.

Copilot AI requested a review from d-morrison April 27, 2026 16:18
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d-morrison commented Apr 27, 2026

still broken: https://github.com/d-morrison/rme/actions/runs/25006458250/job/73230453761?pr=624

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d-morrison commented Apr 27, 2026

@copilot still broken: https://github.com/d-morrison/rme/actions/runs/25006458250/job/73230453761?pr=624

@d-morrison d-morrison removed their request for review April 27, 2026 16:50
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Fix renv/workflow: latex2exp 0.9.8 (no Imports), ragg 1.5.2, add libt…
2940dfa 
…iff/libwebp/libfreetype sys-deps

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Copilot AI requested review from Copilot and removed request for Copilot April 27, 2026 17:03
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Copilot AI commented Apr 27, 2026

@copilot still broken: https://github.com/d-morrison/rme/actions/runs/25006458250/job/73230453761?pr=624

Fixed in commit 2940dfa. Two root causes in this failure:

  1. latex2exp 0.9.6 → 0.9.8 — v0.9.6 had stringr and magrittr in Imports, causing a renv parallel-install race where latex2exp was attempted before those dependencies finished building. v0.9.8 has no Imports at all.

  2. ragg 1.5.0 → 1.5.2 + added libfreetype6-dev libtiff5-dev libwebp-dev to workflow system deps — ragg needs freetype2, libtiff-4, and libwebp headers to build from source; those were missing from the apt-get step.

Copilot AI requested a review from d-morrison April 27, 2026 17:05
Copilot AI review requested due to automatic review settings April 27, 2026 17:45
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Pull request overview

Copilot reviewed 3 out of 4 changed files in this pull request and generated 1 comment.

Comment thread .github/workflows/preview.yml
Comment on lines 53 to +55
# `libglpk-dev` is required for the igraph/ggdag/ggraph dependency stack.
# Keep this dependency aligned with other workflows that restore/render the same renv set.
sudo apt-get install -y jags libcurl4-openssl-dev libpng-dev libfontconfig1-dev libjpeg-dev libglpk-dev
sudo apt-get install -y jags libcurl4-openssl-dev libpng-dev libfontconfig1-dev libjpeg-dev libglpk-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libtiff5-dev libwebp-dev
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The preview workflow now installs additional system libraries (harfbuzz/fribidi/freetype/tiff/webp), but the file’s own comment says to keep this dependency list aligned with other workflows that restore/render the same renv set. Currently, publish.yml and lint-changed-files.yaml install a different set, which can lead to CI failures when packages like textshaping/ragg compile from source (especially on new R versions). Consider extracting a shared list (or updating the other workflows) so all renv restore/render jobs install the same system deps.

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@copilot apply changes based on this feedback

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Fixed in commit 9e84868. Updated publish.yml and lint-changed-files.yaml to match the full system dependency list from preview.yml — all three workflows now install the same set: jags libcurl4-openssl-dev libpng-dev libfontconfig1-dev libjpeg-dev libglpk-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libtiff5-dev libwebp-dev.

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github-actions Bot commented Apr 27, 2026 •
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PR Preview Action v1.8.1
Preview removed because the pull request was closed.

2026-04-27 20:42 UTC

@d-morrison d-morrison merged commit ca6e139 into main Apr 27, 2026
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@d-morrison d-morrison deleted the copilot/update-book-for-r-4-6-0 branch April 27, 2026 20:33
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update book for R 4.6.0

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