* using log directory ‘/srv/hornik/tmp/CRAN/PCBS.Rcheck’
* using R Under development (unstable) (2024-04-16 r86435)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘PCBS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PCBS’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Kathryn Lande <kathryn.lande@mail.mcgill.ca>’

New submission

Possibly misspelled words in DESCRIPTION:
  BiSulfite (3:28)
  WGBS (7:61)

Package has a VignetteBuilder field but no prebuilt vignette index.
* 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 serialization versions ... OK
* checking whether package ‘PCBS’ can be installed ... [3s/3s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] NOTE
CheckOvercompression: no visible binding for global variable ‘n.seeds’
DefineBestPC: no visible binding for global variable ‘best’
DefineBestPC: no visible binding for global variable ‘PC1’
DefineBestPC: no visible binding for global variable ‘ID’
DefineBestPC: no visible binding for global variable ‘PC2’
checkRank: no visible binding for global variable ‘abs.order’
checkRank: no visible binding for global variable ‘PC_Score’
chromDict: no visible binding for global variable ‘pos’
multiple_metagenes: no visible binding for global variable ‘bin’
multiple_metagenes: no visible binding for global variable ‘meanScore’
multiple_metagenes: no visible binding for global variable ‘Set’
multiple_metagenes: no visible binding for global variable ‘se_min’
multiple_metagenes: no visible binding for global variable ‘se_max’
oneSeed: no visible global function definition for ‘.’
plot_metagene: no visible binding for global variable ‘bin’
plot_metagene: no visible binding for global variable ‘meanScore’
plot_metagene: no visible binding for global variable ‘se_min’
plot_metagene: no visible binding for global variable ‘se_max’
rankDist: no visible binding for global variable ‘abs.order’
rankDist: no visible binding for global variable ‘PC_Score’
rankDist: no visible binding for global variable ‘x’
rankDist: no visible binding for global variable ‘y’
score_metagene: no visible binding for global variable ‘meanScore’
score_metagene: no visible binding for global variable ‘se_min’
score_metagene: no visible binding for global variable ‘se_max’
Undefined global functions or variables:
  . ID PC1 PC2 PC_Score Set abs.order best bin meanScore n.seeds pos
  se_max se_min x y
* 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 ... [10s/10s] OK
* checking PDF version of manual ... [3s/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: 2 NOTEs