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BioC 2.12: CHECK report for KCsmart on george2

This page was generated on 2013-10-09 09:37:31 -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: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings KCsmart_2.18.0.tar.gz
StartedAt: 2013-10-09 02:50:18 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:54:11 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 233.6 seconds
RetCode: 0
Status:  OK 
CheckDir: KCsmart.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/KCsmart.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [158s/161s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
KCsmart-package      42.970  0.448  43.893
getSigRegionsCompKC  27.573  0.140  28.155
compareSpmCollection 21.585  0.064  22.875
calcSpmCollection    19.618  0.156  19.874
plotScaleSpace       10.033  0.008  10.290
plot                  7.840  0.068   8.224
getSigSegments        6.069  0.020   6.105
findSigLevelTrad      5.917  0.032   5.957
findSigLevelFdr       5.232  0.036   5.286
* 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-package42.970 0.44843.893
calcSpm2.0400.0242.112
calcSpmCollection19.618 0.15619.874
compKc-class0.0080.0000.007
compKcSigRegions-class0.0080.0000.007
compareSpmCollection21.585 0.06422.875
findSigLevelFdr5.2320.0365.286
findSigLevelTrad5.9170.0325.957
getSigRegionsCompKC27.573 0.14028.155
getSigSegments6.0690.0206.105
idPoints0.0320.0040.035
plot7.8400.0688.224
plotScaleSpace10.033 0.00810.290
samplePointMatrix-class0.0040.0000.005
sigSegments-class0.0000.0000.004
spmCollection-class0.0120.0000.015
write.table4.6920.0004.695