* using log directory ‘/srv/hornik/tmp/CRAN/SKFCPD.Rcheck’
* using R Under development (unstable) (2024-02-15 r85925)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘SKFCPD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SKFCPD’ version ‘0.2.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Hanmo Li <hanmo@pstat.ucsb.edu>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Gu (16:235)
  Hanmo (16:202)
  Kalman (16:25)
  Mengyang (16:226)
  Yuedong (16:212)
  scalable (16:43)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-02-15 as issues were not corrected
    in time.
* 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 ‘SKFCPD’ can be installed ... [20s/20s] OK
* used C++ compiler: ‘Debian clang version 17.0.6 (5)’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] 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 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 ... [5s/5s] ERROR
Running examples in ‘SKFCPD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SKFCPD
> ### Title: Getting the results of the SKFCPD model
> ### Aliases: SKFCPD
> 
> ### ** Examples
> 
>   library(SKFCPD)
>   
>   #------------------------------------------------------------------------------
>   # Example: fast online changepoint detection with DEPENDENT data.
>   # 
>   # Data generation: Data follows a multidimensional Gaussian process with Matern 2.5 kernel.
>   #------------------------------------------------------------------------------
>   # Data Generation
>   set.seed(1)
>   
>   n_obs = 150
>   n_dim = 2
>   seg_len = c(70, 30, 20,30)
>   mean_each_seg = c(0,1,-1,0)
>   
>   x_mat=matrix(1:n_obs)
>   y_mat=matrix(NA, nrow=n_obs, ncol=n_dim)
>   
>   gamma = rep(5, n_dim) # range parameter of the covariance matrix
>   
>   # compute the matern 2.5 kernel
>   construct_cor_matrix = function(input, gamma){
+     n = length(input)
+     R0=abs(outer(input,(input),'-'))
+     matrix_one = matrix(1, n, n)
+     const = sqrt(5) * R0 / gamma
+     Sigma = (matrix_one + const + const^2/3) * (exp(-const))
+     return(Sigma)
+   }
>   
>   for(j in 1:n_dim){
+     y_each_dim = c()
+     for(i in 1:length(seg_len)){
+       nobs_per_seg = seg_len[i]
+       Sigma = construct_cor_matrix(1:nobs_per_seg, gamma[j])
+       L=t(chol(Sigma))
+       theta=rep(mean_each_seg[i],nobs_per_seg)+L%*%rnorm(nobs_per_seg)
+       y_each_dim = c(y_each_dim, theta+0.1*rnorm(nobs_per_seg))
+     }
+     y_mat[,j] = y_each_dim
+   }
>   
>   ## Detect changepoints by SKFCPD
>   Online_CPD_1 = SKFCPD(design = x_mat,
+                         response = y_mat,
+                         train_prop = 1/3)
Starting a new changepoint detection model.
No missing values found in the response.
Starting the training process:
Use first 33.33333% observations for training.
Esimated parameters: 
gamma: 4.35689 4.21304 
eta: 0.01618 0.01088 
sigma_2: 0.42814 0.72252 
Fast changepoint detection algorithm completed. 
Estimated changepoints:  71 101 121 
>   
>   ## visulize the results
>   plot_SKFCPD(Online_CPD_1)
>   
>   #------------------------------------------------------------------------------
>   # Example: iterative fast online changepoint detection
>   #------------------------------------------------------------------------------
>   
>   # train/test split
>   train_index = 1:50
>   test_index = 51:150
>   
>   x_train = x_mat[train_index, , drop=FALSE]
>   y_train = y_mat[train_index, , drop=FALSE]
>   x_test = x_mat[test_index, , drop=FALSE]
>   y_test = y_mat[test_index, , drop=FALSE]
>   
>   # estimate the parameters
>   fast_model = Estimate_GP_params(x_train, y_train) 
>   
>   # detect changepoints sequentially
>   Online_CPD_2 = NULL
>   init_params = list(gamma = 1/fast_model@beta,
+                      eta = fast_model@eta,
+                      sigma_2 = fast_model@sigma_2)
>   for(i in 1:length(test_index)){
+     if(sum(is.na(y_test[i,]))==0){
+       Online_CPD_2 = SKFCPD(design = x_test[i, , drop=FALSE],
+                             response = y_test[i, , drop=FALSE],
+                             FCPD = Online_CPD_2,
+                             init_params = init_params)
+     }
+   }
Starting a new changepoint detection model.
No missing values found in the response.
Esimated parameters: 
gamma:  4.35689 4.21304 
eta:  0.01618 0.01088 
sigma_2:  0.42814 0.72252 
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("SKFCPD", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()

 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: gc()
 2: showConnections()
 3: cleanEx()
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE