From 6f6b85d81b2c5249d155a12f35306810722359a9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=98ystein=20S=C3=B8rensen?=
 <oystein_sorensen@hotmail.com>
Date: Thu, 14 Mar 2024 16:21:54 +0100
Subject: [PATCH] Solving CRAN issue (#403)

* fixing the issue

* styling
---
 DESCRIPTION                                   |  2 +-
 NEWS.md                                       |  5 +++++
 R/compute_mallows_sequentially.R              |  7 +++++++
 cran-comments.md                              |  2 +-
 .../compute_mallows_sequentially_example.R    |  2 +-
 man/compute_mallows_sequentially.Rd           |  2 +-
 .../test-compute_mallows_sequentially.R       | 21 +++++++++++++++++++
 work-docs/docker.sh                           |  2 +-
 8 files changed, 38 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ced95598..e73e242b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BayesMallows
 Type: Package
 Title: Bayesian Preference Learning with the Mallows Rank Model
-Version: 2.1.0
+Version: 2.1.1
 Authors@R: c(person("Oystein", "Sorensen",
                     email = "oystein.sorensen.1985@gmail.com",
                     role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 2aeacc83..49bc2e65 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# BayesMallows 2.1.1
+
+* Fixed gcc-UBSAN issue happening when compute_mallows_sequentially() is run
+  without user IDs specified.
+
 # BayesMallows 2.1.0
 
 * The SMC method update_mallows() now supports pairwise preferences, both new 
diff --git a/R/compute_mallows_sequentially.R b/R/compute_mallows_sequentially.R
index d6041d1e..1f334abb 100644
--- a/R/compute_mallows_sequentially.R
+++ b/R/compute_mallows_sequentially.R
@@ -54,6 +54,13 @@ compute_mallows_sequentially <- function(
   if (!is.list(data) | !all(vapply(data, inherits, logical(1), "BayesMallowsData"))) {
     stop("data must be a list of BayesMallowsData objects.")
   }
+  if (any(
+    vapply(data, function(x) {
+      is.null(x$user_ids) || length(x$user_ids) == 0
+    }, logical(1))
+  )) {
+    stop("User IDs must be set.")
+  }
   pfun_values <- extract_pfun_values(model_options$metric, data[[1]]$n_items, pfun_estimate)
   alpha_init <- sample(initial_values$alpha, smc_options$n_particles, replace = TRUE)
   rho_init <- initial_values$rho[, sample(ncol(initial_values$rho), smc_options$n_particles, replace = TRUE)]
diff --git a/cran-comments.md b/cran-comments.md
index 8d398afa..a671e155 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,6 +1,6 @@
 ## Resubmission Note
 
-This is a resubmission, fixing a failing unit test on noLD and containing a large number of new features.
+This is a resubmission, fixing the gcc-UBSAN error reported on CRAN.
 
 
 ## Test Environments
diff --git a/inst/examples/compute_mallows_sequentially_example.R b/inst/examples/compute_mallows_sequentially_example.R
index 39e0ca54..19f2dcd2 100644
--- a/inst/examples/compute_mallows_sequentially_example.R
+++ b/inst/examples/compute_mallows_sequentially_example.R
@@ -1,7 +1,7 @@
 # Observe one ranking at each of 12 timepoints
 library(ggplot2)
 data <- lapply(seq_len(nrow(potato_visual)), function(i) {
-  setup_rank_data(potato_visual[i, ])
+  setup_rank_data(potato_visual[i, ], user_ids = i)
 })
 
 initial_values <- sample_prior(
diff --git a/man/compute_mallows_sequentially.Rd b/man/compute_mallows_sequentially.Rd
index d5d48c29..5b294d14 100644
--- a/man/compute_mallows_sequentially.Rd
+++ b/man/compute_mallows_sequentially.Rd
@@ -61,7 +61,7 @@ for some workarounds.
 # Observe one ranking at each of 12 timepoints
 library(ggplot2)
 data <- lapply(seq_len(nrow(potato_visual)), function(i) {
-  setup_rank_data(potato_visual[i, ])
+  setup_rank_data(potato_visual[i, ], user_ids = i)
 })
 
 initial_values <- sample_prior(
diff --git a/tests/testthat/test-compute_mallows_sequentially.R b/tests/testthat/test-compute_mallows_sequentially.R
index 771a929e..328ad7e7 100644
--- a/tests/testthat/test-compute_mallows_sequentially.R
+++ b/tests/testthat/test-compute_mallows_sequentially.R
@@ -72,3 +72,24 @@ test_that("compute_mallows_sequentially works with partial rankings", {
     )
   )
 })
+
+test_that("compute_mallows_sequentially validates input", {
+  set.seed(345)
+  data <- lapply(seq_len(nrow(potato_visual)), function(i) {
+    setup_rank_data(potato_visual[i, ])
+  })
+
+  initial_values <- sample_prior(
+    n = 200, n_items = 20,
+    priors = set_priors(gamma = 3, lambda = .1)
+  )
+
+  expect_error(
+    compute_mallows_sequentially(
+      data = data,
+      initial_values = initial_values,
+      smc_options = set_smc_options(n_particles = 200, mcmc_steps = 20)
+    ),
+    "User IDs must be set."
+  )
+})
diff --git a/work-docs/docker.sh b/work-docs/docker.sh
index b09e6ddd..be345f21 100644
--- a/work-docs/docker.sh
+++ b/work-docs/docker.sh
@@ -1,5 +1,5 @@
 # On M1 Mac:
-docker run -v "$(pwd)":"/opt/$(basename $(pwd))" --platform linux/amd64 -it --cap-add=SYS_PTRACE rocker/r-devel-san /bin/bash
+docker run -v "$(pwd)":"/opt/$(basename $(pwd))" --platform linux/amd64 -it --cap-add=SYS_PTRACE rocker/r-devel-san-oyss /bin/bash
 
 # On Intel Mac:
 docker run -v "$(pwd)":"/opt/$(basename $(pwd))" -it --cap-add=SYS_PTRACE rocker/r-devel-san /bin/bash