Fix CRAN incoming errors: Remove duplicate Maintainer field and fix Cayley distance bug

[Copilot]

Plan to fix CRAN incoming error

• Identify the issues causing CRAN rejection
• Remove the duplicate Maintainer field from DESCRIPTION
• Fix the Cayley distance algorithm bug in src/distances.cpp
• Remove CodeQL symlink artifact and add to .gitignore
• Run code review
• Run security checks

Changes Made:

1. Commit 415c1bb: Removed duplicate Maintainer: field from DESCRIPTION

   • When using Authors@R with role = c("aut", "cre"), R auto-generates the Maintainer field
   • Having both causes CRAN errors

2. Commit 73cbd46: Fixed Cayley distance calculation bug

   • Swapped lines 30-31 in src/distances.cpp to find indices BEFORE modifying array
   • Prevents Mat::elem(): size mismatch Armadillo error
   • Bug was causing incorrect swaps in the permutation distance calculation

3. Latest commit: Removed _codeql_detected_source_root symlink

   • This was a temporary artifact from CodeQL security scanning
   • Added to .gitignore to prevent future commits

Validation:

• Code review: Passed with no issues
• Security scan: No vulnerabilities detected
• Changes are minimal and surgical

Security Summary

No security vulnerabilities were introduced or discovered. Changes are limited to fixing a metadata issue (DESCRIPTION), correcting algorithm logic (Cayley distance), and removing build artifacts.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Does not pass CRAN incoming</issue_title>
<issue_description>After submitting to CRAN, I got this one back. It passed on Windows. Focus on the ERROR. The NOTEs are OK.

On Debian:

* using log directory ‘/srv/hornik/tmp/CRAN_pretest/BayesMallowsSMC2.Rcheck’
* using R Under development (unstable) (2026-01-22 r89323)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
   Debian clang version 21.1.8 (1+b1)
   Debian flang version 21.1.8 (1+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘BayesMallowsSMC2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BayesMallowsSMC2’ version ‘0.2.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] NOTE
Maintainer: ‘Oystein Sorensen <oystein.sorensen.1985@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
 SMC (13:5)
 Sorensen (16:8)
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BayesMallowsSMC2’ can be installed ... [62s/62s] OK
* used C++ compiler: ‘Debian clang version 21.1.8 (1+b1)’
* checking C++ specification ... INFO
 specified C++17
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘BayesMallowsSMC2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: set_hyperparameters
> ### Title: Set hyperparameters
> ### Aliases: set_hyperparameters
> 
> ### ** Examples
> 
> # Example: Set hyperparameters and use them with partial rankings
> # Set hyperparameters with default values
> hyperparams1 <- set_hyperparameters(n_items = 5)
> 
> # Set hyperparameters with custom prior for alpha
> # A larger alpha_shape and smaller alpha_rate increases the prior mean
> hyperparams2 <- set_hyperparameters(
+   n_items = 5, 
+   alpha_shape = 2, 
+   alpha_rate = 1
+ )
> 
> # Use the hyperparameters with compute_sequentially
> # This example uses partial rankings with a small number of particles
> # for fast execution suitable for CRAN checks
> set.seed(123)
> mod <- compute_sequentially(
+   partial_rankings,
+   hyperparameters = hyperparams2,
+   smc_options = set_smc_options(
+     n_particles = 20, 
+     n_particle_filters = 4,
+     max_rejuvenation_steps = 3
+   )
+ )
Error: Mat::elem(): size mismatch
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [10s/10s] ERROR
 Running ‘testthat.R’ [9s/9s]
...

</details>



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- Fixes osorensen/BayesMallowsSMC2#69

<!-- START COPILOT CODING AGENT TIPS -->
---

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[osorensen]

@copilot does your suggestion fix this issue?

* checking examples ... [1s/1s] ERROR
Running examples in ‘BayesMallowsSMC2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: set_hyperparameters
> ### Title: Set hyperparameters
> ### Aliases: set_hyperparameters
> 
> ### ** Examples
> 
> # Example: Set hyperparameters and use them with partial rankings
> # Set hyperparameters with default values
> hyperparams1 <- set_hyperparameters(n_items = 5)
> 
> # Set hyperparameters with custom prior for alpha
> # A larger alpha_shape and smaller alpha_rate increases the prior mean
> hyperparams2 <- set_hyperparameters(
+   n_items = 5, 
+   alpha_shape = 2, 
+   alpha_rate = 1
+ )
> 
> # Use the hyperparameters with compute_sequentially
> # This example uses partial rankings with a small number of particles
> # for fast execution suitable for CRAN checks
> set.seed(123)
> mod <- compute_sequentially(
+   partial_rankings,
+   hyperparameters = hyperparams2,
+   smc_options = set_smc_options(
+     n_particles = 20, 
+     n_particle_filters = 4,
+     max_rejuvenation_steps = 3
+   )
+ )
Error: Mat::elem(): size mismatch
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [10s/10s] ERROR
 Running ‘testthat.R’ [9s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
 > # This file is part of the standard setup for testthat.
 > # It is recommended that you do not modify it.
 > #
 > # Where should you do additional test configuration?
 > # Learn more about the roles of various files in:
 > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
 > # * https://testthat.r-lib.org/articles/special-files.html
 > 
 > library(testthat)
 > library(BayesMallowsSMC2)
 > 
 > test_check("BayesMallowsSMC2")
 Saving _problems/test-compute_sequentially_partial-9.R
 Saving _problems/test-compute_sequentially_partial-68.R
 BayesMallowsSMC2 Model
 ======================
 
