BioC 3.0: CHECK report for copynumber on perceval

Package: copynumber

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch copynumber_1.6.0.tar.gz

StartedAt: 2015-04-10 00:18:41 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:24:12 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 330.3 seconds

RetCode: 0

Status:  OK

CheckDir: copynumber.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch copynumber_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/copynumber.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copynumber/DESCRIPTION’ ... OK
* this is package ‘copynumber’ version ‘1.6.0’
* 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 ‘copynumber’ can be installed ... [15s/32s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [88s/111s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotCircle       13.566  0.380  22.848
plotFreq          7.431  0.220   8.517
plotHeatmap       6.170  0.208   7.367
subsetSegments    5.468  0.176   5.660
plotAberration    5.286  0.159   6.115
callAberrations   5.095  0.163   5.299
getGRangesFormat  5.022  0.151   5.175
plotGenome        4.619  0.120   7.049
plotSample        4.261  0.127   6.652
plotAllele        4.175  0.155   6.150
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/copynumber.Rcheck/00check.log’
for details.

* 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	0.025	0.003	0.028
aspcf	3.105	0.115	3.238
callAberrations	5.095	0.163	5.299
getGRangesFormat	5.022	0.151	5.175
imputeMissing	3.571	0.090	3.699
interpolate.pcf	0.760	0.023	0.792
lymphoma	0.001	0.000	0.002
micma	0.001	0.000	0.001
multipcf	0.773	0.013	0.791
pcf	1.346	0.032	1.433
pcfPlain	0.267	0.007	0.320
plotAberration	5.286	0.159	6.115
plotAllele	4.175	0.155	6.150
plotChrom	3.431	0.084	4.218
plotCircle	13.566	0.380	22.848
plotFreq	7.431	0.220	8.517
plotGamma	2.971	0.046	3.956
plotGenome	4.619	0.120	7.049
plotHeatmap	6.170	0.208	7.367
plotSample	4.261	0.127	6.652
selectSegments	1.441	0.005	1.452
subsetData	0.010	0.001	0.011
subsetSegments	5.468	0.176	5.660
winsorize	0.585	0.006	1.094