BioC 3.4: CHECK report for clipper on morelia

Package: clipper

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clipper_1.14.0.tar.gz

StartedAt: 2017-04-15 00:00:21 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:04:48 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 267.2 seconds

RetCode: 0

Status:  OK

CheckDir: clipper.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 clipper_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/clipper.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clipper/DESCRIPTION’ ... OK
* this is package ‘clipper’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘RCytoscape’
* 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 ‘clipper’ 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
clipperAllRoots 11.356  0.194  11.564
pathwayTest      8.207  0.051   8.264
clipper          5.369  0.146   6.061
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.4-bioc/meat/clipper.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
clipper	5.369	0.146	6.061
clipperAllRoots	11.356	0.194	11.564
cliqueMeanTest	2.834	0.044	2.880
cliqueMixedTest	2.609	0.037	2.647
cliquePairedTest	2.634	0.045	2.678
cliqueVarianceTest	2.428	0.045	2.475
deleteEdge	0.097	0.002	0.099
easyClip	2.733	0.035	2.784
getGraphEntryGenes	0.208	0.004	0.211
getJunctionTreePaths	0.211	0.003	0.214
nameCliques	0.001	0.001	0.001
pathwayTest	8.207	0.051	8.264
plotInCytoscape	0.001	0.001	0.001
prunePaths	0.004	0.000	0.005