* using log directory 'd:/RCompile/CRANincoming/R-devel/SCdeconR.Rcheck'
* using R Under development (unstable) (2024-02-20 r85959 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'SCdeconR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SCdeconR' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Yuanhang Liu <liu.yuanhang@mayo.edu>'

New submission

Possibly misspelled words in DESCRIPTION:
  Deconvolution (3:8)
  deconvolution (7:40)

Size of tarball: 32141286 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'SCdeconR' 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [11s] 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 ... [10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s] OK
* checking loading without being on the library search path ... [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 ... [45s] NOTE
bulk_generator: no visible binding for global variable '.'
celltype_expression: no visible global function definition for
  'Reference'
celltype_expression: no visible global function definition for
  'SpatialRNA'
celltype_expression: no visible global function definition for
  'create.RCTD'
celltype_expression: no visible global function definition for
  'fitBulk'
comparedeg_scatter: no visible binding for global variable
  'log2foldchange.x'
comparedeg_scatter: no visible binding for global variable
  'log2foldchange.y'
comparedeg_scatter: no visible binding for global variable 'category'
comparedeg_scatter: no visible binding for global variable 'genename'
comparedeg_scatter: no visible global function definition for
  'ggplotly'
comparegsea_scatter: no visible binding for global variable 'NES.x'
comparegsea_scatter: no visible binding for global variable 'NES.y'
comparegsea_scatter: no visible binding for global variable 'category'
comparegsea_scatter: no visible binding for global variable 'NAME'
comparegsea_scatter: no visible global function definition for
  'ggplotly'
compute_metrics: no visible binding for global variable 'celltype'
compute_metrics: no visible binding for global variable 'mixture_samep'
compute_metrics: no visible binding for global variable
  'observed_values'
compute_metrics: no visible binding for global variable
  'expected_values'
compute_metrics: no visible binding for global variable 'mixture'
construct_ref: no visible binding for global variable 'i'
deconvolution: no visible global function definition for 'CIBERSORT'
deconvolution: no visible global function definition for 'fardeep'
deconvolution: no visible global function definition for 'music_prop'
deconvolution: no visible global function definition for 'SCDC_prop'
deconvolution: no visible global function definition for
  'source_python'
deconvolution: no visible global function definition for
  'tape_deconvolution'
deseq2_fun: no visible global function definition for
  'DESeqDataSetFromMatrix'
deseq2_fun: no visible global function definition for 'nbinomWaldTest'
deseq2_fun: no visible global function definition for 'results'
deseq2_fun: no visible binding for global variable 'lfcSE'
deseq2_fun: no visible binding for global variable 'padj'
deseq2_fun: no visible binding for global variable 'log2FoldChange'
deseq2_fun: no visible binding for global variable 'pvalue'
deseq2_fun: no visible binding for global variable 'baseMean'
deseq2_fun: no visible binding for global variable 'log2foldchange'
deseq2_fun: no visible binding for global variable 'pval'
edger_fun: no visible binding for global variable 'logCPM'
edger_fun: no visible binding for global variable 'PValue'
edger_fun: no visible binding for global variable 'pval'
edger_fun: no visible binding for global variable 'log2foldchange'
gsea_rwplot: no visible binding for global variable 'gsearespath'
gsea_sumplot: no visible binding for global variable 'NES'
gsea_sumplot: no visible binding for global variable 'NAME'
gsea_sumplot: no visible binding for global variable 'SIZE'
gsea_sumplot: no visible global function definition for 'ggplotly'
limma.pfun: no visible global function definition for 'lmFit'
limma.pfun: no visible global function definition for 'eBayes'
limma.pfun: no visible global function definition for 'topTable'
