* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck’
* using R Under development (unstable) (2024-09-06 r87103)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘CAESAR.Suite/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAESAR.Suite’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Xiao Zhang <zhangxiao1994@cuhk.edu.cn>’

New submission

Possibly misspelled words in DESCRIPTION:
  Omics (4:17)
  omics (14:30, 14:174, 14:644)
  scRNA (14:324, 14:588)

Size of tarball: 83434823 bytes
* 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 ‘CAESAR.Suite’ can be installed ... [59s/59s] OK
* used C++ compiler: ‘Debian clang version 18.1.8 (9)’
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘docs’ ‘vignettes_data’
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [42s/42s] 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 ... [2s/2s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [50s/49s] ERROR
Running examples in ‘CAESAR.Suite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cellembedding_matrix
> ### Title: Compute Spatial-Aware Cell Embeddings
> ### Aliases: cellembedding_matrix
> 
> ### ** Examples
> 
> data(toydata)
> 
> seu <- toydata$seu[, 1:1000]
> pos <- toydata$pos[1:1000, ]
> 
> adjm <- ProFAST::AddAdj(as.matrix(pos))
The spatial cooridnates are 2 dimensions
Error in getAdj_auto(pos, lower.med = neighbors - 2, upper.med = neighbors +  : 
  The radius.upper is too smaller that cannot find median neighbors greater than 4.
Calls: <Anonymous> -> getAdj_auto
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
CAESAR.CTDEP 5.513  0.599   5.977
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [191s/160s] OK
* 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, 2 NOTEs