* using log directory ‘/home/hornik/tmp/CRAN_special_donttest/funMoDisco.Rcheck’
* using R Under development (unstable) (2025-11-05 r88988)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (Debian 15.2.0-4) 15.2.0
    GNU Fortran (Debian 15.2.0-4) 15.2.0
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* using option ‘--run-donttest’
* checking for file ‘funMoDisco/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘funMoDisco’ version ‘1.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [8s/8s] OK
* 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 ‘funMoDisco’ can be installed ... [160s/162s] OK
* used C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’
* checking C++ specification ... OK
  Not all R platforms support C++20
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [4s/4s] 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 ... [28s/28s] OK
* checking Rd files ... [1s/1s] 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 ... [1s/1s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/10s] ERROR
Running examples in ‘funMoDisco-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: discoverMotifs
> ### Title: Functional Motif Discovery
> ### Aliases: discoverMotifs
> 
> ### ** Examples
> 
> ## No test: 
> # Example 1: Discover motifs using ProbKMA
> 
> # Define dissimilarity measure and weight parameter
> diss <- 'd0_d1_L2'
> alpha <- 0.5
> 
> # Define number of motifs and their minimum lengths
> K <- c(2, 3)
> c <- c(61, 51)
> n_init <- 3
> 
> # Load simulated data
> data("simulated200")
> 
> # Perform motif discovery using ProbKMA
> tmp_path <- tempdir()  
> 
> results <- funMoDisco::discoverMotifs(
+   Y0 = simulated200$Y0,
+   method = "ProbKMA",
+   stopCriterion = "max",
+   name = tempdir(),
+   plot = FALSE,
+   probKMA_options = list(
+     Y1 = simulated200$Y1,
+     K = K,
+     c = c,
+     n_init = n_init,
+     diss = diss,
+     alpha = alpha
+   ),
+   worker_number = 1
+ )
K 2 _c 61 _random 1 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in dir.create(paste0(name, "K", K, "_c", c), showWarnings = TRUE,  :
  '/home/hornik/tmp/scratch/RtmpnBf4FR/working_dir/RtmpXYQIwe/K2_c61' already exists
K 2 _c 61 _random 2 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
Warning in dir.create(paste0(name, "K", K, "_c", c), showWarnings = TRUE,  :
  '/home/hornik/tmp/scratch/RtmpnBf4FR/working_dir/RtmpXYQIwe/K2_c61' already exists
K 2 _c 61 _random 3 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
K 2 _c 51 _random 1 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
Warning in dir.create(paste0(name, "K", K, "_c", c), showWarnings = TRUE,  :
  '/home/hornik/tmp/scratch/RtmpnBf4FR/working_dir/RtmpXYQIwe/K2_c51' already exists
K 2 _c 51 _random 2 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
Warning in dir.create(paste0(name, "K", K, "_c", c), showWarnings = TRUE,  :
  '/home/hornik/tmp/scratch/RtmpnBf4FR/working_dir/RtmpXYQIwe/K2_c51' already exists
K 2 _c 51 _random 3 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
K 3 _c 61 _random 1 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
Warning in dir.create(paste0(name, "K", K, "_c", c), showWarnings = TRUE,  :
  '/home/hornik/tmp/scratch/RtmpnBf4FR/working_dir/RtmpXYQIwe/K3_c61' already exists
K 3 _c 61 _random 2 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
Warning in dir.create(paste0(name, "K", K, "_c", c), showWarnings = TRUE,  :
  '/home/hornik/tmp/scratch/RtmpnBf4FR/working_dir/RtmpXYQIwe/K3_c61' already exists
K 3 _c 61 _random 3 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
K 3 _c 51 _random 1 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
Warning in dir.create(paste0(name, "K", K, "_c", c), showWarnings = TRUE,  :
  '/home/hornik/tmp/scratch/RtmpnBf4FR/working_dir/RtmpXYQIwe/K3_c51' already exists
K 3 _c 51 _random 2 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
Warning in dir.create(paste0(name, "K", K, "_c", c), showWarnings = TRUE,  :
  '/home/hornik/tmp/scratch/RtmpnBf4FR/working_dir/RtmpXYQIwe/K3_c51' already exists
K 3 _c 51 _random 3 running
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Membership matrix dimensions not valid. Choosing random initial membership matrix.
Warning in initialChecks(Y0, Y1, P0, S0, params, diss, V_init) :
  Shift warping matrix dimensions not valid. Choosing random initial shift warping matrix.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
> 
> # Example 2: Discover motifs using funBIalign
> results_funbialign <- funMoDisco::discoverMotifs(
+   Y0 = simulated200$Y0,
+   method = "funBIalign",
+   stopCriterion = "fMSR",
+   name = tempdir(),
+   plot = FALSE,
+   funBIalign_options = list(
+     portion_len = 60,
+     min_card = 3,
+     cut_off = 1.0
+   ),
+   worker_number = 1
+   ) 
Error: Package 'RcppArmadillo' referenced from LinkingTo directive is not available.
Warning in par(oldpar) : calling par(new=TRUE) with no plot
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [4s/4s] OK
  Running ‘tinytest.R’ [4s/4s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [7s/7s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR