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BioC 3.5: CHECK report for clipper on veracruz2

This page was generated on 2017-08-16 13:30:46 -0400 (Wed, 16 Aug 2017).

Package 228/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.16.0
Paolo Martini
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/clipper
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: clipper
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clipper_1.16.0.tar.gz
StartedAt: 2017-08-16 01:03:26 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:07:56 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 270.3 seconds
RetCode: 0
Status:  OK 
CheckDir: clipper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clipper_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/clipper.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clipper/DESCRIPTION’ ... OK
* this is package ‘clipper’ version ‘1.16.0’
* 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 8.848  0.109   9.163
pathwayTest     6.528  0.045   6.755
* 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-3.5-bioc/meat/clipper.Rcheck/00check.log’
for details.


clipper.Rcheck/00install.out:

* 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)

clipper.Rcheck/clipper-Ex.timings:

nameusersystemelapsed
clipper4.5710.1454.841
clipperAllRoots8.8480.1099.163
cliqueMeanTest2.3200.0412.410
cliqueMixedTest2.3800.0532.489
cliquePairedTest3.1210.0523.252
cliqueVarianceTest2.0000.0352.075
deleteEdge0.1150.0020.119
easyClip1.6850.0251.741
getGraphEntryGenes0.1930.0050.198
getJunctionTreePaths0.1260.0030.130
nameCliques0.0010.0000.001
pathwayTest6.5280.0456.755
plotInCytoscape0.0010.0000.001
prunePaths0.0380.0010.038