* using log directory 'd:/RCompile/CRANincoming/R-devel/proRate.Rcheck'
* using R Under development (unstable) (2025-06-17 r88325 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 ... NOTE
Maintainer: 'Yu Liu <yuabrahamliu@gmail.com>'

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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'proRate' 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 ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [11s] 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 ... 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 ... 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 ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [183s] OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 NOTEs