* using log directory 'd:/RCompile/CRANincoming/R-devel/SingleCellComplexHeatMap.Rcheck'
* using R Under development (unstable) (2025-06-16 r88324 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'SingleCellComplexHeatMap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SingleCellComplexHeatMap' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'XueCheng <xuecheng328@gmail.com>'

New submission

License components with restrictions and base license permitting such:
  MIT + file LICENSE
File 'LICENSE':
  MIT License
  
  Copyright (c) 2024 XueCheng
  
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:
  
  The above copyright notice and this permission notice shall be included in all
  copies or substantial portions of the Software.
  
  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  SOFTWARE.
  
  YEAR: 2024
  COPYRIGHT HOLDER: XueCheng

Possibly misspelled words in DESCRIPTION:
  ComplexHeatmap (11:34)

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(family = "XueCheng",
                    role = c("aut", "cre"),
                    email = "xuecheng328@gmail.com")
as necessary.

Found the following (possibly) invalid URLs:
  URL: https://github.com/xuecheng328/SingleCellComplexHeatMap
    From: DESCRIPTION
    Status: 404
    Message: Not Found
  URL: https://github.com/xuecheng328/SingleCellComplexHeatMap/issues
    From: DESCRIPTION
          inst/doc/SingleCellComplexHeatMap.html
    Status: 404
    Message: Not Found
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SingleCellComplexHeatMap' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  'Test.ipynb' 'project_folder.tar.gz'
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: 'png'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [27s] NOTE
create_cell_annotations: no visible global function definition for
  '%>%'
create_cell_annotations: no visible binding for global variable
  'TimePoint'
create_cell_annotations: no visible binding for global variable
  'CellType'
create_cell_annotations: no visible global function definition for
  'setNames'
create_gene_annotations: no visible global function definition for
  '%>%'
create_gene_annotations: no visible binding for global variable
  'GeneGroup'
create_gene_annotations: no visible binding for global variable 'Gene'
create_gene_annotations: no visible global function definition for
  'setNames'
create_single_cell_complex_heatmap: no visible global function
  definition for 'png'
create_single_cell_complex_heatmap: no visible global function
  definition for 'dev.off'
prepare_expression_matrices: no visible global function definition for
  '%>%'
prepare_expression_matrices: no visible binding for global variable
  'pct.exp'
prepare_expression_matrices: no visible binding for global variable
  'avg.exp'
prepare_expression_matrices: no visible binding for global variable
  'id'
prepare_expression_matrices: no visible binding for global variable
  'avg.exp.scaled'
Undefined global functions or variables:
  %>% CellType Gene GeneGroup TimePoint avg.exp avg.exp.scaled dev.off
  id pct.exp png setNames
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("stats", "setNames")
to your NAMESPACE file.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'create_cell_annotations' 'create_gene_annotations'
  'create_single_cell_complex_heatmap' 'prepare_expression_matrices'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library(testthat)
  > library(SingleCellComplexHeatMap)
  > 
  > test_check("SingleCellComplexHeatMap")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 1 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • Requires mock Seurat object for testing (2):
    'test-prepare_expression_matrices.R:6:3',
    'test-prepare_expression_matrices.R:17:3'
  • empty test (2): 'test-main-functions.R:15:1', 'test-main-functions.R:22:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-main-functions.R:9:3'): create_single_cell_complex_heatmap handles invalid inputs ──
  `create_single_cell_complex_heatmap(mock_seurat, character(0))` threw an error with unexpected message.
  Expected match: "features must be a non-empty character vector"
  Actual message: "object 'mock_seurat' not found"
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test-main-functions.R:9:3
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─SingleCellComplexHeatMap::create_single_cell_complex_heatmap(...)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 1 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'data(package=)' call not declared from: 'SeuratObject'
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 5 NOTEs