* using log directory ‘/srv/hornik/tmp/CRAN_pretest/GeneralizedUmatrixGPU.Rcheck’
* using R Under development (unstable) (2025-09-27 r88882)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘GeneralizedUmatrixGPU/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneralizedUmatrixGPU’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] NOTE
Maintainer: ‘Quirin Stier <Quirin_Stier@gmx.de>’

New submission

Possibly misspelled words in DESCRIPTION:
  Thrun (8:358, 8:482, 8:660)
  Umatrix (8:547)
  coercively (8:346)
* 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 serialization versions ... OK
* checking whether package ‘GeneralizedUmatrixGPU’ can be installed ... [9s/9s] WARNING
Found the following significant warnings:
  trainSESOM.cpp:171:6: warning: variable 'err' is uninitialized when used here [-Wuninitialized]
See ‘/srv/hornik/tmp/CRAN_pretest/GeneralizedUmatrixGPU.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 19.1.7 (3+b2)’
* 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 ... [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
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* checking R code for possible problems ... [5s/5s] 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... NOTE
Found the following Makefile(s) without a final LF:
  src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
* 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 ... [4s/4s] ERROR
Running examples in ‘GeneralizedUmatrixGPU-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GeneralizedUmatrixGPU
> ### Title: Generalized U-Matrix on GPU for Projection Methods published in
> ###   [Thrun/Ultsch, 2020]
> ### Aliases: GeneralizedUmatrixGPU getUmatrix4Projection
> ### Keywords: visualization U-Matrix Umatrix GeneralizedUmatrixGPU
> ###   GeneralizedUmatrix
> 
> ### ** Examples
> 
> library(GeneralizedUmatrix)
> data("Chainlink")
> Data=Chainlink$Data
> Cls=Chainlink$Cls
> InputDistances=as.matrix(dist(Data))
> res=cmdscale(d=InputDistances, k = 2, eig = TRUE, add = FALSE, x.ret = FALSE)
> ProjectedPoints=as.matrix(res$points)
> ## Not run: 
> ##D Stress = ProjectionBasedClustering::KruskalStress(InputDistances,
> ##D as.matrix(dist(ProjectedPoints)))
> ## End(Not run)
> ## Don't show: 
> resUmatrix=GeneralizedUmatrixGPU(Data[1:2,], ProjectedPoints[1:2,])
Loading required namespace: mgcv

 *** caught segfault ***
address 0x10, cause 'memory not mapped'

Traceback:
 1: trainSESOM(Data, BMUs, RadiusVector, N = dim(Data)[1], DIM = dim(Data)[2],     MinData, MaxData, Lines = k, Columns = m, Weights = d, toroid = toroid,     NumDataPerEpoch = NumDataPerEpoch)
 2: GeneralizedUmatrixGPU(Data[1:2, ], ProjectedPoints[1:2, ])
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs