BioC 3.0: CHECK report for DMRforPairs on perceval

Package: DMRforPairs

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DMRforPairs_1.2.0.tar.gz

StartedAt: 2015-04-10 00:52:18 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:00:38 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 499.8 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 --no-vignettes --timings --no-multiarch DMRforPairs_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/DMRforPairs.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRforPairs/DESCRIPTION’ ... OK
* this is package ‘DMRforPairs’ version ‘1.2.0’
* 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 ... [45s/45s] 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 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
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’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [37s/37s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
DMRforPairs 4.911  0.117   5.358
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/DMRforPairs.Rcheck/00check.log’
for details.

* installing *source* package ‘DMRforPairs’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DMRforPairs)

name	user	system	elapsed
DMRforPairs	4.911	0.117	5.358
calc_stats	0.000	0.000	0.001
export_data	2.640	0.114	2.995
merge_classes	0.001	0.001	0.001
plot_annotate_custom_region	1.459	0.031	1.503
plot_annotate_gene	1.431	0.029	1.471
plot_annotate_probes	0.001	0.001	0.000
plot_annotate_region	1.309	0.029	1.342
regionfinder	0.000	0.000	0.001
testregion	0.000	0.000	0.001
tune_parameters	1.702	0.028	1.733