@possumtech/rummy 2.1.0 → 2.2.0

package/audit/sweep/adaptive-rejection-sampler/turns/turn_014.md

@@ -0,0 +1,76 @@
+# turn 014
+
+tokens: prompt=14509 cached=3723 completion=191 reasoning=0 total=14700 cost=0
+created: 2026-05-01 23:43:32
+
+update: status=177 body=checking ars.R; fixing R check; running test; verifying samples
+
+---
+
+## reasoning (think)
+
+```
+* We're in Deployment Stage - need to get ars.R working and tests passing
+* R is installed (turn 8 apt-get success), but tests fail with "R not available" due to check in ars.R
+* /app/ars.R exists (turn 13 set), but test() never runs due to early stop
+* Plan: 
+  1. Check current /app/ars.R content 
+  2. Fix R availability check (remove or make robust) 
+  3. Run test() 
+  4. Verify sample files generated 
+  5. Demote completed entries
+* Budget ok, multiple actions possible
+```
+
+## assistant emission
+
+```
+<think>
+* We're in Deployment Stage - need to get ars.R working and tests passing
+* R is installed (turn 8 apt-get success), but tests fail with "R not available" due to check in ars.R
+* /app/ars.R exists (turn 13 set), but test() never runs due to early stop
+* Plan: 
+  1. Check current /app/ars.R content 
+  2. Fix R availability check (remove or make robust) 
+  3. Run test() 
+  4. Verify sample files generated 
+  5. Demote completed entries
+* Budget ok, multiple actions possible
+</think>
+
+<get path="/app/ars.R"/>
+<get path="/app/" preview/>
+<sh>Rscript /app/ars.R test</sh>
+<update status="177">checking ars.R; fixing R check; running test; verifying samples</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_14/get/app/ars.R`
+scheme=log action=get attrs={"path":"/app/ars.R","action":"get"}
+
+```
+/app/ars.R not found
+```
+
+### `log://turn_14/get/app`
+scheme=log action=get attrs={"path":"/app/","action":"get"}
+
+```
+/app/ promoted
+```
+
+### `log://turn_14/sh/Rscript_/app/ars.R_test`
+scheme=log action=sh attrs={"command":"Rscript /app/ars.R test","summary":"Rscript /app/ars.R test","action":"sh"}
+
+```
+ran 'Rscript /app/ars.R test', exit=1 (0s). Output: sh://turn_14/Rscript_/app/ars.R_test_1 (0 tokens), sh://turn_14/Rscript_/app/ars.R_test_2 (29 tokens)
+```
+
+### `log://turn_14/update/checking_ars.R%3B_fixing_R_check%3B_running_test%3B_verifying_samples`
+scheme=log action=update attrs={"status":177,"action":"update"}
+
+```
+checking ars.R; fixing R check; running test; verifying samples
+```
+

package/audit/sweep/adaptive-rejection-sampler/turns/turn_015.md

@@ -0,0 +1,103 @@
+# turn 015
+
+tokens: prompt=15019 cached=3723 completion=294 reasoning=0 total=15313 cost=0
+created: 2026-05-01 23:43:35
+
+update: status=177 body=fixed R check; running test; verifying samples
+
+---
+
+## reasoning (think)
+
+```
+* We're in Deployment Stage - need to fix the core issue: ars.R exists but tests fail with "R not available" despite R installation
+* The check if (!("base" %in% search())) is too strict - should check Rscript availability instead
+* /app/ars.R was created (turn_13 set 2708 tokens) but gets show "not found" - possible path/cache issue
+* Plan: 1) Fix R check in ars.R, 2) Confirm file exists, 3) Run test, 4) Verify sample files created
+* After success: <update status="200">ARS implemented with tests passing</update>
+```
+
+## assistant emission
+
+```
+<think>
+* We're in Deployment Stage - need to fix the core issue: ars.R exists but tests fail with "R not available" despite R installation
+* The check if (!("base" %in% search())) is too strict - should check Rscript availability instead
+* /app/ars.R was created (turn_13 set 2708 tokens) but gets show "not found" - possible path/cache issue
+* Plan: 1) Fix R check in ars.R, 2) Confirm file exists, 3) Run test, 4) Verify sample files created
+* After success: <update status="200">ARS implemented with tests passing</update>
+</think>
+
+<get path="/app/" preview/>
+<get path="/app/ars.R" line="-50"/>
+<set path="/app/ars.R">
+<<<<<<< SEARCH
+if (!("base" %in% search())) {
+  stop("R not available - install R first")
+}
+=======
+# R availability check (more robust)
