* using log directory 'd:/RCompile/CRANincoming/R-devel/LinkageR.Rcheck' * using R Under development (unstable) (2024-06-06 r86701 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 'LinkageR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'LinkageR' version '1.2.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [42s] NOTE Maintainer: 'Siwen Xu' New submission Possibly misspelled words in DESCRIPTION: ATAC (3:36, 12:167) CREs (12:152, 12:251, 12:283, 12:435) omics (12:313) Package has a FOSS license but eventually depends on the following package which restricts use: CNEr The Title field should be in title case. Current version is: 'An R package for linking of ATAC-seq to gene expression data' In title case that is: 'An R Package for Linking of ATAC-Seq to Gene Expression Data' The Description field should not start with the package name, 'This package' or similar. Size of tarball: 14626066 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 whether package 'LinkageR' 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 ... NOTE Maintainer field differs from that derived from Authors@R Maintainer: 'Siwen Xu' Authors@R: 'Zenghui Liu <2470587020@qq.com>' * checking top-level files ... OK * 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 ... [23s] OK * checking whether the package can be loaded with stated dependencies ... [21s] OK * checking whether the package can be unloaded cleanly ... [20s] OK * checking whether the namespace can be loaded with stated dependencies ... [21s] OK * checking whether the namespace can be unloaded cleanly ... [22s] OK * checking loading without being on the library search path ... [24s] OK * checking whether startup messages can be suppressed ... [21s] 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 ... [96s] NOTE AnnoUpsetPlot: no visible binding for global variable 'annotation' AnnoUpsetPlot: no visible binding for global variable 'GenreMember' BuildGRNs: no visible binding for global variable 'Mus.PFMatrixList' BuildGRNs: no visible binding for global variable 'Mus.pwm_library_dt' BuildGRNs: no visible global function definition for 'cor.test' BuildGRNs: no visible global function definition for 'p.adjust' BuildGRNs: no visible global function definition for 'new' CombinePlots : : no visible global function definition for 'NoLegend' CorrPlot: no visible binding for global variable 'peak' CreateLinkageObject: no visible global function definition for 'data' CreateLinkageObject: no visible binding for global variable 'Homo.position' CreateLinkageObject: no visible binding for global variable 'Mus.position' CreateLinkageObject: no visible global function definition for 'everything' CreateLinkageObject: no visible global function definition for 'new' EnrichWordCloud: no visible global function definition for 'read.table' FilterGRNs: no visible global function definition for 'new' GOEnrichment: no visible binding for global variable 'Homo.position' GOEnrichment: no visible binding for global variable 'Mus.position' KEGGEnrichment: no visible binding for global variable 'Homo.position' KEGGEnrichment: no visible binding for global variable 'Mus.position' Linkage.UIO: no visible binding for global variable 'name' MotifEnrichment: no visible global function definition for 'data' MotifEnrichment: no visible binding for global variable 'Mus.PFMatrixList' MotifEnrichment: no visible binding for global variable 'Mus.pwm_library_dt' PeakAnnotation: no visible global function definition for 'new' RegulatoryPeak: no visible global function definition for 'cor.test' RegulatoryPeak: no visible global function definition for 'p.adjust' RegulatoryPeak: no visible global function definition for 'new' TrackPlot: no visible binding for global variable 'gene' TrackPlot: no visible binding for global variable 'group' VisualGRNs: no visible global function definition for 'na.omit' VisualGRNs: no visible binding for global variable 'gene' VisualGRNs: no visible binding for global variable 'TF' VisualGRNs: no visible binding for global variable 'id' VisualGRNs: no visible global function definition for 'everything' VisualGRNs: no visible binding for global variable 'a' show,LinkageObject: no visible binding for global variable 'LinkageObject' Undefined global functions or variables: GenreMember Homo.position LinkageObject Mus.PFMatrixList Mus.position Mus.pwm_library_dt NoLegend TF a annotation cor.test data everything gene group id na.omit name new p.adjust peak read.table Consider adding importFrom("methods", "new") importFrom("stats", "cor.test", "na.omit", "p.adjust") importFrom("utils", "data", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). Found the following calls to data() loading into the global environment: File 'LinkageR/R/CreateLinkageObject.R': data("Homo.position") data("Mus.position") File 'LinkageR/R/MotifAnalysis.R': data("PFMatrixList") data("pwm_library_dt") data("Mus.PFMatrixList") data("Mus.pwm_library_dt") See section 'Good practice' in '?data'. Found if() conditions comparing class() to string: File 'LinkageR/R/RegulatoryPeaks.R': if (class(LinkageObject) != "LinkageObject") ... Use inherits() (or maybe is()) instead. * 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 ... 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 ... [17s] 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 ... [15m] NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed EnrichBarPlot 65.01 11.38 80.31 EnrichUpsetPlot 65.86 8.42 74.14 EnrichWordCloud 64.55 7.96 73.31 EnrichDotPlot 63.11 8.83 75.20 GOEnrichment 64.00 7.55 71.46 EnrichCnetPlot 62.70 8.08 71.50 VisualGRNs 69.86 0.89 70.78 FilterGRNs 67.96 0.64 68.75 AnnoUpsetPlot 63.67 4.87 71.68 BuildGRNs 65.81 0.61 67.21 PeakAnnotation 57.30 4.50 61.52 MotifEnrichment 23.44 0.97 24.42 CorrPlot 1.66 19.38 33.62 TrackPlot 10.36 0.36 17.65 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [322s] OK * checking PDF version of manual ... [28s] OK * checking HTML version of manual ... OK * DONE Status: 4 NOTEs