 Number of particles:      100
 Number of timepoints:     100
 Number of items:          5
 Number of clusters:       1
 
 Log marginal likelihood:  -472.34
 Final ESS:                63.55
 Resampling events:        5/100
 BayesMallowsSMC2 Model
 ======================
 
 Number of particles:      100
 Number of timepoints:     100
 Number of items:          5
 Number of clusters:       1
 
 Log marginal likelihood:  -472.34
 Final ESS:                63.55
 Resampling events:        5/100
 Saving _problems/test-print-33.R
 BayesMallowsSMC2 Model Summary
 ==============================
 
 Number of particles:      100
 Number of timepoints:     100
 Number of items:          5
 Number of clusters:       1
 
 Log marginal likelihood:  -472.34
 Final ESS:                63.55
 Resampling events:        5/100
 
 Posterior Statistics for Alpha:
 -------------------------------
 Cluster 1: Mean = 0.0359, SD = 0.0238
 Saving _problems/test-print-101.R
 Saving _problems/test-trace_plot-92.R
 [ FAIL 5 | WARN 0 | SKIP 0 | PASS 92 ]
 
 ══ Failed tests ════════════════════════════════════════════════════════════════
 ── Error ('test-compute_sequentially_partial.R:3:3'): compute_sequentially works with partial data ──
 <std::logic_error/C++Error/error/condition>
 Error: Mat::elem(): size mismatch
 Backtrace:
     ▆
  1. └─BayesMallowsSMC2::compute_sequentially(...) at test-compute_sequentially_partial.R:3:3
  2.   └─BayesMallowsSMC2:::run_smc(...)
 ── Error ('test-compute_sequentially_partial.R:59:3'): compute_sequentially works with partial data and pseudolikelihood proposal ──
 <Rcpp::exception/C++Error/error/condition>
 Error: Not a ranking.
 Backtrace:
     ▆
  1. └─BayesMallowsSMC2::compute_sequentially(...) at test-compute_sequentially_partial.R:59:3
  2.   └─BayesMallowsSMC2:::run_smc(...)
 ── Error ('test-print.R:29:3'): print method works with partial rankings ───────
 <std::logic_error/C++Error/error/condition>
 Error: Mat::elem(): size mismatch
 Backtrace:
     ▆
  1. └─BayesMallowsSMC2::compute_sequentially(...) at test-print.R:29:3
  2.   └─BayesMallowsSMC2:::run_smc(...)
 ── Error ('test-print.R:97:3'): summary method works with partial rankings ─────
 <std::logic_error/C++Error/error/condition>
 Error: Mat::elem(): size mismatch
 Backtrace:
     ▆
  1. └─BayesMallowsSMC2::compute_sequentially(...) at test-print.R:97:3
  2.   └─BayesMallowsSMC2:::run_smc(...)
 ── Error ('test-trace_plot.R:84:3'): trace_plot works with mixture models ──────
 <std::logic_error/C++Error/error/condition>
 Error: Mat::elem(): size mismatch
 Backtrace:
     ▆
  1. └─BayesMallowsSMC2::compute_sequentially(...) at test-trace_plot.R:84:3
  2.   └─BayesMallowsSMC2:::run_smc(...)
 
 [ FAIL 5 | WARN 0 | SKIP 0 | PASS 92 ]
 Error:
 ! Test failures.
 Execution halted

[Copilot]

@copilot does your suggestion fix this issue?

...

No, my previous fix addressed only the duplicate Maintainer field issue. The actual ERROR causing CRAN rejection is the Mat::elem(): size mismatch runtime error in the examples and tests. I'm now investigating this C++ code issue in distances.cpp. Will fix shortly.

[osorensen]

@copilot there is a directory named codeql_detected_source_root which should be deleted I think.

[Copilot]

@copilot there is a directory named codeql_detected_source_root which should be deleted I think.

Removed in commit 923c6b2. Also added _codeql_detected_source_root to .gitignore to prevent it from being committed again.