Package: DMRforPairs

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DMRforPairs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DMRforPairs_1.22.0.tar.gz

StartedAt: 2020-04-15 01:55:06 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:00:58 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 352.0 seconds

RetCode: 0

Status:  OK

CheckDir: DMRforPairs.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DMRforPairs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DMRforPairs_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/DMRforPairs.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRforPairs/DESCRIPTION’ ... OK
* this is package ‘DMRforPairs’ version ‘1.22.0’
* 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 ‘DMRforPairs’ 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 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
DMRforPairs: no visible global function definition for 'combn'
DMRforPairs: no visible global function definition for 'p.adjust'
calc_stats: no visible global function definition for 'combn'
calc_stats: no visible binding for global variable 'median'
calc_stats: no visible global function definition for 'wilcox.test'
calc_stats: no visible global function definition for 'kruskal.test'
export_data: no visible global function definition for 'write.table'
plot_annotate_probes: no visible global function definition for
  'rainbow'
plot_annotate_probes: no visible global function definition for 'png'
plot_annotate_probes: no visible global function definition for 'par'
plot_annotate_probes: no visible global function definition for 'plot'
plot_annotate_probes: no visible global function definition for 'lines'
plot_annotate_probes: no visible global function definition for
  'extendrange'
plot_annotate_probes: no visible global function definition for
  'dev.off'
plot_annotate_probes: no visible global function definition for 'pdf'
plot_annotate_probes: no visible global function definition for 'combn'
plot_annotate_probes: no visible global function definition for
  'legend'
plot_annotate_probes: no visible global function definition for 'axis'
plot_annotate_probes: no visible global function definition for 'box'
plot_annotate_probes: no visible global function definition for
  'seqlevels<-'
plot_annotate_probes: no visible global function definition for 'Rle'
plot_annotate_probes: no visible global function definition for
  'IRanges'
Undefined global functions or variables:
  IRanges Rle axis box combn dev.off extendrange kruskal.test legend
  lines median p.adjust par pdf plot png rainbow seqlevels<-
  wilcox.test write.table
Consider adding
  importFrom("grDevices", "dev.off", "extendrange", "pdf", "png",
             "rainbow")
  importFrom("graphics", "axis", "box", "legend", "lines", "par", "plot")
  importFrom("stats", "kruskal.test", "median", "p.adjust",
             "wilcox.test")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/DMRforPairs.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DMRforPairs
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DMRforPairs’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DMRforPairs)

name	user	system	elapsed
DMRforPairs	2.827	0.060	2.914
calc_stats	0	0	0
export_data	1.582	0.078	1.658
merge_classes	0	0	0
plot_annotate_custom_region	1.252	0.025	1.287
plot_annotate_gene	1.041	0.025	1.073
plot_annotate_probes	0	0	0
plot_annotate_region	1.095	0.022	1.124
regionfinder	0.001	0.000	0.001
testregion	0	0	0
tune_parameters	1.321	0.018	1.349