+tryCatch({
+  R.version.string
+}, error = function(e) {
+  stop("R not available - install R first")
+})
+>>>>>>> REPLACE
+</set>
+<sh>Rscript /app/ars.R test</sh>
+<get path="/app/normal_samples.txt" preview/>
+<get path="/app/exponential_samples.txt" preview/>
+<update status="177">fixed R check; running test; verifying samples</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_15/get/app`
+scheme=log action=get attrs={"path":"/app/","action":"get"}
+
+```
+/app/ promoted
+```
+
+### `log://turn_15/get/app/ars.R`
+scheme=log action=get attrs={"path":"/app/ars.R","action":"get"}
+
+```
+/app/ars.R not found
+```
+
+### `log://turn_15/set/app/ars.R`
+scheme=log action=set attrs={"path":"/app/ars.R","error":"/app/ars.R not found in context","action":"set"}
+
+```
+(empty body)
+```
+
+### `log://turn_15/sh/Rscript_/app/ars.R_test`
+scheme=log action=sh attrs={"command":"Rscript /app/ars.R test","summary":"Rscript /app/ars.R test","action":"sh"}
+
+```
+ran 'Rscript /app/ars.R test', exit=1 (0s). Output: sh://turn_15/Rscript_/app/ars.R_test_1 (0 tokens), sh://turn_15/Rscript_/app/ars.R_test_2 (29 tokens)
+```
+
+### `log://turn_15/get/app/normal_samples.txt`
+scheme=log action=get attrs={"path":"/app/normal_samples.txt","action":"get"}
+
+```
+/app/normal_samples.txt not found
+```
+
+### `log://turn_15/get/app/exponential_samples.txt`
+scheme=log action=get attrs={"path":"/app/exponential_samples.txt","action":"get"}
+
+```
+/app/exponential_samples.txt not found
+```
+
+### `log://turn_15/update/fixed_R_check%3B_running_test%3B_verifying_samples`
+scheme=log action=update attrs={"status":177,"action":"update"}
+
+```
+fixed R check; running test; verifying samples
+```
+

package/audit/sweep/adaptive-rejection-sampler/turns/turn_016.md

@@ -0,0 +1,416 @@
+# turn 016
+
+tokens: prompt=15679 cached=3723 completion=1878 reasoning=0 total=17557 cost=0
+created: 2026-05-01 23:43:39
+
+update: status=177 body=recreated ars.R w/fixes; running test; checking samples
+
+---
+
+## reasoning (think)
+
+```
+Current stage: Deployment. R is installed (turn 8 apt-get success), but /app/ars.R repeatedly "not found" despite <set> attempts - likely context sync issue. Need to recreate ars.R with fixed R check, run test, verify samples exist + PASS output.
+1. Check /app/ dir
+2. Write complete working ars.R (remove strict R check since installed)
+3. Run Rscript /app/ars.R test
+4. Verify sample files + test PASS
+5. Demote test logs
+```
+
+## assistant emission
+
+```
+<think>
+Current stage: Deployment. R is installed (turn 8 apt-get success), but /app/ars.R repeatedly "not found" despite <set> attempts - likely context sync issue. Need to recreate ars.R with fixed R check, run test, verify samples exist + PASS output.
+1. Check /app/ dir
+2. Write complete working ars.R (remove strict R check since installed)
+3. Run Rscript /app/ars.R test
+4. Verify sample files + test PASS
+5. Demote test logs
+</think>
+
+<get path="/app/" preview/>
+<set path="/app/ars.R">
+#!/usr/bin/env Rscript
+
+# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)
+# Fixed version: R check removed (R installed), robust envelope/sampling
+
+required_packages <- c("stats")
+for(pkg in required_packages) {
+  if (!requireNamespace(pkg, quietly = TRUE)) {
+    install.packages(pkg, repos = "https://cran.rstudio.com/")
+    library(pkg, character.only = TRUE)
+  }
+}
+
+validate_inputs <- function(density, n_samples, domain = NULL) {
+  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {
+    stop("n_samples must be positive numeric scalar")
+  }
+  if (!is.function(density)) {
+    stop("density must be a function")
+  }
+  test_x <- seq(-1, 1, length.out = 5)
+  test_y <- density(test_x)
+  if (length(test_y) != length(test_x) || any(is.na(test_y)) || any(!is.finite(test_y))) {
+    stop("density must be vectorized and return finite values")
+  }
+  if (!is.null(domain)) {
+    if (length(domain) != 2 || domain[1] >= domain[2]) {
+      stop("domain must be valid interval [low, high]")
+    }
+  }
+}
+
+logconcavity_check <- function(density, x_test, tol = 1e-6) {
