##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings coMethDMR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/coMethDMR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘coMethDMR/DESCRIPTION’ ... OK
* this is package ‘coMethDMR’ version ‘1.4.0’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘coMethDMR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 R 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 startup messages can be suppressed ... 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 ... NOTE
File ‘coMethDMR/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("Checking for cached SeSAMe data.")
    packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.")

See section ‘Good practice’ in '?.onAttach'.
* checking Rd files ... OK
* checking Rd metadata ... 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
CoMethSingleRegion  30.476  1.355  33.569
CloseBySingleRegion 25.988  1.595  29.235
lmmTest             23.581  0.725  25.561
CpGsInfoOneRegion   18.041  0.708  19.639
lmmTestAllRegions   17.347  0.313  18.321
SplitCpGDFbyRegion  16.683  0.489  18.116
CoMethAllRegions    12.014  1.080  13.446
GetCpGsInRegion     11.389  0.344  12.530
AnnotateResults     10.526  0.620  11.147
CpGsInfoAllRegions   6.724  0.272   7.189
CreateOutputDF       5.842  0.140   6.300
OrderCpGsByLocation  5.787  0.192   6.277
ImportSesameData     5.507  0.168   5.980
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ using ‘UTF-8’... OK
  ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/coMethDMR.Rcheck/00check.log’
for details.