* using log directory 'd:/RCompile/CRANincoming/R-devel/gapr.Rcheck'
* using R Under development (unstable) (2025-05-11 r88197 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'gapr/DESCRIPTION' ... OK
* this is package 'gapr' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [11s] NOTE
Maintainer: 'ShuYu Lin <shuyuuu89@gmail.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  HCT (6:329)
  Tien (6:840)
  seriation (6:359)
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'gapr' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.2.0'
* checking installed package size ... OK
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [22s] OK
* checking Rd files ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [13s] ERROR
Running examples in 'gapr-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: computeProximity
> ### Title: Compute Proximity Matrix
> ### Aliases: computeProximity
> 
> ### ** Examples
> 
> # =======================
> # Example 1: Crabs dataset with distance method (Euclidean distance)
> # =======================
> # Step 1: Compute proximity matrix
> if (requireNamespace("MASS", quietly = TRUE)) {
+   df_crabs <- as.matrix(MASS::crabs[, -c(1:3)])  # Use continuous variables only
+   row_prox_crabs <- computeProximity(
+     data = df_crabs,
+     proxType = 0,               # 0 = Euclidean distance
+     side = 0,                   # 0 = row-wise proximity
+     isContainMissingValue = 0
+   )
+ 
+   # Step 2: Obtain R2E ordering
+   r2e_order_crabs <- ellipse_sort(row_prox_crabs)  # R2E ordering
+ 
+   # Step 3: Apply AVG-R2E ordering
+   hctree_result_crabs <- hctree_sort(
+     row_prox_crabs,                   # use distance matrix directly
+     externalOrder = r2e_order_crabs,  # apply r2e order
+     orderType = 2,                    # 2 = Average-linkage
+     flipType = 1                      # 1 = Flip based on externalOrder
+   )
+ 
+   avg_r2e_order_crabs <- hctree_result_crabs$order + 1
+ 
+   # Inspect results
+   avg_r2e_order_crabs
+ 
+   rm(df_crabs, row_prox_crabs, r2e_order_crabs, hctree_result_crabs, avg_r2e_order_crabs)
+   gc()
+ }
          used  (Mb) gc trigger  (Mb) max used  (Mb)
Ncells 2633697 140.7    4398324 234.9  4398324 234.9
Vcells 4596817  35.1   10146329  77.5  8370290  63.9
> 
> # =======================
> # Example 2: Crabs dataset with distance method (Pearson correlation)
> # =======================
> if (requireNamespace("MASS", quietly = TRUE)) {
+   df_crabs <- as.matrix(MASS::crabs[, -c(1:3)])  # Use continuous variables only
+   row_prox_pearson <- computeProximity(
+     data = df_crabs,
+     proxType = 1,               # 1 = Pearson correlation (internally 1 - cor)
+     side = 0,                   # 0 = row-wise proximity
+     isContainMissingValue = 0
+   )
+ 
+   # Step 2: Obtain R2E ordering
+   r2e_order_pearson <- ellipse_sort(row_prox_pearson)  # R2E ordering
+ 
+   # Step 3: Inspect results
+   dist_pearson <- as.dist(1 - row_prox_pearson) # convert correlation matrix to distance matrix
+   dist_pearson_MT <- as.matrix(dist_pearson)
+ 
+   hctree_result_pearson <- hctree_sort(
+     dist_pearson_MT,                    # use distance matrix directly
+     externalOrder = r2e_order_pearson,  # apply r2e order
+     orderType = 2,                      # 2 = Average-linkage
+     flipType = 1                        # 1 = Flip based on externalOrder
+   )
+ 
+   avg_r2e_order_pearson <- hctree_result_pearson$order + 1
+ 
+   # Inspect results
+   avg_r2e_order_pearson
+ 
+   rm(df_crabs, row_prox_pearson, r2e_order_pearson, dist_pearson, dist_pearson_MT)
+   rm(hctree_result_pearson, avg_r2e_order_pearson)
+   gc()
+ }
Error in gc() : 
  GC encountered a node (00000246977FDC60) with an unknown SEXP type: 27 at memory.c:1840
Execution halted
* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE