* 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 ... WARNING
Maintainer: 'Yuanhang Liu <liu.yuanhang@mayo.edu>'

New submission

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

FOSS licence with BuildVignettes: false

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid URLs:
  URL: http://www.gsea-msigdb.org/gsea/downloads.jsp (moved to https://www.gsea-msigdb.org:443/gsea/downloads.jsp)
    From: inst/doc/Cell_type_deconvolution_and_differential_analysis.html
    Status: 301
    Message: Moved Permanently
  URL: https://cran.r-project.org/web/packages/FARDEEP/index.html
    From: man/scdecon.Rd
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/MASS/index.html
    From: man/scdecon.Rd
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/nnls/index.html
    From: man/scdecon.Rd
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  The canonical URL of the CRAN page for a package is 
    https://CRAN.R-project.org/package=pkgname
  For content that is 'Moved Permanently', please change http to https,
  add trailing slashes, or replace the old by the new URL.

The Title field should be in title case. Current version is:
'Deconvolution of bulk RNA-seq data using single-cell RNA-seq data as reference'
In title case that is:
'Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference'

Size of tarball: 33825729 bytes
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'dplyr', 'edgeR', 'foreach', 'ggplot2', 'glmGamPoi', 'Seurat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... NOTE
Found the following non-portable file paths:
  SCdeconR/inst/extdata/gsea/results/age_adjust/ranked_gene_list_na_pos_versus_na_neg_1680642129036.tsv
  SCdeconR/inst/extdata/gsea/results/age_unadjust/GLYCOSYLPHOSPHATIDYLINOSITOL_(GPI)-ANCHOR_BIOSYNTHESIS.html
  SCdeconR/inst/extdata/gsea/results/age_unadjust/GLYCOSYLPHOSPHATIDYLINOSITOL_(GPI)-ANCHOR_BIOSYNTHESIS.tsv
  SCdeconR/inst/extdata/gsea/results/age_unadjust/enplot_GLYCOSYLPHOSPHATIDYLINOSITOL_(GPI)-ANCHOR_BIOSYNTHESIS_1.png
  SCdeconR/inst/extdata/gsea/results/age_unadjust/ranked_gene_list_na_pos_versus_na_neg_1680642330325.tsv

