* using log directory 'd:/RCompile/CRANincoming/R-devel/UCASpatial.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'UCASpatial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'UCASpatial' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Yin Xu <xuy@big.ac.cn>'

New submission

Non-FOSS package license (CC-BY-NC-ND 4.0)

Possibly misspelled words in DESCRIPTION:
  Deconvolute (16:14)
  Deconvolution (3:8)
  Transcriptomics (3:34)
  referne (16:97)
  scRNA (16:105)
  transcriptomics (16:38)

Suggests or Enhances not in mainstream repositories:
  COSG
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: 'COSG'
* 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 'UCASpatial' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  CC-BY-NC-ND 4.0
Standardizable: FALSE
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'NAMESPACE_all'
* 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
'::' or ':::' imports not declared from:
  'DropletUtils' 'cowplot' 'ggplot2' 'jpeg' 'matrixStats' 'png'
  'scatterpie' 'stringr' 'tibble' 'tidyr'
'library' or 'require' calls not declared from:
  'DropletUtils' 'Matrix' 'Metrics' 'NMF' 'RcppML' 'SPOTlight' 'Seurat'
  'cowplot' 'dplyr' 'edgeR' 'entropy' 'ggplot2' 'grid' 'imager' 'jpeg'
  'nnls' 'philentropy' 'png' 'purrr' 'reshape2' 'stringr' 'tibble'
  'tidyr'
'library' or 'require' calls in package code:
  'COSG' 'DropletUtils' 'Matrix' 'Metrics' 'NMF' 'RcppML' 'SPOTlight'
  'Seurat' 'cowplot' 'dplyr' 'edgeR' 'entropy' 'ggplot2' 'grid'
  'imager' 'jpeg' 'nnls' 'philentropy' 'png' 'purrr' 'reshape2'
  'stringr' 'tibble' 'tidyr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CalculateEntropy: no visible global function definition for 'Idents'
CalculateEntropy: no visible global function definition for
  'WhichCells'
CalculateEntropy: no visible global function definition for '%>%'
CalculateEntropy: no visible global function definition for 'group_by'
CalculateEntropy: no visible binding for global variable 'gene'
CalculateEntropy: no visible global function definition for 'mutate'
CalculateEntropy: no visible binding for global variable 'avg_logFC'
CalculateEntropy: no visible binding for global variable 'pre_weight'
CalculateEntropy: no visible global function definition for 'top_n'
CalculateEntropy: no visible binding for global variable 'p_val'
CalculateEntropy: no visible global function definition for
  'txtProgressBar'
CalculateEntropy: no visible global function definition for
  'setTxtProgressBar'
CalculateEntropy: no visible binding for global variable
  'entropy.adjust'
CalculateEntropy: no visible binding for global variable 'cluster'
CalculateEntropy: no visible binding for global variable 'weight'
UCASpatial_deconv: no visible global function definition for 'is'
UCASpatial_deconv: no visible global function definition for
  'DefaultAssay<-'
UCASpatial_deconv: no visible global function definition for 'Idents<-'
UCASpatial_deconv: no visible global function definition for '%>%'
UCASpatial_deconv: no visible global function definition for 'rename'
UCASpatial_deconv: no visible binding for global variable 'avg_log2FC'
UCASpatial_deconv: no visible binding for global variable 'cluster'
UCASpatial_deconv: no visible global function definition for 'cosg'
UCASpatial_deconv: no visible global function definition for 'group_by'
UCASpatial_deconv: no visible binding for global variable 'gene'
UCASpatial_deconv: no visible global function definition for 'filter'
UCASpatial_deconv: no visible binding for global variable 'weight'
UCASpatial_deconv: no visible global function definition for 'mutate'
UCASpatial_deconv: no visible binding for global variable 'ent_weight'
UCASpatial_deconv: no visible binding for global variable 'ent.adj'
UCASpatial_deconv: no visible binding for global variable 'cos_weight'
UCASpatial_deconvolution_nmf: no visible global function definition for
  'txtProgressBar'
UCASpatial_deconvolution_nmf: no visible global function definition for
  'setTxtProgressBar'
UCASpatial_downsample: no visible global function definition for
  'Idents<-'
UCASpatial_downsample : <anonymous>: no visible global function
  definition for 'WhichCells'
UCASpatial_downsample : <anonymous>: no visible global function
  definition for 'if_else'
UCASpatial_downsample : <anonymous> : <anonymous>: no visible global
  function definition for 'GetAssayData'
UCASpatial_downsample : <anonymous> : <anonymous>: no visible binding
  for global variable 'var'
cut_markers2: no visible global function definition for '%>%'
cut_markers2: no visible binding for global variable 'cluster'
cut_markers2: no visible binding for global variable 'weight'
cut_markers2: no visible binding for global variable 'gene'
dot_plot_profiles_fun: no visible global function definition for '%>%'
dot_plot_profiles_fun: no visible binding for global variable
  'clust_vr'
dot_plot_profiles_fun: no visible binding for global variable 'id'
dot_plot_profiles_fun: no visible binding for global variable 'weights'
dot_plot_profiles_fun: no visible global function definition for 'aes'
dot_plot_profiles_fun: no visible binding for global variable 'topics'
dot_plot_profiles_fun: no visible binding for global variable 'median'
dot_plot_profiles_fun: no visible binding for global variable '.'
dot_plot_profiles_fun: no visible binding for global variable 'Cell
  type'
dot_plot_profiles_fun: no visible binding for global variable 'value'
dot_plot_profiles_fun: no visible binding for global variable 'Topics'
init_nmf_matr: no visible global function definition for '%>%'
init_nmf_matr: no visible binding for global variable 'cluster'
init_nmf_matr: no visible binding for global variable 'weight'
