Remove cutoff package dependency (removed from CRAN) (#302)

* Initial plan

* fix: remove cutoff package dependency (removed from CRAN)

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

* fix: use GitHub version of cutoff package (choisy/cutoff) since it was removed from CRAN

Instead of removing the cutoff dependency entirely, switch to installing
from GitHub to keep the tutorial unchanged.

Closes #301

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

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

* fix: add set, do, tmcn as direct Imports so pak resolves them from Remotes

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.

* Remove fastStat and its broken deps (set, do, tmcn) — unused and incompatible with current data.table

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>

Author: Copilot

DESCRIPTION

@@ -168,7 +168,6 @@ Imports:
     EnhancedVolcano,
     ggradar,
     streamgraph,
-    fastStat,
     apyramid,
     flow,
     survminer,
@@ -262,7 +261,6 @@ Remotes:
     kevinblighe/EnhancedVolcano,
     ricardo-bion/ggradar,
     hrbrmstr/streamgraph,
-    yikeshu0611/fastStat,
     wch/extrafont,
     hrbrmstr/hrbrthemes,
     hrbrmstr/waffle,
@@ -280,4 +278,5 @@ Remotes:
     jinworks/CellChat,
     cran/smoother,
     cran/regplot,
-    YuLab-SMU/fanyi
+    YuLab-SMU/fanyi,
+    choisy/cutoff

Hiplot/155-risk-plot.qmd

@@ -19,7 +19,7 @@ This page is the tutorial for source code version of the Hiplot `Risk Factor Ana
 
 -   Programming language: R
 
--   Dependent packages: `data.table`; `jsonlite`; `survminer`; `fastStat`; `cutoff`; `ggplot2`; `cowplot`
+-   Dependent packages: `data.table`; `jsonlite`; `survminer`; `cutoff`; `ggplot2`; `cowplot`
 
 ```{r packages setup, message=FALSE, warning=FALSE, output=FALSE}
 # Install packages
@@ -32,11 +32,8 @@ if (!requireNamespace("jsonlite", quietly = TRUE)) {
 if (!requireNamespace("survminer", quietly = TRUE)) {
   install.packages("survminer")
 }
-if (!requireNamespace("fastStat", quietly = TRUE)) {
-  remotes::install_github("yikeshu0611/fastStat")
-}
 if (!requireNamespace("cutoff", quietly = TRUE)) {
-  install.packages("cutoff")
+  remotes::install_github("choisy/cutoff")
 }
 if (!requireNamespace("ggplot2", quietly = TRUE)) {
   install.packages("ggplot2")
@@ -49,7 +46,6 @@ if (!requireNamespace("cowplot", quietly = TRUE)) {
 library(data.table)
 library(jsonlite)
 library(survminer)
-library(fastStat)
 library(cutoff)
 library(ggplot2)
 library(cowplot)

Hiplot/155-risk-plot.zh.qmd

@@ -19,7 +19,7 @@ author:
 
 -   编程语言: R
 
--   依赖包: `data.table`; `jsonlite`; `survminer`; `fastStat`; `cutoff`; `ggplot2`; `cowplot`
+-   依赖包: `data.table`; `jsonlite`; `survminer`; `cutoff`; `ggplot2`; `cowplot`
 
 ```{r packages setup, message=FALSE, warning=FALSE, output=FALSE}
 # 安装包
@@ -32,11 +32,8 @@ if (!requireNamespace("jsonlite", quietly = TRUE)) {
 if (!requireNamespace("survminer", quietly = TRUE)) {
   install.packages("survminer")
 }
-if (!requireNamespace("fastStat", quietly = TRUE)) {
-  remotes::install_github("yikeshu0611/fastStat")
-}
 if (!requireNamespace("cutoff", quietly = TRUE)) {
-  install.packages("cutoff")
+  remotes::install_github("choisy/cutoff")
 }
 if (!requireNamespace("ggplot2", quietly = TRUE)) {
   install.packages("ggplot2")
@@ -49,7 +46,6 @@ if (!requireNamespace("cowplot", quietly = TRUE)) {
 library(data.table)
 library(jsonlite)
 library(survminer)
-library(fastStat)
 library(cutoff)
 library(ggplot2)
 library(cowplot)