Package: BadRegionFinder

Version: 1.8.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BadRegionFinder_1.8.0.tar.gz

StartedAt: 2018-10-15 22:35:23 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 22:38:23 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 179.2 seconds

RetCode: 0

Status:  OK

CheckDir: BadRegionFinder.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BadRegionFinder_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/BadRegionFinder.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BadRegionFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BadRegionFinder’ version ‘1.8.0’
* 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 ‘BadRegionFinder’ 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
determineCoverage: no visible global function definition for ‘path’
Undefined global functions or variables:
  path
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotDetailed     6.688  0.116  10.326
plotSummaryGenes 2.036  0.012   5.918
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/BadRegionFinder.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL BadRegionFinder
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘BadRegionFinder’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BadRegionFinder)

name	user	system	elapsed
BadRegionFinder-package	0.160	0.016	0.178
determineCoverage	0.004	0.004	0.027
determineCoverageQuality	0.008	0.000	0.006
determineQuantiles	0.196	0.016	0.214
determineRegionsOfInterest	0.004	0.000	0.004
plotDetailed	6.688	0.116	10.326
plotSummary	0.156	0.000	0.155
plotSummaryGenes	2.036	0.012	5.918
reportBadRegionsDetailed	0.152	0.004	0.159
reportBadRegionsGenes	0.140	0.000	0.141
reportBadRegionsSummary	0.136	0.008	0.144