+  if (length(x_test) < 3) return(TRUE)
+  h <- 1e-5
+  f1 <- (density(x_test + h) - density(x_test - h)) / (2 * h)
+  f2 <- (f1[2:length(f1)] - f1[1:(length(f1)-1)]) / h
+  if (any(f2 > tol, na.rm = TRUE)) {
+    warning("Possible log-concavity violation")
+    return(FALSE)
+  }
+  return(TRUE)
+}
+
+envelope_build <- function(x_nodes, y_nodes, y_deriv_nodes) {
+  slopes <- y_deriv_nodes
+  envelope_func <- function(x) {
+    n <- length(x_nodes)
+    result <- numeric(length(x))
+    for (i in seq_along(x)) {
+      xi <- x[i]
+      j <- findInterval(xi, x_nodes)
+      if (j == 0) j <- 1
+      if (j >= n) j <- n
+      result[i] <- y_nodes[j] + slopes[j] * (xi - x_nodes[j])
+    }
+    pmax(exp(result), 1e-300)
+  }
+  list(func = envelope_func, x_nodes = x_nodes, y_nodes = y_nodes, slopes = slopes)
+}
+
+sample_proposal <- function(envelope, domain = NULL) {
+  n_seg <- length(envelope$x_nodes) - 1
+  if (n_seg < 1) return(rnorm(1))
+  seg <- sample(1:n_seg, 1, prob = diff(envelope$x_nodes) * exp(envelope$y_nodes[-length(envelope$y_nodes)]))
+  x_left <- envelope$x_nodes[seg]
+  slope <- envelope$slopes[seg]
+  rate <- -slope
+  if (rate < 1e-6) rate <- 1
+  x_prop <- x_left + rexp(1, rate) * sign(slope)
+  if (!is.null(domain)) x_prop <- pmax(domain[1], pmin(domain[2], x_prop))
+  x_prop
+}
+
+ars <- function(density, n_samples = 1000, domain = NULL, max_iter = 50000) {
+  validate_inputs(density, n_samples, domain)
+  
+  if (is.null(domain)) {
+    x_nodes <- c(-5, 0, 5)
+  } else {
+    x_nodes <- seq(domain[1], domain[2], length.out = 3)
+  }
+  
+  y_nodes <- density(x_nodes)
+  h <- 1e-4
+  y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
+  
+  if (!logconcavity_check(density, x_nodes)) warning("Initial log-concavity warning")
+  
+  envelope <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)
+  samples <- numeric(n_samples)
+  n_collected <- 0
+  iter <- 0
+  rejects <- c()
+  
+  while (n_collected < n_samples && iter < max_iter) {
+    iter <- iter + 1
+    x_prop <- sample_proposal(envelope, domain)
+    
+    f_prop <- density(x_prop)
+    g_prop <- envelope$func(x_prop)
+    u <- runif(1)
+    
+    if (u <= f_prop / g_prop) {
+      n_collected <- n_collected + 1
+      samples[n_collected] <- x_prop
+    } else {
+      rejects <- c(rejects, x_prop)
+    }
+    
+    if (n_collected %% 20 == 0 || length(rejects) > 10) {
+      x_nodes <- sort(c(x_nodes, tail(samples, 3), tail(rejects, 2)))
+      if (length(x_nodes) > 15) x_nodes <- quantile(x_nodes, probs = seq(0,1,length.out=15))
+      y_nodes <- density(x_nodes)
+      y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
+      envelope <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)
+      rejects <- c()
+    }
+  }
+  
+  if (n_collected < n_samples) {
+    warning(sprintf("%d/%d samples after %d iter", n_collected, n_samples, max_iter))
+  }
+  samples[1:n_collected]
+}
+
+test <- function(n_test = 10000, ks_alpha = 0.01) {
+  cat("Running ARS test suite...\n\n")
+  
+  set.seed(42)
+  cat("Normal test:\n")
+  ars_norm <- ars(dnorm, n_test)
+  truth_norm <- rnorm(n_test)
+  ks_norm <- ks.test(ars_norm, truth_norm)$p.value
+  m_n <- mean(ars_norm); s_n <- sd(ars_norm)
+  pass_n <- abs(m_n) < 0.1 & abs(s_n-1) < 0.1 & ks_norm > ks_alpha
+  cat(sprintf("NORMAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\n", 
+              ifelse(pass_n,"PASS","FAIL"), m_n, s_n, ks_norm))
+  writeLines(as.character(ars_norm), "/app/normal_samples.txt")
+  
+  cat("\nExponential test:\n")
+  ars_exp <- ars(dexp, n_test, domain=c(0,10))
+  truth_exp <- rexp(n_test)
+  ks_exp <- ks.test(ars_exp, truth_exp)$p.value
+  m_e <- mean(ars_exp); s_e <- sd(ars_exp)
+  pass_e <- abs(m_e-1) < 0.15 & abs(s_e-1) < 0.3 & ks_exp > ks_alpha
+  cat(sprintf("EXPONENTIAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\n", 
+              ifelse(pass_e,"PASS","FAIL"), m_e, s_e, ks_exp))
+  writeLines(as.character(ars_exp), "/app/exponential_samples.txt")
+  
+  cat("\nTest complete. Samples saved.\n")
+}
+
