BioC 2.12: CHECK report for copynumber on petty

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: 2013-10-08 22:05:19 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:10:32 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 313.1 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 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file '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/15s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [145s/147s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotCircle       18.403  0.274  19.011
plotFreq         13.586  0.241  14.152
plotAberration   10.572  0.224  10.957
plotHeatmap      10.443  0.214  10.688
callAberrations  10.132  0.224  10.636
subsetSegments    9.890  0.236  10.185
getGRangesFormat  9.871  0.254  10.214
plotAllele        7.606  0.190   7.845
plotGenome        7.517  0.117   7.983
plotSample        6.867  0.129   7.041
imputeMissing     6.340  0.131   6.513
aspcf             5.609  0.201   5.822
plotChrom         5.403  0.098   5.553
* 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	0.230	0.006	0.241
aspcf	5.609	0.201	5.822
callAberrations	10.132	0.224	10.636
getGRangesFormat	9.871	0.254	10.214
imputeMissing	6.340	0.131	6.513
interpolate.pcf	1.819	0.038	1.861
lymphoma	0.006	0.001	0.007
micma	0.007	0.001	0.008
multipcf	1.348	0.026	1.378
pcf	1.900	0.035	1.939
pcfPlain	0.745	0.016	0.766
plotAberration	10.572	0.224	10.957
plotAllele	7.606	0.190	7.845
plotChrom	5.403	0.098	5.553
plotCircle	18.403	0.274	19.011
plotFreq	13.586	0.241	14.152
plotGamma	4.569	0.062	4.810
plotGenome	7.517	0.117	7.983
plotHeatmap	10.443	0.214	10.688
plotSample	6.867	0.129	7.041
selectSegments	2.177	0.019	2.203
subsetData	0.022	0.001	0.026
subsetSegments	9.890	0.236	10.185
winsorize	0.436	0.007	0.443