* using log directory ‘/srv/hornik/tmp/CRAN/SCdeconR.Rcheck’ * using R Under development (unstable) (2024-02-21 r85960) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * 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 ... [4s/5s] WARNING Maintainer: ‘Yuanhang Liu ’ 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 executable files ... 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 for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘SCdeconR’ can be installed ... [33s/33s] 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 ... [7s/7s] OK * checking whether the package can be loaded with stated dependencies ... [7s/7s] OK * checking whether the package can be unloaded cleanly ... [7s/7s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [7s/7s] 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 ... [11s/11s] NOTE Normalization: no visible global function definition for ‘DGEList’ Normalization: no visible global function definition for ‘calcNormFactors’ bulk_generator : : 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 ... [0s/0s] 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 Package unavailable to check Rd xrefs: ‘Linnorm’ 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 ... [6s/6s] 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/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 ... [0s/0s] NONE ‘Cell_type_deconvolution_and_differential_analysis.Rmd’ using ‘UTF-8’... [0s/0s] OK * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 8 NOTEs