* using log directory ‘/srv/hornik/tmp/CRAN_pretest/proRate.Rcheck’ * using R Under development (unstable) (2025-06-05 r88281) * 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/5s] 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’ calpauseidx: no visible global function definition for ‘p.adjust’ calrate: no visible global function definition for ‘read.table’ calrate: no visible global function definition for ‘p.adjust’ 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’ calsig: no visible global function definition for ‘wilcox.test’ 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’ fishermean: no visible global function definition for ‘fisher.test’ 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 global function definition for ‘read.table’ 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 global function definition for ‘read.table’ getgc: no visible binding for global variable ‘gene_id’ getkmer: no visible global function definition for ‘read.table’ 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’ intercompare: no visible global function definition for ‘p.adjust’ 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’ limmacomp: no visible global function definition for ‘as.formula’ limmacomp: no visible global function definition for ‘model.matrix’ makegenelist: no visible global function definition for ‘complete.cases’ makegenelist: no visible binding for global variable ‘gene’ makepauseregion: no visible binding for global variable ‘pauseidxtargetfile’ makepauseregion: no visible global function definition for ‘read.table’ 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 global function definition for ‘read.table’ 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’ parsereadsfile: no visible global function definition for ‘as’ pausefunction: no visible binding for global variable ‘parallellist’ pausefunction: no visible binding for global variable ‘readsdepth’ pausefunction: no visible binding for global variable ‘savegenenames’ pausefunction: no visible global function definition for ‘fisher.test’ 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 ‘time’ plotpairs: no visible binding for global variable ‘xcoord’ plotpairs: no visible binding for global variable ‘reads’ plotprocessing: no visible global function definition for ‘quantile’ 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’ quantileattr: no visible global function definition for ‘quantile’ removeoverlap: no visible binding for global variable ‘genecoords’ selectfisher: no visible binding for global variable ‘kmerres2’ selectfisher: no visible binding for global variable ‘kmerres1’ selectfisher: no visible global function definition for ‘fisher.test’ selectfisher: no visible global function definition for ‘p.adjust’ smooth_fun: no visible global function definition for ‘predict’ transpoint: no visible global function definition for ‘wilcox.test’ 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’ wilcoxcomp: no visible global function definition for ‘wilcox.test’ Undefined global functions or variables: GeneBodysinglefwdFPMs TSSfwdFPMmeans TSSrevFPMmeans TSSsinglefwdFPMs TTSsinglefwdFPMs as as.formula binres combinefwdFPMmeans combinerevFPMmeans complete.cases condition dat1 dat2 datalist depth distance endcoord fisher.test gbfwdcount gene gene_id genecoords genefpm1 genefpm2 geneinfo genes genes1 hmm_r kmerres1 kmerres2 maxtssradius mergerefs mixexts1 model.matrix p.adjust parallellist pauseidxtargetfile plotgenenames predict quantile quantilenum rates read.table reads reads1 reads1depth readsdepth savegenenames significance startcoord strand strandmethod subreads1 subreads2 time time1file time1files tssfwdcount tssradius ttsradius wilcox.test xcoord Consider adding importFrom("methods", "as") importFrom("stats", "as.formula", "complete.cases", "fisher.test", "model.matrix", "p.adjust", "predict", "quantile", "time", "wilcox.test") importFrom("utils", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'addtrack.Rd': \examples lines wider than 100 characters: wt0file <- 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt0.bam' wt15file <- 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt15.bam' Rd file 'calrate.Rd': \examples lines wider than 100 characters: wt0file <- 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt0.bam' wt15file <- 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt15.bam' Rd file 'mmetaplot.Rd': \examples lines wider than 100 characters: wt0file <- 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt0.bam' wt15file <- 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt15.bam' Rd file 'plotprocessing.Rd': \examples lines wider than 100 characters: wt0file <- 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt0.bam' wt15file <- 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt15.bam' These lines will be truncated in the PDF manual. * 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 ... [39s/60s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘tutorial_proRate.Rmd’ using rmarkdown trying URL 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt0.bam' Content type 'application/octet-stream' length 34518219 bytes (32.9 MB) ================================================== downloaded 32.9 MB trying URL 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/wt15.bam' Content type 'application/octet-stream' length 32596672 bytes (31.1 MB) ================================================== downloaded 31.1 MB trying URL 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/ko0.bam' Content type 'application/octet-stream' length 25708037 bytes (24.5 MB) ================================================== downloaded 24.5 MB trying URL 'https://raw.githubusercontent.com/yuabrahamliu/proRate/refs/heads/master/inst/extdata/ko15.bam' Content type 'application/octet-stream' length 32984728 bytes (31.5 MB) ================================================== downloaded 31.5 MB ** Processing: /srv/hornik/tmp/CRAN_pretest/proRate.Rcheck/vign_test/proRate/vignettes/tutorial_proRate_files/figure-html/unnamed-chunk-5-1.png 768x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 39383 bytes Input file size = 39509 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30435 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30435 Output IDAT size = 30435 bytes (8948 bytes decrease) Output file size = 30513 bytes (8996 bytes = 22.77% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/proRate.Rcheck/vign_test/proRate/vignettes/tutorial_proRate_files/figure-html/unnamed-chunk-5-2.png 768x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 39218 bytes Input file size = 39344 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31371 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31371 Output IDAT size = 31371 bytes (7847 bytes decrease) Output file size = 31449 bytes (7895 bytes = 20.07% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/proRate.Rcheck/vign_test/proRate/vignettes/tutorial_proRate_files/figure-html/unnamed-chunk-7-1.png 768x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23801 bytes Input file size = 23903 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20939 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20939 Output IDAT size = 20939 bytes (2862 bytes decrease) Output file size = 21017 bytes (2886 bytes = 12.07% decrease) Quitting from tutorial_proRate.Rmd:263-268 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! Unable to find conda binary. Is Anaconda installed? --- Backtrace: ▆ 1. └─reticulate::conda_list() 2. └─reticulate::conda_binary(conda) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'tutorial_proRate.Rmd' failed with diagnostics: Unable to find conda binary. Is Anaconda installed? --- failed re-building ‘tutorial_proRate.Rmd’ SUMMARY: processing the following file failed: ‘tutorial_proRate.Rmd’ Error: Vignette re-building failed. Execution halted * 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: 1 ERROR, 3 NOTEs