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BioC 2.12: CHECK report for KCsmart on petty

This page was generated on 2013-10-09 09:39:43 -0700 (Wed, 09 Oct 2013).

Package 355/671HostnameOS / ArchBUILDCHECKBUILD BIN
KCsmart 2.18.0
Jorma de Ronde
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/KCsmart
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: KCsmart
Version: 2.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KCsmart_2.18.0.tar.gz
StartedAt: 2013-10-08 22:53:32 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:57:33 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 240.2 seconds
RetCode: 0
Status:  OK 
CheckDir: KCsmart.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/KCsmart.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 'KCsmart/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KCsmart' version '2.18.0'
* 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 'KCsmart' can be installed ... [7s/7s] 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [154s/157s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
KCsmart-package      39.588  2.904  43.919
getSigRegionsCompKC  21.201  2.435  23.675
calcSpmCollection    20.069  2.946  23.388
compareSpmCollection 19.673  2.818  22.701
plotScaleSpace        9.320  0.992  10.366
plot                  5.263  0.580   5.885
findSigLevelFdr       5.166  0.596   5.786
findSigLevelTrad      4.853  0.579   5.462
* 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

KCsmart.Rcheck/00install.out:

* installing *source* package 'KCsmart' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'write.table' from package 'utils' in package 'KCsmart'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (KCsmart)

KCsmart.Rcheck/KCsmart-Ex.timings:

nameusersystemelapsed
KCsmart-package39.588 2.90443.919
calcSpm2.6780.2872.988
calcSpmCollection20.069 2.94623.388
compKc-class0.0080.0070.014
compKcSigRegions-class0.0030.0040.007
compareSpmCollection19.673 2.81822.701
findSigLevelFdr5.1660.5965.786
findSigLevelTrad4.8530.5795.462
getSigRegionsCompKC21.201 2.43523.675
getSigSegments3.8710.5444.421
idPoints0.0340.0130.048
plot5.2630.5805.885
plotScaleSpace 9.320 0.99210.366
samplePointMatrix-class0.0030.0040.007
sigSegments-class0.0130.0050.018
spmCollection-class0.0030.0030.007
write.table4.1970.4644.669