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BioC 2.12: CHECK report for copynumber on george2

This page was generated on 2013-10-09 09:38:02 -0700 (Wed, 09 Oct 2013).

Package 150/671HostnameOS / ArchBUILDCHECKBUILD BIN
copynumber 1.1.1
Gro Nilsen
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/copynumber
Last Changed Rev: 75693 / Revision: 81334
Last Changed Date: 2013-04-16 05:30:28 -0700 (Tue, 16 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: copynumber
Version: 1.1.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings copynumber_1.1.1.tar.gz
StartedAt: 2013-10-09 01:09:09 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:14:03 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 293.3 seconds
RetCode: 0
Status:  OK 
CheckDir: copynumber.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/copynumber.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 ‘copynumber/DESCRIPTION’ ... OK
* this is package ‘copynumber’ version ‘1.1.1’
* 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 ‘copynumber’ can be installed ... [14s/14s] 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [130s/131s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotCircle       19.274  0.032  19.346
plotFreq         13.652  0.036  13.800
plotAberration    8.924  0.008   9.144
callAberrations   8.457  0.024   8.775
subsetSegments    7.941  0.004   7.941
plotHeatmap       7.837  0.012   7.946
getGRangesFormat  7.656  0.008   7.669
plotAllele        7.269  0.036   7.381
plotGenome        6.064  0.036   6.103
plotSample        5.688  0.032   5.750
aspcf             5.472  0.024   5.509
plotChrom         5.424  0.036   5.496
imputeMissing     5.093  0.016   5.109
* 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

copynumber.Rcheck/00install.out:

* installing *source* package ‘copynumber’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (copynumber)

copynumber.Rcheck/copynumber-Ex.timings:

nameusersystemelapsed
SNPdata0.3760.0080.381
aspcf5.4720.0245.509
callAberrations8.4570.0248.775
getGRangesFormat7.6560.0087.669
imputeMissing5.0930.0165.109
interpolate.pcf1.6080.0041.612
lymphoma0.020.000.02
micma0.0240.0000.025
multipcf1.1840.0041.191
pcf1.5680.0081.577
pcfPlain0.7640.0000.762
plotAberration8.9240.0089.144
plotAllele7.2690.0367.381
plotChrom5.4240.0365.496
plotCircle19.274 0.03219.346
plotFreq13.652 0.03613.800
plotGamma4.7970.0204.815
plotGenome6.0640.0366.103
plotHeatmap7.8370.0127.946
plotSample5.6880.0325.750
selectSegments2.2240.0082.232
subsetData0.020.000.02
subsetSegments7.9410.0047.941
winsorize0.3200.0080.329