init_nmf_matr: no visible global function definition for 'bind_rows'
meta_filter: no visible global function definition for 'DefaultAssay<-'
meta_filter: no visible global function definition for
  'FindVariableFeatures'
meta_filter: no visible global function definition for 'ScaleData'
meta_filter: no visible global function definition for 'RunPCA'
meta_filter: no visible global function definition for
  'VariableFeatures'
meta_filter: no visible global function definition for 'FindNeighbors'
meta_filter: no visible global function definition for 'FindClusters'
meta_filter: no visible global function definition for '%>%'
new_simulate: no visible global function definition for 'is'
new_simulate: no visible binding for global variable 'n.celltype'
new_simulate: no visible binding for global variable 'n.cell'
new_simulate: no visible global function definition for
  'txtProgressBar'
new_simulate : <anonymous>: no visible global function definition for
  '%>%'
new_simulate : <anonymous>: no visible global function definition for
  'mutate'
new_simulate : <anonymous>: no visible global function definition for
  'all_of'
new_simulate : <anonymous>: no visible binding for global variable
  'weight'
new_simulate : <anonymous>: no visible global function definition for
  'sym'
new_simulate : <anonymous>: no visible binding for global variable
  'sum_weights'
new_simulate : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
new_simulate: no visible global function definition for '%>%'
new_simulate: no visible binding for global variable '.'
predict_spatial_mixtures_nmf_weighted: no visible binding for global
  variable 'sd'
predict_spatial_mixtures_nmf_weighted: no visible global function
  definition for '%>%'
predict_spatial_mixtures_nmf_weighted: no visible global function
  definition for 'group_by'
predict_spatial_mixtures_nmf_weighted: no visible binding for global
  variable 'gene'
predict_spatial_mixtures_nmf_weighted: no visible binding for global
  variable 'weight'
prep_seobj_topic_fun: no visible global function definition for 'is'
seed_init_mtrx_nmf: no visible global function definition for '%>%'
seed_init_mtrx_nmf: no visible global function definition for
  'bind_rows'
spatial_scatterpie: no visible global function definition for 'is'
spatial_scatterpie: no visible global function definition for '%>%'
spatial_scatterpie: no visible binding for global variable '.'
spatial_scatterpie: no visible binding for global variable 'rsum'
spatial_scatterpie: no visible binding for global variable 'imagerow'
spatial_scatterpie: no visible binding for global variable 'imagecol'
spatial_scatterpie: no visible binding for global variable
  'imagecol_scaled'
spatial_scatterpie: no visible binding for global variable
  'imagerow_scaled'
spatial_scatterpie: no visible global function definition for
  'scale_fill_manual'
test_MultiIndex: no visible global function definition for 'JSD'
test_MultiIndex: no visible global function definition for 'quantile'
test_Pearson: no visible global function definition for 'cor'
test_Pearson_spotlevel: no visible global function definition for 'cor'
test_RMSE: no visible global function definition for 'rmse'
test_RMSE_spotlevel: no visible global function definition for 'rmse'
test_Spearman: no visible global function definition for 'cor'
test_Spearman_spotlevel: no visible global function definition for
  'cor'
topic_profile_per_cluster_nmf: no visible global function definition
  for 'is'
topic_profile_per_cluster_nmf: no visible global function definition
  for '%>%'
topic_profile_per_cluster_nmf: no visible binding for global variable
  'clust_vr'
topic_profile_per_cluster_nmf: no visible binding for global variable
  'median'
train_nsnmfmod: no visible binding for global variable 'sd'
Undefined global functions or variables:
  %>% . Cell type DefaultAssay<- FindClusters FindNeighbors
  FindVariableFeatures GetAssayData Idents Idents<- JSD RunPCA
  ScaleData Topics VariableFeatures WhichCells aes all_of avg_log2FC
  avg_logFC bind_rows clust_vr cluster cor cos_weight cosg ent.adj
  ent_weight entropy.adjust filter gene group_by id if_else imagecol
  imagecol_scaled imagerow imagerow_scaled is median mutate n.cell
  n.celltype p_val pre_weight quantile rename rmse rsum
  scale_fill_manual sd setTxtProgressBar sum_weights sym top_n topics
  txtProgressBar value var weight weights
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "cor", "filter", "median", "quantile", "sd", "var",
             "weights")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... 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 ... WARNING
Functions or methods with usage in Rd file 'hello.Rd' but not in code:
  'hello'

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'UCASpatial_deconv.Rd'
  'output_path' 'min.pct' 'logfc.threshold' 'min.diff.pct'
  'downsample_n' 'remove.RPL' 'remove.MT' 'cos.filter' 'cos.mu'
  'cos.n_genes_user' 'marker.slot' 'unit' 'random.seed' 'meta.filter'
  'nmf.tol' 'meta.assay' 'meta.ndims' 'meta.resolution' 'meta.purity'
  'ent.filter.threshold' 'cos.filter.threshold'
  'weight.filter.threshold'

Undocumented arguments in Rd file 'UCASpatial_deconvolution_nmf.Rd'
  'nmf_mod' 'cluster_markers' 'mixture_transcriptome' 'normalize'
  'reference_profiles' 'min_cont'

Undocumented arguments in Rd file 'new_simulate.Rd'
  'verbose'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in 'UCASpatial-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hello
> ### Title: Hello, World!
> ### Aliases: hello
> 
> ### ** Examples
> 
> hello()
Error in hello() : could not find function "hello"
Execution halted
* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 3 NOTEs