Package: copynumber

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch copynumber_1.1.1.tar.gz

StartedAt: 2013-05-01 04:09:08 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 04:13:38 -0700 (Wed, 01 May 2013)

EllapsedTime: 270.8 seconds

RetCode: 0

Status:  OK

CheckDir: copynumber.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/copynumber.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [13s/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 ... [120s/122s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotCircle       15.741  0.308  16.258
plotFreq         10.816  0.264  11.241
plotHeatmap       8.526  0.248   8.941
plotAberration    8.358  0.270   8.742
callAberrations   7.953  0.274   8.370
getGRangesFormat  7.857  0.254   8.235
subsetSegments    7.531  0.231   7.902
plotGenome        6.270  0.146   6.564
plotAllele        6.181  0.187   6.428
plotSample        5.268  0.141   5.514
aspcf             4.982  0.211   5.242
imputeMissing     5.035  0.147   5.244
* 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

* 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)

name	user	system	elapsed
SNPdata	0.228	0.007	0.238
aspcf	4.982	0.211	5.242
callAberrations	7.953	0.274	8.370
getGRangesFormat	7.857	0.254	8.235
imputeMissing	5.035	0.147	5.244
interpolate.pcf	1.191	0.044	1.261
lymphoma	0.010	0.001	0.010
micma	0.010	0.001	0.011
multipcf	1.337	0.028	1.378
pcf	1.523	0.054	1.593
pcfPlain	0.463	0.008	0.475
plotAberration	8.358	0.270	8.742
plotAllele	6.181	0.187	6.428
plotChrom	4.535	0.114	4.718
plotCircle	15.741	0.308	16.258
plotFreq	10.816	0.264	11.241
plotGamma	4.204	0.058	4.477
plotGenome	6.270	0.146	6.564
plotHeatmap	8.526	0.248	8.941
plotSample	5.268	0.141	5.514
selectSegments	2.329	0.030	2.385
subsetData	0.018	0.004	0.022
subsetSegments	7.531	0.231	7.902
winsorize	0.563	0.010	0.582