BioC 3.1: CHECK report for saps on morelia

Package: saps

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings saps_2.0.0.tar.gz

StartedAt: 2015-10-09 06:06:11 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:07:53 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 101.7 seconds

RetCode: 0

Status:  OK

CheckDir: saps.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 saps_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/saps.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘saps/DESCRIPTION’ ... OK
* this is package ‘saps’ version ‘2.0.0’
* 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 ‘saps’ can be installed ... [4s/5s] 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [53s/53s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
plotSapsScoreDensity 20.972  1.057  22.035
calculateQValue       9.067  0.172   9.248
* 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: OK

* installing *source* package ‘saps’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘igraph::union’ when loading ‘piano’
Warning: replacing previous import by ‘igraph::normalize’ when loading ‘piano’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘igraph::union’ when loading ‘piano’
Warning: replacing previous import by ‘igraph::normalize’ when loading ‘piano’
* DONE (saps)

name	user	system	elapsed
calculatePEnrichment	1.454	0.024	1.492
calculatePPure	0.012	0.000	0.012
calculatePRandom	0.520	0.012	0.533
calculateQValue	9.067	0.172	9.248
plotEnrichment	4.679	0.121	4.812
plotKM	3.473	0.224	3.697
plotRandomDensity	3.993	0.360	4.354
plotSapsScoreDensity	20.972	1.057	22.035
rankConcordance	0.037	0.000	0.037
saps	4.293	0.217	4.510