limma.pfun: no visible binding for global variable 'adj.P.Val'
limma.pfun: no visible binding for global variable 'P.Value'
limma.pfun: no visible binding for global variable 'AveExpr'
limma.pfun: no visible binding for global variable 'pval'
limma.pfun: no visible binding for global variable 'padj_method'
limma.pfun: no visible binding for global variable 'log2foldchange'
limma_voom_fun: no visible global function definition for 'voom'
limma_voom_fun: no visible global function definition for 'lmFit'
limma_voom_fun: no visible global function definition for 'eBayes'
limma_voom_fun: no visible global function definition for 'topTable'
limma_voom_fun: no visible binding for global variable 'adj.P.Val'
limma_voom_fun: no visible binding for global variable 'P.Value'
limma_voom_fun: no visible binding for global variable 'AveExpr'
limma_voom_fun: no visible binding for global variable 'pval'
limma_voom_fun: no visible binding for global variable 'log2foldchange'
load_scdata: no visible binding for global variable 'cc.genes'
marker_strategies: no visible binding for global variable 'log2FC'
marker_strategies: no visible binding for global variable 'CT'
marker_strategies: no visible binding for global variable 'AveExpr'
markerfc: no visible global function definition for 'topTable'
markerfc: no visible binding for global variable 'CT'
markerfc: no visible binding for global variable 'log2FC'
prop_barplot: no visible binding for global variable 'ct'
prop_barplot: no visible binding for global variable 'ct_prop'
prop_barplot: no visible binding for global variable 'sampleid'
prop_barplot: no visible global function definition for 'ggplotly'
run_de: no visible global function definition for 'limma_fun'
scaling: no visible global function definition for
  'DESeqDataSetFromMatrix'
scaling: no visible global function definition for 'vst'
scaling: no visible global function definition for 'Linnorm'
scdecon: no visible global function definition for 'voom'
scdecon: no visible global function definition for 'lmFit'
scdecon: no visible global function definition for 'contrasts.fit'
scdecon: no visible global function definition for 'eBayes'
transformation: no visible global function definition for
  'varianceStabilizingTransformation'
Undefined global functions or variables:
  . AveExpr CIBERSORT CT DESeqDataSetFromMatrix Linnorm NAME NES NES.x
  NES.y P.Value PValue Reference SCDC_prop SIZE SpatialRNA adj.P.Val
  baseMean category cc.genes celltype contrasts.fit create.RCTD ct
  ct_prop eBayes expected_values fardeep fitBulk genename ggplotly
  gsearespath i lfcSE limma_fun lmFit log2FC log2FoldChange
  log2foldchange log2foldchange.x log2foldchange.y logCPM mixture
  mixture_samep music_prop nbinomWaldTest observed_values padj
  padj_method pval pvalue results sampleid source_python
  tape_deconvolution topTable varianceStabilizingTransformation voom
  vst

Found the following calls to data() loading into the global environment:
File 'SCdeconR/R/helpers.R':
  data("ffpemodel")
File 'SCdeconR/R/reference_construction.R':
  data("cc.genes")
See section 'Good practice' in '?data'.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'construct_ref.Rd':
  \examples lines wider than 100 characters:
     phenodata_list <- c(paste0(system.file("extdata", package = "SCdeconR"), "/refdata/phenodata_sample1.txt"),
                         paste0(system.file("extdata", package = "SCdeconR"), "/refdata/phenodata_sample2.txt"))

Rd file 'load_scdata.Rd':
  \examples lines wider than 100 characters:
     phenodata_list <- c(paste0(system.file("extdata", package = "SCdeconR"), "/refdata/phenodata_sample1.txt"),
                         paste0(system.file("extdata", package = "SCdeconR"), "/refdata/phenodata_sample2.txt"))

These lines will be truncated in the PDF manual.
* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [15s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... NOTE
Package vignette without corresponding tangle output:
  'Cell_type_deconvolution_and_differential_analysis.Rmd'
* checking re-building of vignette outputs ... [357s] OK
* checking PDF version of manual ... [26s] OK
* checking HTML version of manual ... OK
* DONE
Status: 4 NOTEs