* using log directory ‘/srv/hornik/tmp/CRAN/BioEnricher.Rcheck’ * using R Under development (unstable) (2023-12-02 r85657) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.5 (1) Debian flang-new version 17.0.5 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘BioEnricher/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioEnricher’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Zaoqu Liu ’ New submission Possibly misspelled words in DESCRIPTION: BioEnricher (8:38) CMAP (11:52) CellMarker (11:36) DisGeNET (11:26) KEGG (10:33) MsigDB (10:63) PROGENy (12:31) PubMed (13:5) Reactome (10:53) WikiPathways (10:39) bioinformatic (3:49) Package has a FOSS license but eventually depends on the following package which may restrict use: viper The Title field should be in title case. Current version is: ‘Integrate analysis and visualization for bioinformatic enrichment analyzer’ In title case that is: ‘Integrate Analysis and Visualization for Bioinformatic Enrichment Analyzer’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... NOTE Subdirectory ‘BioEnricher’ seems to contain an installed version of the package. * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BioEnricher’ can be installed ... [31s/31s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘BioEnricher’ ‘docs’ ‘test.R’ * 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 ... [10s/10s] OK * checking whether the package can be loaded with stated dependencies ... [9s/9s] OK * checking whether the package can be unloaded cleanly ... [9s/9s] OK * checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK * checking whether the namespace can be unloaded cleanly ... [10s/10s] OK * checking loading without being on the library search path ... [10s/10s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘RColorBrewer’ ‘RCurl’ ‘XML’ ‘cowplot’ ‘fst’ ‘ggrepel’ ‘paletteer’ ‘showtext’ ‘stringi’ ‘tibble’ ‘tidyr’ ‘viridis’ ‘xml2’ 'library' or 'require' call not declared from: ‘pathview’ 'library' or 'require' call to ‘pathview’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing or unexported object: ‘enrichplot::gsInfo’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [41s/41s] NOTE gene.info : ensOrg_name_data: no visible binding for global variable ‘.genekitrEnv’ gene.info : mapEnsOrg: no visible binding for global variable ‘ensOrg_name’ gene.info : mapEnsOrg: no visible binding for global variable ‘.genekitrEnv’ gene.info : mapEnsOrg: no visible binding for global variable ‘.’ gene.info : mapEnsOrg: no visible binding for global variable ‘latin_short_name’ gene.info: no visible binding for global variable ‘.’ lzq_GSEA: no visible binding for global variable ‘cellName’ lzq_GSEA: no visible binding for global variable ‘gs_name’ lzq_GSEA: no visible binding for global variable ‘entrez_gene’ lzq_GSEA: no visible binding for global variable ‘CMAPfromDSEATM’ lzq_GSEA.barplot1: no visible binding for global variable ‘cols_brown_green’ lzq_GSEA.barplot1: no visible binding for global variable ‘pvalue’ lzq_GSEA.barplot1: no visible binding for global variable ‘NES’ lzq_GSEA.barplot1: no visible binding for global variable ‘sig’ lzq_GSEA.barplot1: no visible binding for global variable ‘p.adjust’ lzq_GSEA.barplot1: no visible binding for global variable ‘Description’ lzq_GSEA.barplot2: no visible binding for global variable ‘pvalue’ lzq_GSEA.barplot2: no visible binding for global variable ‘NES’ lzq_GSEA.barplot2: no visible binding for global variable ‘p.adjust’ lzq_GSEA.barplot2: no visible binding for global variable ‘Description’ lzq_GSEA.barplot2: no visible binding for global variable ‘Type’ lzq_GSEA.dotplot1: no visible binding for global variable ‘cols_brown_green’ lzq_GSEA.dotplot1: no visible binding for global variable ‘pvalue’ lzq_GSEA.dotplot1: no visible binding for global variable ‘NES’ lzq_GSEA.dotplot1: no visible binding for global variable ‘sig’ lzq_GSEA.dotplot1: no visible binding for global variable ‘p.adjust’ lzq_GSEA.dotplot1: no visible binding for global variable ‘Description’ lzq_GSEA.integrated: no visible binding for global variable ‘cellName’ lzq_GSEA.integrated: no visible binding for global variable ‘gs_name’ lzq_GSEA.integrated: no visible binding for global variable ‘entrez_gene’ lzq_GSEA.integrated: no visible binding for global variable ‘CMAPfromDSEATM’ lzq_ORA: no visible binding for global variable ‘cellName’ lzq_ORA: no visible binding for global variable ‘gs_name’ lzq_ORA: no visible binding for global variable ‘entrez_gene’ lzq_ORA: no visible binding for global variable ‘CMAPfromDSEATM’ lzq_ORA.barplot1: no visible binding for global variable ‘cols_brown_green’ lzq_ORA.barplot1: no visible binding for global variable ‘pvalue’ lzq_ORA.barplot1: no visible binding for global variable ‘.’ lzq_ORA.barplot1: no visible binding for global variable ‘Description’ lzq_ORA.barplot2: no visible binding for global variable ‘pvalue’ lzq_ORA.barplot2: no visible binding for global variable ‘p.adjust’ lzq_ORA.barplot2: no visible binding for global variable ‘Description’ lzq_ORA.barplot2: no visible binding for global variable ‘Type’ lzq_ORA.barplot2: no visible binding for global variable ‘log10P’ lzq_ORA.dotplot1: no visible binding for global variable ‘cols_brown_green’ lzq_ORA.dotplot1: no visible binding for global variable ‘pvalue’ lzq_ORA.dotplot1: no visible binding for global variable ‘.’ lzq_ORA.dotplot1: no visible binding for global variable ‘Description’ lzq_ORA.integrated: no visible binding for global variable ‘cellName’ lzq_ORA.integrated: no visible binding for global variable ‘gs_name’ lzq_ORA.integrated: no visible binding for global variable ‘entrez_gene’ lzq_ORA.integrated: no visible binding for global variable ‘CMAPfromDSEATM’ lzq_gseaplot: no visible binding for global variable ‘x’ lzq_gseaplot: no visible binding for global variable ‘runningScore’ lzq_gseaplot: no visible binding for global variable ‘ymax’ lzq_gseaplot: no visible binding for global variable ‘geneList’ lzq_progeny.dea : : no visible binding for global variable ‘term’ lzq_progeny.dea: no visible binding for global variable ‘.’ lzq_progeny.dea: no visible binding for global variable ‘pathways’ lzq_progeny.dea: no visible binding for global variable ‘statistic’ lzq_progeny.dea: no visible binding for global variable ‘p.value’ lzq_progeny.gene.details: no visible binding for global variable ‘p.value’ lzq_progeny.gene.details: no visible binding for global variable ‘weight’ lzq_progeny.gene.details: no visible binding for global variable ‘color’ lzq_progeny.gene.details: no visible binding for global variable ‘Gene2’ lzq_updateSymbol: no visible binding for global variable ‘Approved’ lzq_updateSymbol : : no visible binding for global variable ‘ID’ lzq_updateSymbol : : no visible binding for global variable ‘Symbol’ lzq_updateSymbol : : no visible binding for global variable ‘.’ lzq_updateSymbol: no visible binding for global variable ‘.’ lzq_updateSymbol: no visible binding for global variable ‘ID’ lzq_updateSymbol: no visible binding for global variable ‘Symbol’ lzq_updateSymbolforDL: no visible binding for global variable ‘Approved’ lzq_updateSymbolforDL : : no visible binding for global variable ‘ID’ lzq_updateSymbolforDL : : no visible binding for global variable ‘Symbol’ lzq_updateSymbolforDL : : no visible binding for global variable ‘.’ lzq_updateSymbolforDL: no visible binding for global variable ‘.’ lzq_updateSymbolforDL: no visible binding for global variable ‘ID’ lzq_updateSymbolforDL: no visible binding for global variable ‘Symbol’ Undefined global functions or variables: . .genekitrEnv Approved CMAPfromDSEATM Description Gene2 ID NES Symbol Type cellName color cols_brown_green ensOrg_name entrez_gene geneList gs_name latin_short_name log10P p.adjust p.value pathways pvalue runningScore sig statistic term weight x ymax Consider adding importFrom("stats", "p.adjust") to your NAMESPACE file. * checking Rd files ... [0s/0s] 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 ... 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 ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [12s/12s] OK * checking PDF version of manual ... [4s/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, 4 NOTEs