* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SVG.Rcheck’
* using R Under development (unstable) (2026-01-22 r89323)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1+b1)
    Debian flang version 21.1.8 (1+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘SVG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SVG’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] NOTE
Maintainer: ‘Zaoqu Liu <liuzaoqu@163.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  SVGs (11:74)
  Transcriptomics (4:9)
  Zhu (20:5)
  al (18:40, 19:14, 20:12, 21:14)
  binSpect (14:38)
  et (18:37, 19:11, 20:9, 21:11)
  nnSVG (15:53)
  transcriptomics (12:16)
  vectorization (17:13)
* 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 ‘SVG’ can be installed ... [13s/13s] OK
* used C compiler: ‘Debian clang version 21.1.8 (1+b1)’
* used C++ compiler: ‘Debian clang version 21.1.8 (1+b1)’
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking whether startup messages can be suppressed ... [0s/0s] 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 ... [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 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 ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] ERROR
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(SVG)
  SVG: Spatially Variable Genes Detection Methods
  Version: 1.0.0
  Author: Zaoqu Liu (liuzaoqu@163.com)
  GitHub: https://github.com/Zaoqu-Liu/SVG
  ---
  Available methods: MERINGUE, binSpect, SPARK-X, nnSVG
  Use CalSVG() for unified interface or CalSVG_*() for specific methods
  > 
  > test_check("SVG")
  Saving _problems/test-simulation-10.R
  Saving _problems/test-simulation-28.R
  Saving _problems/test-simulation-45.R
  Saving _problems/test-simulation-56.R
  Saving _problems/test-simulation-74.R
  Saving _problems/test-simulation-88.R
  Saving _problems/test-simulation-99.R
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 65 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-simulation.R:5:5'): simulate_spatial_data returns correct structure ──
  Error in `simulate_spatial_data(n_spots = 100, n_genes = 50, n_svg = 10, seed = 42)`: unused argument (seed = 42)
  ── Error ('test-simulation.R:23:5'): simulate_spatial_data returns correct dimensions ──
  Error in `simulate_spatial_data(n_spots = n_spots, n_genes = n_genes, n_svg = 10, seed = 42)`: unused argument (seed = 42)
  ── Error ('test-simulation.R:40:5'): simulate_spatial_data creates correct number of SVGs ──
  Error in `simulate_spatial_data(n_spots = 100, n_genes = 50, n_svg = n_svg, seed = 42)`: unused argument (seed = 42)
  ── Error ('test-simulation.R:51:5'): simulate_spatial_data generates valid counts ──
  Error in `simulate_spatial_data(n_spots = 100, n_genes = 50, n_svg = 10, seed = 42)`: unused argument (seed = 42)
  ── Error ('test-simulation.R:68:9'): different grid types work correctly ───────
  Error in `simulate_spatial_data(n_spots = 50, n_genes = 20, n_svg = 5, grid_type = grid, seed = 42)`: unused argument (seed = 42)
  ── Error ('test-simulation.R:82:5'): different pattern types are assigned correctly ──
  Error in `simulate_spatial_data(n_spots = 100, n_genes = 50, n_svg = 20, pattern_types = c("gradient", "hotspot", "periodic", "cluster"), seed = 42)`: unused argument (seed = 42)
  ── Error ('test-simulation.R:99:5'): reproducibility with same seed ────────────
  Error in `simulate_spatial_data(n_spots = 50, n_genes = 20, n_svg = 5, seed = 123)`: unused argument (seed = 123)
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 65 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [6s/6s] OK
* checking PDF version of manual ... [5s/5s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character μ (U+03BC)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character φ (U+03C6)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘SVG-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 2 NOTEs