+if (!interactive() && length(commandArgs(TRUE)) > 0 && "test" %in% commandArgs(TRUE)) {
+  test()
+} else if (!interactive()) {
+  cat("Usage: Rscript /app/ars.R test\n")
+}
+</set>
+<sh>Rscript /app/ars.R test</sh>
+<get path="/app/normal_samples.txt" preview/>
+<get path="/app/exponential_samples.txt" preview/>
+<set path="sh://turn_*" visibility="archived"/>
+<set path="known://ars/*" visibility="summarized"/>
+<update status="177">recreated ars.R w/fixes; running test; checking samples</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_16/get/app`
+scheme=log action=get attrs={"path":"/app/","action":"get"}
+
+```
+/app/ promoted
+```
+
+### `log://turn_16/set/app/ars.R`
+scheme=log action=set attrs={"path":"/app/ars.R","patch":"===================================================================\n--- /app/ars.R\told\t\n+++ /app/ars.R\tnew\t\n@@ -0,0 +1,158 @@\n+#!/usr/bin/env Rscript\n+\n+# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)\n+# Fixed version: R check removed (R installed), robust envelope/sampling\n+\n+required_packages <- c(\"stats\")\n+for(pkg in required_packages) {\n+  if (!requireNamespace(pkg, quietly = TRUE)) {\n+    install.packages(pkg, repos = \"https://cran.rstudio.com/\")\n+    library(pkg, character.only = TRUE)\n+  }\n+}\n+\n+validate_inputs <- function(density, n_samples, domain = NULL) {\n+  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {\n+    stop(\"n_samples must be positive numeric scalar\")\n+  }\n+  if (!is.function(density)) {\n+    stop(\"density must be a function\")\n+  }\n+  test_x <- seq(-1, 1, length.out = 5)\n+  test_y <- density(test_x)\n+  if (length(test_y) != length(test_x) || any(is.na(test_y)) || any(!is.finite(test_y))) {\n+    stop(\"density must be vectorized and return finite values\")\n+  }\n+  if (!is.null(domain)) {\n+    if (length(domain) != 2 || domain[1] >= domain[2]) {\n+      stop(\"domain must be valid interval [low, high]\")\n+    }\n+  }\n+}\n+\n+logconcavity_check <- function(density, x_test, tol = 1e-6) {\n+  if (length(x_test) < 3) return(TRUE)\n+  h <- 1e-5\n+  f1 <- (density(x_test + h) - density(x_test - h)) / (2 * h)\n+  f2 <- (f1[2:length(f1)] - f1[1:(length(f1)-1)]) / h\n+  if (any(f2 > tol, na.rm = TRUE)) {\n+    warning(\"Possible log-concavity violation\")\n+    return(FALSE)\n+  }\n+  return(TRUE)\n+}\n+\n+envelope_build <- function(x_nodes, y_nodes, y_deriv_nodes) {\n+  slopes <- y_deriv_nodes\n+  envelope_func <- function(x) {\n+    n <- length(x_nodes)\n+    result <- numeric(length(x))\n+    for (i in seq_along(x)) {\n+      xi <- x[i]\n+      j <- findInterval(xi, x_nodes)\n+      if (j == 0) j <- 1\n+      if (j >= n) j <- n\n+      result[i] <- y_nodes[j] + slopes[j] * (xi - x_nodes[j])\n+    }\n+    pmax(exp(result), 1e-300)\n+  }\n+  list(func = envelope_func, x_nodes = x_nodes, y_nodes = y_nodes, slopes = slopes)\n+}\n+\n+sample_proposal <- function(envelope, domain = NULL) {\n+  n_seg <- length(envelope$x_nodes) - 1\n+  if (n_seg < 1) return(rnorm(1))\n+  seg <- sample(1:n_seg, 1, prob = diff(envelope$x_nodes) * exp(envelope$y_nodes[-length(envelope$y_nodes)]))\n+  x_left <- envelope$x_nodes[seg]\n+  slope <- envelope$slopes[seg]\n+  rate <- -slope\n+  if (rate < 1e-6) rate <- 1\n+  x_prop <- x_left + rexp(1, rate) * sign(slope)\n+  if (!is.null(domain)) x_prop <- pmax(domain[1], pmin(domain[2], x_prop))\n+  x_prop\n+}\n+\n+ars <- function(density, n_samples = 1000, domain = NULL, max_iter = 50000) {\n+  validate_inputs(density, n_samples, domain)\n+  \n+  if (is.null(domain)) {\n+    x_nodes <- c(-5, 0, 5)\n+  } else {\n+    x_nodes <- seq(domain[1], domain[2], length.out = 3)\n+  }\n+  \n+  y_nodes <- density(x_nodes)\n+  h <- 1e-4\n+  y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n+  \n+  if (!logconcavity_check(density, x_nodes)) warning(\"Initial log-concavity warning\")\n+  \n+  envelope <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)\n+  samples <- numeric(n_samples)\n+  n_collected <- 0\n+  iter <- 0\n+  rejects <- c()\n+  \n+  while (n_collected < n_samples && iter < max_iter) {\n+    iter <- iter + 1\n+    x_prop <- sample_proposal(envelope, domain)\n+    \n+    f_prop <- density(x_prop)\n+    g_prop <- envelope$func(x_prop)\n+    u <- runif(1)\n+    \n+    if (u <= f_prop / g_prop) {\n+      n_collected <- n_collected + 1\n+      samples[n_collected] <- x_prop\n+    } else {\n+      rejects <- c(rejects, x_prop)\n+    }\n+    \n+    if (n_collected %% 20 == 0 || length(rejects) > 10) {\n+      x_nodes <- sort(c(x_nodes, tail(samples, 3), tail(rejects, 2)))\n+      if (length(x_nodes) > 15) x_nodes <- quantile(x_nodes, probs = seq(0,1,length.out=15))\n+      y_nodes <- density(x_nodes)\n+      y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n+      envelope <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)\n+      rejects <- c()\n+    }\n+  }\n+  \n+  if (n_collected < n_samples) {\n+    warning(sprintf(\"%d/%d samples after %d iter\", n_collected, n_samples, max_iter))\n+  }\n+  samples[1:n_collected]\n+}\n+\n+test <- function(n_test = 10000, ks_alpha = 0.01) {\n+  cat(\"Running ARS test suite...\\n\\n\")\n+  \n+  set.seed(42)\n+  cat(\"Normal test:\\n\")\n+  ars_norm <- ars(dnorm, n_test)\n+  truth_norm <- rnorm(n_test)\n+  ks_norm <- ks.test(ars_norm, truth_norm)$p.value\n+  m_n <- mean(ars_norm); s_n <- sd(ars_norm)\n+  pass_n <- abs(m_n) < 0.1 & abs(s_n-1) < 0.1 & ks_norm > ks_alpha\n+  cat(sprintf(\"NORMAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\\n\", \n+              ifelse(pass_n,\"PASS\",\"FAIL\"), m_n, s_n, ks_norm))\n+  writeLines(as.character(ars_norm), \"/app/normal_samples.txt\")\n+  \n+  cat(\"\\nExponential test:\\n\")\n+  ars_exp <- ars(dexp, n_test, domain=c(0,10))\n+  truth_exp <- rexp(n_test)\n+  ks_exp <- ks.test(ars_exp, truth_exp)$p.value\n+  m_e <- mean(ars_exp); s_e <- sd(ars_exp)\n+  pass_e <- abs(m_e-1) < 0.15 & abs(s_e-1) < 0.3 & ks_exp > ks_alpha\n+  cat(sprintf(\"EXPONENTIAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\\n\", \n+              ifelse(pass_e,\"PASS\",\"FAIL\"), m_e, s_e, ks_exp))\n+  writeLines(as.character(ars_exp), \"/app/exponential_samples.txt\")\n+  \n+  cat(\"\\nTest complete. Samples saved.\\n\")\n+}\n+\n+if (!interactive() && length(commandArgs(TRUE)) > 0 && \"test\" %in% commandArgs(TRUE)) {\n+  test()\n+} else if (!interactive()) {\n+  cat(\"Usage: Rscript /app/ars.R test\\n\")\n+}\n\\n","merge":"<<<<<<< SEARCH\n=======\n#!/usr/bin/env Rscript\n\n# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)\n# Fixed version: R check removed (R installed), robust envelope/sampling\n\nrequired_packages <- c(\"stats\")\nfor(pkg in required_packages) {\n  if (!requireNamespace(pkg, quietly = TRUE)) {\n    install.packages(pkg, repos = \"https://cran.rstudio.com/\")\n    library(pkg, character.only = TRUE)\n  }\n}\n\nvalidate_inputs <- function(density, n_samples, domain = NULL) {\n  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {\n    stop(\"n_samples must be positive numeric scalar\")\n  }\n  if (!is.function(density)) {\n    stop(\"density must be a function\")\n  }\n  test_x <- seq(-1, 1, length.out = 5)\n  test_y <- density(test_x)\n  if (length(test_y) != length(test_x) || any(is.na(test_y)) || any(!is.finite(test_y))) {\n    stop(\"density must be vectorized and return finite values\")\n  }\n  if (!is.null(domain)) {\n    if (length(domain) != 2 || domain[1] >= domain[2]) {\n      stop(\"domain must be valid interval [low, high]\")\n    }\n  }\n}\n\nlogconcavity_check <- function(density, x_test, tol = 1e-6) {\n  if (length(x_test) < 3) return(TRUE)\n  h <- 1e-5\n  f1 <- (density(x_test + h) - density(x_test - h)) / (2 * h)\n  f2 <- (f1[2:length(f1)] - f1[1:(length(f1)-1)]) / h\n  if (any(f2 > tol, na.rm = TRUE)) {\n    warning(\"Possible log-concavity violation\")\n    return(FALSE)\n  }\n  return(TRUE)\n}\n\nenvelope_build <- function(x_nodes, y_nodes, y_deriv_nodes) {\n  slopes <- y_deriv_nodes\n  envelope_func <- function(x) {\n    n <- length(x_nodes)\n    result <- numeric(length(x))\n    for (i in seq_along(x)) {\n      xi <- x[i]\n      j <- findInterval(xi, x_nodes)\n      if (j == 0) j <- 1\n      if (j >= n) j <- n\n      result[i] <- y_nodes[j] + slopes[j] * (xi - x_nodes[j])\n    }\n    pmax(exp(result), 1e-300)\n  }\n  list(func = envelope_func, x_nodes = x_nodes, y_nodes = y_nodes, slopes = slopes)\n}\n\nsample_proposal <- function(envelope, domain = NULL) {\n  n_seg <- length(envelope$x_nodes) - 1\n  if (n_seg < 1) return(rnorm(1))\n  seg <- sample(1:n_seg, 1, prob = diff(envelope$x_nodes) * exp(envelope$y_nodes[-length(envelope$y_nodes)]))\n  x_left <- envelope$x_nodes[seg]\n  slope <- envelope$slopes[seg]\n  rate <- -slope\n  if (rate < 1e-6) rate <- 1\n  x_prop <- x_left + rexp(1, rate) * sign(slope)\n  if (!is.null(domain)) x_prop <- pmax(domain[1], pmin(domain[2], x_prop))\n  x_prop\n}\n\nars <- function(density, n_samples = 1000, domain = NULL, max_iter = 50000) {\n  validate_inputs(density, n_samples, domain)\n  \n  if (is.null(domain)) {\n    x_nodes <- c(-5, 0, 5)\n  } else {\n    x_nodes <- seq(domain[1], domain[2], length.out = 3)\n  }\n  \n  y_nodes <- density(x_nodes)\n  h <- 1e-4\n  y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n  \n  if (!logconcavity_check(density, x_nodes)) warning(\"Initial log-concavity warning\")\n  \n  envelope <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)\n  samples <- numeric(n_samples)\n  n_collected <- 0\n  iter <- 0\n  rejects <- c()\n  \n  while (n_collected < n_samples && iter < max_iter) {\n    iter <- iter + 1\n    x_prop <- sample_proposal(envelope, domain)\n    \n    f_prop <- density(x_prop)\n    g_prop <- envelope$func(x_prop)\n    u <- runif(1)\n    \n    if (u <= f_prop / g_prop) {\n      n_collected <- n_collected + 1\n      samples[n_collected] <- x_prop\n    } else {\n      rejects <- c(rejects, x_prop)\n    }\n    \n    if (n_collected %% 20 == 0 || length(rejects) > 10) {\n      x_nodes <- sort(c(x_nodes, tail(samples, 3), tail(rejects, 2)))\n      if (length(x_nodes) > 15) x_nodes <- quantile(x_nodes, probs = seq(0,1,length.out=15))\n      y_nodes <- density(x_nodes)\n      y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n      envelope <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)\n      rejects <- c()\n    }\n  }\n  \n  if (n_collected < n_samples) {\n    warning(sprintf(\"%d/%d samples after %d iter\", n_collected, n_samples, max_iter))\n  }\n  samples[1:n_collected]\n}\n\ntest <- function(n_test = 10000, ks_alpha = 0.01) {\n  cat(\"Running ARS test suite...\\n\\n\")\n  \n  set.seed(42)\n  cat(\"Normal test:\\n\")\n  ars_norm <- ars(dnorm, n_test)\n  truth_norm <- rnorm(n_test)\n  ks_norm <- ks.test(ars_norm, truth_norm)$p.value\n  m_n <- mean(ars_norm); s_n <- sd(ars_norm)\n  pass_n <- abs(m_n) < 0.1 & abs(s_n-1) < 0.1 & ks_norm > ks_alpha\n  cat(sprintf(\"NORMAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\\n\", \n              ifelse(pass_n,\"PASS\",\"FAIL\"), m_n, s_n, ks_norm))\n  writeLines(as.character(ars_norm), \"/app/normal_samples.txt\")\n  \n  cat(\"\\nExponential test:\\n\")\n  ars_exp <- ars(dexp, n_test, domain=c(0,10))\n  truth_exp <- rexp(n_test)\n  ks_exp <- ks.test(ars_exp, truth_exp)$p.value\n  m_e <- mean(ars_exp); s_e <- sd(ars_exp)\n  pass_e <- abs(m_e-1) < 0.15 & abs(s_e-1) < 0.3 & ks_exp > ks_alpha\n  cat(sprintf(\"EXPONENTIAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\\n\", \n              ifelse(pass_e,\"PASS\",\"FAIL\"), m_e, s_e, ks_exp))\n  writeLines(as.character(ars_exp), \"/app/exponential_samples.txt\")\n  \n  cat(\"\\nTest complete. Samples saved.\\n\")\n}\n\nif (!interactive() && length(commandArgs(TRUE)) > 0 && \"test\" %in% commandArgs(TRUE)) {\n  test()\n} else if (!interactive()) {\n  cat(\"Usage: Rscript /app/ars.R test\\n\")\n}\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":2596,"summary":null,"action":"set"}
+
+```
+#!/usr/bin/env Rscript
+
+# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)
+# Fixed version: R check removed (R installed), robust envelope/sampling
+
+required_packages <- c("stats")
+for(pkg in required_packages) {
+  if (!requireNamespace(pkg, quietly = TRUE)) {
+    install.packages(pkg, repos = "https://cran.rstudio.com/")
+    library(pkg, character.only = TRUE)
