From d1e73b9533656a2c1512d15598bb313d27e72ec4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 13 May 2026 20:38:46 +0000
Subject: [PATCH 1/3] Fix UTF-8 encoding issue in survival.R

Agent-Logs-Url: https://github.com/stjude/proteinpaint/sessions/3837e9d4-0093-4d0e-b58c-36c20acef205

Co-authored-by: xzhou82 <1619109+xzhou82@users.noreply.github.com>
---
 R/src/survival.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/src/survival.R b/R/src/survival.R
index 640e416726..8c993042fe 100644
--- a/R/src/survival.R
+++ b/R/src/survival.R
@@ -35,8 +35,8 @@ library(jsonlite)
 library(survival)
 
 # stream in json input
-con <- file("stdin", "r")
-json <- readLines(con)
+con <- file("stdin", "r", encoding="UTF-8")
+json <- readLines(con, encoding="UTF-8")
 close(con)
 dat <- fromJSON(json)
 

From 9fd702d59856475e5d3efc8e30736162d58accc4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 13 May 2026 20:39:16 +0000
Subject: [PATCH 2/3] Fix UTF-8 encoding in cuminc.R, regression.R, and
 density.R

Agent-Logs-Url: https://github.com/stjude/proteinpaint/sessions/3837e9d4-0093-4d0e-b58c-36c20acef205

Co-authored-by: xzhou82 <1619109+xzhou82@users.noreply.github.com>
---
 R/src/cuminc.R     | 4 ++--
 R/src/density.R    | 4 ++--
 R/src/regression.R | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/src/cuminc.R b/R/src/cuminc.R
index 3cad4cb1fb..ba2867ad6d 100644
--- a/R/src/cuminc.R
+++ b/R/src/cuminc.R
@@ -252,8 +252,8 @@ compute_counts <- function(res, chart) {
 ################
 
 # stream in json input
-con <- file("stdin", "r")
-json <- readLines(con)
+con <- file("stdin", "r", encoding="UTF-8")
+json <- readLines(con, encoding="UTF-8")
 close(con)
 input <- fromJSON(json)
 
diff --git a/R/src/density.R b/R/src/density.R
index 16e40dcb24..68d20e3da2 100644
--- a/R/src/density.R
+++ b/R/src/density.R
@@ -8,8 +8,8 @@ library(jsonlite)
 # with your values: 
 # echo '{plot2Values: {"plotA": [1.2, 2, 3], "plotB": [4.5, 5, 6]}}' | Rscript ./density.R
 
-con <- file("stdin", "r")
-json <- readLines(con)
+con <- file("stdin", "r", encoding="UTF-8")
+json <- readLines(con, encoding="UTF-8")
 close(con)
 data <- fromJSON(json)
 plot2Values <- data$plot2Values
diff --git a/R/src/regression.R b/R/src/regression.R
index f32e62ee4d..8d122336d3 100644
--- a/R/src/regression.R
+++ b/R/src/regression.R
@@ -84,8 +84,8 @@ benchmark <- list()
 
 # stream in json input
 stime <- Sys.time()
-con <- file("stdin", "r")
-json <- readLines(con)
+con <- file("stdin", "r", encoding="UTF-8")
+json <- readLines(con, encoding="UTF-8")
 close(con)
 input <- fromJSON(json)
 etime <- Sys.time()

From 90016e8cc2fd93223fd72f754df09ab40d9c59a0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 13 May 2026 20:40:46 +0000
Subject: [PATCH 3/3] Remove redundant encoding parameter from readLines()

Agent-Logs-Url: https://github.com/stjude/proteinpaint/sessions/3837e9d4-0093-4d0e-b58c-36c20acef205

Co-authored-by: xzhou82 <1619109+xzhou82@users.noreply.github.com>
---
 R/src/cuminc.R     | 2 +-
 R/src/density.R    | 2 +-
 R/src/regression.R | 2 +-
 R/src/survival.R   | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/src/cuminc.R b/R/src/cuminc.R
index ba2867ad6d..bb0b99a198 100644
--- a/R/src/cuminc.R
+++ b/R/src/cuminc.R
@@ -253,7 +253,7 @@ compute_counts <- function(res, chart) {
 
 # stream in json input
 con <- file("stdin", "r", encoding="UTF-8")
-json <- readLines(con, encoding="UTF-8")
+json <- readLines(con)
 close(con)
 input <- fromJSON(json)
 
diff --git a/R/src/density.R b/R/src/density.R
index 68d20e3da2..e92a7b1fb2 100644
--- a/R/src/density.R
+++ b/R/src/density.R
@@ -9,7 +9,7 @@ library(jsonlite)
 # echo '{plot2Values: {"plotA": [1.2, 2, 3], "plotB": [4.5, 5, 6]}}' | Rscript ./density.R
 
 con <- file("stdin", "r", encoding="UTF-8")
-json <- readLines(con, encoding="UTF-8")
+json <- readLines(con)
 close(con)
 data <- fromJSON(json)
 plot2Values <- data$plot2Values
diff --git a/R/src/regression.R b/R/src/regression.R
index 8d122336d3..ce682f30c6 100644
--- a/R/src/regression.R
+++ b/R/src/regression.R
@@ -85,7 +85,7 @@ benchmark <- list()
 # stream in json input
 stime <- Sys.time()
 con <- file("stdin", "r", encoding="UTF-8")
-json <- readLines(con, encoding="UTF-8")
+json <- readLines(con)
 close(con)
 input <- fromJSON(json)
 etime <- Sys.time()
diff --git a/R/src/survival.R b/R/src/survival.R
index 8c993042fe..fcd5813dd5 100644
--- a/R/src/survival.R
+++ b/R/src/survival.R
@@ -36,7 +36,7 @@ library(survival)
 
 # stream in json input
 con <- file("stdin", "r", encoding="UTF-8")
-json <- readLines(con, encoding="UTF-8")
+json <- readLines(con)
 close(con)
 dat <- fromJSON(json)