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* 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 DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'LICENSE.md'
* 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 ... 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 ... [11s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'Seurat' 'dplyr' 'edgeR' 'foreach' 'ggplot2' 'glmGamPoi'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s] NOTE
Normalization: no visible global function definition for 'DGEList'
Normalization: no visible global function definition for
  'calcNormFactors'
bulk_generator : <anonymous>: no visible global function definition for
  '%>%'
bulk_generator: no visible global function definition for '%>%'
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 global function definition for
  'inner_join'
comparedeg_scatter: no visible global function definition for 'ggplot'
comparedeg_scatter: no visible global function definition for
  'geom_point'
comparedeg_scatter: no visible global function definition for 'aes'
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
  'theme_classic'
comparedeg_scatter: no visible global function definition for 'labs'
comparedeg_scatter: no visible global function definition for
  'scale_color_manual'
comparedeg_scatter: no visible global function definition for 'lims'
comparedeg_scatter: no visible global function definition for
  'geom_hline'
comparedeg_scatter: no visible global function definition for
  'geom_vline'
comparedeg_scatter: no visible global function definition for
  'geom_abline'
comparedeg_scatter: no visible global function definition for
  'ggplotly'
comparegsea_scatter: no visible global function definition for
  'inner_join'
comparegsea_scatter: no visible global function definition for 'ggplot'
comparegsea_scatter: no visible global function definition for
  'geom_point'
comparegsea_scatter: no visible global function definition for 'aes'
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
  'theme_classic'
comparegsea_scatter: no visible global function definition for 'labs'
comparegsea_scatter: no visible global function definition for
  'scale_color_manual'
comparegsea_scatter: no visible global function definition for 'lims'
comparegsea_scatter: no visible global function definition for
  'geom_hline'
comparegsea_scatter: no visible global function definition for
  'geom_vline'
comparegsea_scatter: no visible global function definition for
  'geom_abline'
comparegsea_scatter: no visible global function definition for
  'ggplotly'
compute_metrics: no visible global function definition for '%>%'
compute_metrics: no visible global function definition for 'group_by'
compute_metrics: no visible binding for global variable 'celltype'
compute_metrics: no visible binding for global variable 'mixture_samep'
compute_metrics: no visible global function definition for 'summarise'
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 global function definition for '%dopar%'
construct_ref: no visible global function definition for 'foreach'
construct_ref: no visible binding for global variable 'i'
construct_ref: no visible global function definition for
  'SelectIntegrationFeatures'
construct_ref: no visible global function definition for
  'PrepSCTIntegration'
construct_ref: no visible global function definition for
  'FindIntegrationAnchors'
construct_ref: no visible global function definition for
  'IntegrateData'
construct_ref: no visible global function definition for
  'VariableFeatures<-'
construct_ref: no visible global function definition for 'RunPCA'
construct_ref: no visible global function definition for
  'VariableFeatures'
construct_ref: no visible global function definition for 'RunTSNE'
construct_ref: no visible global function definition for 'RunUMAP'
construct_ref: no visible global function definition for
  'FindNeighbors'
construct_ref: no visible global function definition for 'FindClusters'
construct_ref: no visible global function definition for
  'PrepSCTFindMarkers'
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 global function definition for '%>%'
deseq2_fun: no visible global function definition for 'select'
deseq2_fun: no visible binding for global variable 'lfcSE'
deseq2_fun: no visible binding for global variable 'stat'
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 global function definition for 'mutate'
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 global function definition for 'DGEList'
edger_fun: no visible global function definition for 'calcNormFactors'
edger_fun: no visible global function definition for
  'estimateGLMRobustDisp'
edger_fun: no visible global function definition for 'glmQLFit'
edger_fun: no visible global function definition for 'glmQLFTest'
edger_fun: no visible global function definition for 'cpm'
edger_fun: no visible global function definition for '%>%'
edger_fun: no visible global function definition for 'select'
edger_fun: no visible binding for global variable 'logCPM'
edger_fun: no visible binding for global variable 'PValue'
edger_fun: no visible global function definition for 'rename_with'
edger_fun: no visible global function definition for 'mutate'
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_rwplot: no visible global function definition for
  'colorRampPalette'
gsea_sumplot: no visible global function definition for 'ggplot'
gsea_sumplot: no visible global function definition for 'aes'
gsea_sumplot: no visible binding for global variable 'NES'
gsea_sumplot: no visible binding for global variable 'NAME'
gsea_sumplot: no visible global function definition for 'geom_point'
gsea_sumplot: no visible binding for global variable 'SIZE'
gsea_sumplot: no visible global function definition for 'labs'
gsea_sumplot: no visible global function definition for
  'scale_color_gradientn'
gsea_sumplot: no visible global function definition for 'rainbow'
gsea_sumplot: no visible global function definition for 'geom_vline'
gsea_sumplot: no visible global function definition for 'theme'