+  }
+}
+
+validate_inputs <- function(density, n_samples, domain = NULL) {
+  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {
+    stop("n_samples must be positive numeric scalar")
+  }
+  if (!is.function(density)) {
+    stop("density must be a function")
+  }
+  test_x <- seq(-1, 1, length.out = 5)
+  test_y <- density(test_x)
+  if (length(test_y) != length(test_x) || any(is.na(test_y)) || any(!is.finite(test_y))) {
+    stop("density must be vectorized and return finite values")
+  }
+  if (!is.null(domain)) {
+    if (length(domain) != 2 || domain[1] >= domain[2]) {
+      stop("domain must be valid interval [low, high]")
+    }
+  }
+}
+
+logconcavity_check <- function(density, x_test, tol = 1e-6) {
+  if (length(x_test) < 3) return(TRUE)
+  h <- 1e-5
+  f1 <- (density(x_test + h) - density(x_test - h)) / (2 * h)
+  f2 <- (f1[2:length(f1)] - f1[1:(length(f1)-1)]) / h
+  if (any(f2 > tol, na.rm = TRUE)) {
+    warning("Possible log-concavity violation")
+    return(FALSE)
+  }
+  return(TRUE)
+}
+
+envelope_build <- function(x_nodes, y_nodes, y_deriv_nodes) {
+  slopes <- y_deriv_nodes
+  envelope_func <- function(x) {
+    n <- length(x_nodes)
+    result <- numeric(length(x))
+    for (i in seq_along(x)) {
+      xi <- x[i]
+      j <- findInterval(xi, x_nodes)
+      if (j == 0) j <- 1
+      if (j >= n) j <- n
+      result[i] <- y_nodes[j] + slopes[j] * (xi - x_nodes[j])
+    }
+    pmax(exp(result), 1e-300)
+  }
+  list(func = envelope_func, x_nodes = x_nodes, y_nodes = y_nodes, slopes = slopes)
+}
+
+sample_proposal <- function(envelope, domain = NULL) {
+  n_seg <- length(envelope$x_nodes) - 1
+  if (n_seg < 1) return(rnorm(1))
+  seg <- sample(1:n_seg, 1, prob = diff(envelope$x_nodes) * exp(envelope$y_nodes[-length(envelope$y_nodes)]))
+  x_left <- envelope$x_nodes[seg]
+  slope <- envelope$slopes[seg]
+  rate <- -slope
+  if (rate < 1e-6) rate <- 1
+  x_prop <- x_left + rexp(1, rate) * sign(slope)
+  if (!is.null(domain)) x_prop <- pmax(domain[1], pmin(domain[2], x_prop))
+  x_prop
+}
+
+ars <- function(density, n_samples = 1000, domain = NULL, max_iter = 50000) {
+  validate_inputs(density, n_samples, domain)
+  
+  if (is.null(domain)) {
+    x_nodes <- c(-5, 0, 5)
+  } else {
+    x_nodes <- seq(domain[1], domain[2], length.out = 3)
+  }
+  
+  y_nodes <- density(x_nodes)
+  h <- 1e-4
+  y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
+  
+  if (!logconcavity_check(density, x_nodes)) warning("Initial log-concavity warning")
+  
+  envelope <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)
+  samples <- numeric(n_samples)
+  n_collected <- 0
+  iter <- 0
+  rejects <- c()
+  
+  while (n_collected < n_samples && iter < max_iter) {
+    iter <- iter + 1
+    x_prop <- sample_proposal(envelope, domain)
+    
+    f_prop <- density(x_prop)
+    g_prop <- envelope$func(x_prop)
+    u <- runif(1)
+    
+    if (u <= f_prop / g_prop) {
+      n_collected <- n_collected + 1
+      samples[n_collected] <- x_prop
+    } else {
+      rejects <- c(rejects, x_prop)
+    }
+    
+    if (n_collected %% 20 == 0 || length(rejects) > 10) {
+      x_nodes <- sort(c(x_nodes, tail(samples, 3), tail(rejects, 2)))
+      if (length(x_nodes) > 15) x_nodes <- quantile(x_nodes, probs = seq(0,1,length.out=15))
+      y_nodes <- density(x_nodes)
+      y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
+      envelope <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)
+      rejects <- c()
+    }
+  }
+  
+  if (n_collected < n_samples) {
+    warning(sprintf("%d/%d samples after %d iter", n_collected, n_samples, max_iter))
+  }
+  samples[1:n_collected]
+}
+
+test <- function(n_test = 10000, ks_alpha = 0.01) {
+  cat("Running ARS test suite...\n\n")
+  
+  set.seed(42)
+  cat("Normal test:\n")
+  ars_norm <- ars(dnorm, n_test)
+  truth_norm <- rnorm(n_test)
+  ks_norm <- ks.test(ars_norm, truth_norm)$p.value
+  m_n <- mean(ars_norm); s_n <- sd(ars_norm)
+  pass_n <- abs(m_n) < 0.1 & abs(s_n-1) < 0.1 & ks_norm > ks_alpha
+  cat(sprintf("NORMAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\n", 
