BioC 3.1: CHECK report for copynumber on petty

Package: copynumber

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings copynumber_1.8.0.tar.gz

StartedAt: 2015-10-08 22:19:03 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:23:30 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 266.7 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 copynumber_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/copynumber.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.8.0’
* 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 ... [12s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... [107s/110s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotCircle       16.515  0.466  17.108
plotFreq          8.738  0.158   8.905
plotHeatmap       7.986  0.188   8.187
subsetSegments    7.353  0.179   7.552
getGRangesFormat  7.284  0.178   7.468
callAberrations   6.984  0.193   7.182
plotAberration    6.845  0.147   6.995
plotGenome        5.543  0.104   5.700
plotAllele        5.233  0.123   8.663
* 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (copynumber)

name	user	system	elapsed
SNPdata	0.034	0.005	0.039
aspcf	4.051	0.115	4.168
callAberrations	6.984	0.193	7.182
getGRangesFormat	7.284	0.178	7.468
imputeMissing	4.158	0.075	4.235
interpolate.pcf	1.259	0.024	1.283
lymphoma	0.001	0.000	0.001
micma	0.002	0.001	0.001
multipcf	0.932	0.016	0.949
pcf	1.361	0.026	1.388
pcfPlain	0.401	0.006	0.408
plotAberration	6.845	0.147	6.995
plotAllele	5.233	0.123	8.663
plotChrom	3.957	0.058	4.024
plotCircle	16.515	0.466	17.108
plotFreq	8.738	0.158	8.905
plotGamma	3.157	0.037	3.196
plotGenome	5.543	0.104	5.700
plotHeatmap	7.986	0.188	8.187
plotSample	4.611	0.097	4.717
selectSegments	1.900	0.007	1.910
subsetData	0.010	0.000	0.011
subsetSegments	7.353	0.179	7.552
winsorize	0.335	0.007	0.342