* using log directory ‘/srv/hornik/tmp/CRAN_pretest/proRate.Rcheck’ * using R Under development (unstable) (2025-06-17 r88325) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘proRate/DESCRIPTION’ ... OK * this is package ‘proRate’ version ‘0.99.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Yu Liu ’ New submission Possibly misspelled words in DESCRIPTION: Gro (20:50) LSS (27:24, 28:62) metagene (30:58) polyadenylation (17:47) polymerase (19:36) proRate (2:8, 26:16, 29:41) transcriptional (16:30) The Title field starts with the package name. * 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 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 ‘proRate’ can be installed ... [3s/3s] 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [8s/8s] NOTE addtrack: no visible binding for global variable ‘xcoord’ addtrack: no visible binding for global variable ‘reads’ calpauseidx: no visible binding for global variable ‘datalist’ calrate: no visible binding for global variable ‘significance’ calrate: no visible binding for global variable ‘gene_id’ calsig: no visible binding for global variable ‘binres’ calsig: no visible binding for global variable ‘distance’ combinesingle: no visible binding for global variable ‘TSSsinglefwdFPMs’ combinesingle: no visible binding for global variable ‘TTSsinglefwdFPMs’ combinesingle: no visible binding for global variable ‘GeneBodysinglefwdFPMs’ compressgblength: no visible binding for global variable ‘gbfwdcount’ convertartifical: no visible binding for global variable ‘subreads1’ convertartifical: no visible binding for global variable ‘subreads2’ countregion: no visible binding for global variable ‘tssfwdcount’ countregion: no visible binding for global variable ‘maxtssradius’ countregion: no visible binding for global variable ‘depth’ expandratio: no visible binding for global variable ‘binres’ expandratio: no visible binding for global variable ‘startcoord’ expandratio: no visible binding for global variable ‘endcoord’ extendgblength: no visible binding for global variable ‘gbfwdcount’ extractfeature: no visible binding for global variable ‘genes1’ geneexonfreq: no visible binding for global variable ‘genes’ genegccont: no visible binding for global variable ‘genes’ geneintervalscreen: no visible binding for global variable ‘genes’ getexon: no visible binding for global variable ‘gene_id’ getfpkm: no visible binding for global variable ‘genes’ getfpkm: no visible binding for global variable ‘reads1’ getfpkm: no visible binding for global variable ‘reads1depth’ getgc: no visible binding for global variable ‘gene_id’ getkmer: no visible binding for global variable ‘gene_id’ getreadslist: no visible binding for global variable ‘time1files’ getreadslist: no visible binding for global variable ‘mergerefs’ getreadslist: no visible binding for global variable ‘strandmethod’ intracompare: no visible binding for global variable ‘significance’ intracompare: no visible binding for global variable ‘gene_id’ limmacomp: no visible binding for global variable ‘dat1’ limmacomp: no visible binding for global variable ‘dat2’ makegenelist: no visible binding for global variable ‘gene’ makepauseregion: no visible binding for global variable ‘pauseidxtargetfile’ mapfunction: no visible binding for global variable ‘parallellist’ mapfunction: no visible binding for global variable ‘readsdepth’ mapfunction: no visible binding for global variable ‘plotgenenames’ metaplot: no visible binding for global variable ‘datalist’ mixscan: no visible binding for global variable ‘mixexts1’ orgintercompareinput: no visible binding for global variable ‘significance’ parsereadsfile: no visible binding for global variable ‘time1file’ pausefunction: no visible binding for global variable ‘parallellist’ pausefunction: no visible binding for global variable ‘readsdepth’ pausefunction: no visible binding for global variable ‘savegenenames’ plotends: no visible binding for global variable ‘TSSfwdFPMmeans’ plotends: no visible binding for global variable ‘TSSrevFPMmeans’ plotends: no visible binding for global variable ‘tssradius’ plotends: no visible binding for global variable ‘xcoord’ plotends: no visible binding for global variable ‘reads’ plotends: no visible binding for global variable ‘condition’ plotpairs: no visible binding for global variable ‘genefpm1’ plotpairs: no visible binding for global variable ‘genefpm2’ plotpairs: no visible binding for global variable ‘geneinfo’ plotpairs: no visible binding for global variable ‘xcoord’ plotpairs: no visible binding for global variable ‘reads’ plotprocessing: no visible binding for global variable ‘strand’ plotprocessing: no visible binding for global variable ‘xcoord’ plotprocessing: no visible binding for global variable ‘reads’ plotprocessing: no visible binding for global variable ‘condition’ plotregions: no visible binding for global variable ‘combinefwdFPMmeans’ plotregions: no visible binding for global variable ‘combinerevFPMmeans’ plotregions: no visible binding for global variable ‘tssradius’ plotregions: no visible binding for global variable ‘ttsradius’ plotregions: no visible binding for global variable ‘xcoord’ plotregions: no visible binding for global variable ‘reads’ plotregions: no visible binding for global variable ‘condition’ quantileattr: no visible binding for global variable ‘rates’ quantileattr: no visible binding for global variable ‘quantilenum’ removeoverlap: no visible binding for global variable ‘genecoords’ selectfisher: no visible binding for global variable ‘kmerres2’ selectfisher: no visible binding for global variable ‘kmerres1’ transpoint: no visible global function definition for ‘hmm_r’ wilcoxcomp: no visible binding for global variable ‘dat1’ wilcoxcomp: no visible binding for global variable ‘dat2’ Undefined global functions or variables: GeneBodysinglefwdFPMs TSSfwdFPMmeans TSSrevFPMmeans TSSsinglefwdFPMs TTSsinglefwdFPMs binres combinefwdFPMmeans combinerevFPMmeans condition dat1 dat2 datalist depth distance endcoord gbfwdcount gene gene_id genecoords genefpm1 genefpm2 geneinfo genes genes1 hmm_r kmerres1 kmerres2 maxtssradius mergerefs mixexts1 parallellist pauseidxtargetfile plotgenenames quantilenum rates reads reads1 reads1depth readsdepth savegenenames significance startcoord strand strandmethod subreads1 subreads2 time1file time1files tssfwdcount tssradius ttsradius xcoord * 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 ... [2s/2s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [0s/0s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [117s/145s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 NOTEs