Remove `cutoff` package dependency (removed from CRAN) by Copilot · Pull Request #302 · openbiox/Bizard

Copilot · 2026-07-29T02:22:42Z

The cutoff package was removed from CRAN, causing pak::lockfile_create to fail during CI dependency resolution.

The package was loaded in Hiplot/155-risk-plot.qmd but never actually called — the cutoff calculation uses median() from base R.

Removed cutoff from DESCRIPTION imports
Removed install guard, library(cutoff) call, and dependency list entry from Hiplot/155-risk-plot.qmd and its .zh.qmd counterpart

Fixes build failure JUL 2026 #301

The `cutoff` package was removed from CRAN, causing the CI build to fail when resolving dependencies. The package was loaded but never actually used in the tutorial code (the cutoff calculation uses base R's median()). Closes #301

github-actions · 2026-07-29T02:28:26Z

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Hiplot/155-risk-plot.qmd

Missing recommended section: ## Example
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ShixiangWang · 2026-07-29T02:31:22Z

考虑该包使用github 的版本依赖 https://github.com/choisy/cutoff ，以尽量保持对现有文档教程的不变动和支持？ @copilot

ShixiangWang · 2026-07-29T02:34:20Z

考虑该包使用github 的版本依赖 https://github.com/choisy/cutoff ，以尽量保持对现有文档教程的不变动和支持？ @copilot

…s removed from CRAN Instead of removing the cutoff dependency entirely, switch to installing from GitHub to keep the tutorial unchanged. Closes #301

Copilot · 2026-07-29T02:36:07Z

考虑该包使用github 的版本依赖 https://github.com/choisy/cutoff ，以尽量保持对现有文档教程的不变动和支持？ @copilot

Done — switched to remotes::install_github("choisy/cutoff") in both .qmd files and added choisy/cutoff to the Remotes: field in DESCRIPTION. The tutorial content remains unchanged. See commit e2a2e6a.

github-actions · 2026-07-29T02:36:37Z

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Hiplot/155-risk-plot.qmd

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ShixiangWang · 2026-07-29T02:43:15Z

@copilot 为什么action失败，能解决不？

These packages were also removed from CRAN, causing pak to fail when resolving the dependency chain: fastStat → set → do → tmcn.

Copilot · 2026-07-29T02:46:50Z

@copilot 为什么action失败，能解决不？

CI 失败的原因已经变了——不再是 cutoff 的问题，而是 yikeshu0611/fastStat 的传递依赖 set、do、tmcn 也被从 CRAN 移除了。pak 在解析依赖链 fastStat → set → do → tmcn 时找不到这些包。

已在 DESCRIPTION 的 Remotes: 中添加了 yikeshu0611/set、yikeshu0611/do、cran/tmcn，应该可以解决了。

github-actions · 2026-07-30T02:15:44Z

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ShixiangWang · 2026-07-30T02:21:29Z

@copilot 还是失败了

…motes pak only resolves Remotes for packages listed as direct dependencies. Adding these as Imports ensures pak looks for them in our Remotes field instead of failing to find them on CRAN.

Copilot · 2026-07-30T02:23:43Z

@copilot 还是失败了

问题是 pak 只为项目的直接依赖查找 Remotes: 中的 GitHub 源，不会为间接依赖（fastStat → set/do/tmcn）自动匹配。

已将 set、do、tmcn 也加入 DESCRIPTION 的 Imports 中，这样 pak 会从我们的 Remotes: 字段找到它们的 GitHub 源。

github-actions · 2026-07-30T02:35:56Z

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Hiplot/155-risk-plot.qmd

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See contribution guidance for the expected tutorial format.

ShixiangWang · 2026-07-30T05:39:06Z

@copilot 还是有问题，彻底解决下？

…mpatible with current data.table

Copilot · 2026-07-30T05:42:51Z

@copilot 还是有问题，彻底解决下？

CI 失败原因是 do 包（fastStat 的间接依赖，链路：fastStat → set → do）与当前版本的 data.table 不兼容——do 试图导出 .__T__[:base，但该符号已从 data.table 命名空间中移除，导致编译失败。

由于 fastStat 在教程中只是被 library() 加载，实际代码中从未调用（cutoff 计算用的是 base R 的 median()），已将 fastStat 及其整条依赖链（set、do、tmcn）从 DESCRIPTION 和两个 .qmd 文件中移除。cutoff 保持 GitHub 安装不变。

github-actions · 2026-07-30T07:44:27Z

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github-actions · 2026-07-30T08:17:11Z

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Modified files:

Hiplot/155-risk-plot.qmd Hiplot/155-risk-plot.zh.qmd

Initial plan

f881790

Copilot AI assigned Copilot and ShixiangWang Jul 29, 2026

Copilot AI linked an issue Jul 29, 2026 that may be closed by this pull request

build failure JUL 2026 #301

Open

Copilot started work on behalf of ShixiangWang July 29, 2026 02:23 View session

Copilot AI changed the title ~~[WIP] Fix build failure during website render and deploy~~ Remove cutoff package dependency (removed from CRAN) Jul 29, 2026

Copilot finished work on behalf of ShixiangWang July 29, 2026 02:25

Copilot AI requested a review from ShixiangWang July 29, 2026 02:25

Copilot started work on behalf of ShixiangWang July 29, 2026 02:34 View session

fix: use GitHub version of cutoff package (choisy/cutoff) since it wa…

8a9a635

…s removed from CRAN Instead of removing the cutoff dependency entirely, switch to installing from GitHub to keep the tutorial unchanged. Closes #301

Copilot finished work on behalf of ShixiangWang July 29, 2026 02:36

Copilot started work on behalf of ShixiangWang July 29, 2026 02:44 View session

fix: add GitHub remotes for fastStat transitive deps (set, do, tmcn)

868cc6c

These packages were also removed from CRAN, causing pak to fail when resolving the dependency chain: fastStat → set → do → tmcn.

Copilot finished work on behalf of ShixiangWang July 29, 2026 02:47

Copilot started work on behalf of ShixiangWang July 30, 2026 02:22 View session

fix: add set, do, tmcn as direct Imports so pak resolves them from Re…

19b0bca

…motes pak only resolves Remotes for packages listed as direct dependencies. Adding these as Imports ensures pak looks for them in our Remotes field instead of failing to find them on CRAN.

Copilot finished work on behalf of ShixiangWang July 30, 2026 02:24

Copilot started work on behalf of ShixiangWang July 30, 2026 05:39 View session

Remove fastStat and its broken deps (set, do, tmcn) — unused and inco…

8a55fd0

…mpatible with current data.table

Copilot finished work on behalf of ShixiangWang July 30, 2026 05:43

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