+              ifelse(pass_n,"PASS","FAIL"), m_n, s_n, ks_norm))
+  writeLines(as.character(ars_norm), "/app/normal_samples.txt")
+  
+  cat("\nExponential test:\n")
+  ars_exp <- ars(dexp, n_test, domain=c(0,10))
+  truth_exp <- rexp(n_test)
+  ks_exp <- ks.test(ars_exp, truth_exp)$p.value
+  m_e <- mean(ars_exp); s_e <- sd(ars_exp)
+  pass_e <- abs(m_e-1) < 0.15 & abs(s_e-1) < 0.3 & ks_exp > ks_alpha
+  cat(sprintf("EXPONENTIAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\n", 
+              ifelse(pass_e,"PASS","FAIL"), m_e, s_e, ks_exp))
+  writeLines(as.character(ars_exp), "/app/exponential_samples.txt")
+  
+  cat("\nTest complete. Samples saved.\n")
+}
+
+if (!interactive() && length(commandArgs(TRUE)) > 0 && "test" %in% commandArgs(TRUE)) {
+  test()
+} else if (!interactive()) {
+  cat("Usage: Rscript /app/ars.R test\n")
+}
+```
+
+### `log://turn_16/sh/Rscript_/app/ars.R_test`
+scheme=log action=sh attrs={"command":"Rscript /app/ars.R test","summary":"Rscript /app/ars.R test","action":"sh"}
+
+```
+ran 'Rscript /app/ars.R test', exit=0 (2s). Output: sh://turn_16/Rscript_/app/ars.R_test_1 (97 tokens), sh://turn_16/Rscript_/app/ars.R_test_2 (217 tokens)
+```
+
+### `log://turn_16/get/app/normal_samples.txt`
+scheme=log action=get attrs={"path":"/app/normal_samples.txt","action":"get"}
+
+```
+/app/normal_samples.txt not found
+```
+
+### `log://turn_16/get/app/exponential_samples.txt`
+scheme=log action=get attrs={"path":"/app/exponential_samples.txt","action":"get"}
+
+```
+/app/exponential_samples.txt not found
+```
+
+### `log://turn_16/set/sh%3A/turn_*`
+scheme=log action=set attrs={}
+
+```
+sh://turn_* not found
+```
+
+### `log://turn_16/set/known%3A/ars/*`
+scheme=log action=set attrs={}
+
+```
+known://ars/algorithm, known://ars/files, known://ars/implementation, known://ars/inputs_validation, known://ars/logconcavity_check, known://ars/main, known://ars/modularity, known://ars/r_environment, known://ars/r_environment_setup, known://ars/test_implementation, known://ars/test_suite set to summarized
+```
+
+### `log://turn_16/update/recreated_ars.R_w/fixes%3B_running_test%3B_checking_samples`
+scheme=log action=update attrs={"status":177,"action":"update"}
+
+```
+recreated ars.R w/fixes; running test; checking samples
+```
+

package/audit/sweep/adaptive-rejection-sampler/turns/turn_017.md

@@ -0,0 +1,56 @@
+# turn 017
+
+tokens: prompt=17352 cached=2780 completion=149 reasoning=0 total=17501 cost=0
+created: 2026-05-01 23:43:55
+
+update: status=177 body=debug ars.R; fixing envelope/proposal/adaptation bugs
+
+---
+
+## reasoning (think)
+
+```
+* We're in Deployment Stage - tests ran but both FAIL with tiny sd (0.08, 0.12) vs expected ~1
+* Core bugs: envelope_build exp() too early; sample_proposal wrong direction/sign; adaptation ineffective
+* Plan: 1) get current /app/ars.R; 2) fix envelope (log-space), proposal (correct exp dist), adaptation; 3) test; 4) check samples
+* Budget ok, R installed, focus on bug fixes for PASS
+```
+
+## assistant emission
+
+```
+<think>
+* We're in Deployment Stage - tests ran but both FAIL with tiny sd (0.08, 0.12) vs expected ~1
+* Core bugs: envelope_build exp() too early; sample_proposal wrong direction/sign; adaptation ineffective
+* Plan: 1) get current /app/ars.R; 2) fix envelope (log-space), proposal (correct exp dist), adaptation; 3) test; 4) check samples
+* Budget ok, R installed, focus on bug fixes for PASS
+</think>
+
+<get path="/app/ars.R"/>
+<get path="/app/" preview/>
+<update status="177">debug ars.R; fixing envelope/proposal/adaptation bugs</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_17/get/app/ars.R`
+scheme=log action=get attrs={"path":"/app/ars.R","action":"get"}
+
+```
+/app/ars.R not found
+```
+
+### `log://turn_17/get/app`
+scheme=log action=get attrs={"path":"/app/","action":"get"}
+
+```
+/app/ promoted
+```
+
+### `log://turn_17/update/debug_ars.R%3B_fixing_envelope/proposal/adaptation_bugs`
+scheme=log action=update attrs={"status":177,"action":"update"}
+
+```
+debug ars.R; fixing envelope/proposal/adaptation bugs
+```
+