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BioC 2.12: CHECK report for GSEABase on petty

This page was generated on 2013-10-09 09:39:36 -0700 (Wed, 09 Oct 2013).

Package 300/671HostnameOS / ArchBUILDCHECKBUILD BIN
GSEABase 1.22.0
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GSEABase
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GSEABase
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.22.0.tar.gz
StartedAt: 2013-10-08 22:40:53 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:46:29 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 336.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GSEABase.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GSEABase.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '1.22.0'
* 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 'GSEABase' can be installed ... [22s/22s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 examples ... [35s/35s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
GeneSetCollection-methods 16.995  0.361  17.439
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'unitTests.R' [80s/82s]
 [81s/82s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

GSEABase.Rcheck/00install.out:

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

GSEABase.Rcheck/GSEABase-Ex.timings:

nameusersystemelapsed
CollectionType-class1.4890.0831.579
CollectionType-constructors0.7080.0210.744
GSEABase-package0.3580.0330.425
GeneColorSet-class0.4160.0230.449
GeneIdentifierType-class0.3730.0230.399
GeneIdentifierType-constructors0.9730.0271.050
GeneSet-class0.9730.0351.010
GeneSet-methods0.3480.0220.373
GeneSetCollection-class0.1140.0070.121
GeneSetCollection-methods16.995 0.36117.439
OBOCollection-class0.2410.0130.255
getOBOCollection0.1710.0130.185
getObjects0.1630.0170.181
goSlim-methods1.5070.0941.618
incidence-methods0.0950.0110.106