gsea_sumplot: no visible global function definition for 'element_rect'
gsea_sumplot: no visible global function definition for 'element_line'
gsea_sumplot: no visible global function definition for 'element_blank'
gsea_sumplot: no visible global function definition for
  'scale_y_discrete'
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 global function definition for '%>%'
limma.pfun: no visible global function definition for 'select'
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 global function definition for 'rename_with'
limma.pfun: no visible global function definition for 'all_of'
limma.pfun: no visible global function definition for 'mutate'
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
  'calcNormFactors'
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 global function definition for '%>%'
limma_voom_fun: no visible global function definition for 'select'
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 global function definition for 'rename_with'
limma_voom_fun: no visible global function definition for 'all_of'
limma_voom_fun: no visible global function definition for 'mutate'
limma_voom_fun: no visible binding for global variable 'pval'
limma_voom_fun: no visible binding for global variable 'log2foldchange'
load_scdata: no visible global function definition for 'Read10X'
load_scdata: no visible global function definition for 'Read10X_h5'
load_scdata: no visible global function definition for
  'CreateSeuratObject'
load_scdata: no visible global function definition for
  'PercentageFeatureSet'
load_scdata: no visible global function definition for 'NormalizeData'
load_scdata: no visible global function definition for
  'CellCycleScoring'
load_scdata: no visible binding for global variable 'cc.genes'
load_scdata: no visible global function definition for 'SCTransform'
marker_strategies: no visible global function definition for '%>%'
marker_strategies: no visible binding for global variable 'log2FC'
marker_strategies: no visible global function definition for 'arrange'
marker_strategies: no visible binding for global variable 'CT'
marker_strategies: no visible global function definition for 'desc'
marker_strategies: no visible global function definition for 'group_by'
marker_strategies: no visible global function definition for 'top_n'
marker_strategies: no visible global function definition for 'n'
marker_strategies: no visible binding for global variable 'AveExpr'
markerfc: no visible global function definition for 'topTable'
markerfc: no visible global function definition for '%>%'
markerfc: no visible global function definition for 'arrange'
markerfc: no visible binding for global variable 'CT'
markerfc: no visible global function definition for 'desc'
markerfc: no visible binding for global variable 'log2FC'
prop_barplot: no visible global function definition for '%>%'
prop_barplot: no visible global function definition for 'mutate'
prop_barplot: no visible global function definition for 'group_by'
prop_barplot: no visible binding for global variable 'ct'
prop_barplot: no visible global function definition for 'summarise'
prop_barplot: no visible binding for global variable 'ct_prop'
prop_barplot: no visible global function definition for 'ggplot'
prop_barplot: no visible global function definition for 'geom_col'
prop_barplot: no visible global function definition for 'aes'
prop_barplot: no visible binding for global variable 'sampleid'
prop_barplot: no visible global function definition for 'theme_classic'
prop_barplot: no visible global function definition for 'labs'
prop_barplot: no visible global function definition for 'theme'
prop_barplot: no visible global function definition for 'element_text'
prop_barplot: no visible global function definition for 'element_blank'
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 'LogNormalize'
scaling: no visible global function definition for 'DGEList'
scaling: no visible global function definition for 'calcNormFactors'
scaling: no visible global function definition for 'cpm'
scaling: no visible global function definition for
  'DESeqDataSetFromMatrix'
scaling: no visible global function definition for '%>%'
scaling: no visible global function definition for 'rpkm'
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:
  %>% %dopar% . AveExpr CIBERSORT CT CellCycleScoring
  CreateSeuratObject DESeqDataSetFromMatrix DGEList FindClusters
  FindIntegrationAnchors FindNeighbors IntegrateData Linnorm
  LogNormalize NAME NES NES.x NES.y NormalizeData P.Value PValue
  PercentageFeatureSet PrepSCTFindMarkers PrepSCTIntegration Read10X
  Read10X_h5 Reference RunPCA RunTSNE RunUMAP SCDC_prop SCTransform
  SIZE SelectIntegrationFeatures SpatialRNA VariableFeatures
  VariableFeatures<- adj.P.Val aes all_of arrange baseMean
  calcNormFactors category cc.genes celltype colorRampPalette
  contrasts.fit cpm create.RCTD ct ct_prop desc eBayes element_blank
  element_line element_rect element_text estimateGLMRobustDisp
  expected_values fardeep fitBulk foreach genename geom_abline geom_col
  geom_hline geom_point geom_vline ggplot ggplotly glmQLFTest glmQLFit
  group_by gsearespath i inner_join labs lfcSE limma_fun lims lmFit
  log2FC log2FoldChange log2foldchange log2foldchange.x
  log2foldchange.y logCPM mixture mixture_samep music_prop mutate n
  nbinomWaldTest observed_values padj padj_method pval pvalue rainbow
  rename_with results rpkm sampleid scale_color_gradientn
  scale_color_manual scale_y_discrete select source_python stat
  summarise tape_deconvolution theme theme_classic topTable top_n
  varianceStabilizingTransformation voom vst
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
to your NAMESPACE file.

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 ... NOTE
Unknown packages 'spacexr', 'gamObject' in Rd xrefs
* 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 ... [11s] 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 running R code from vignettes ... NONE
  'Cell_type_deconvolution_and_differential_analysis.Rmd' using 'UTF-8'... OK
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 WARNING, 8 NOTEs