BioC 3.2: CHECK report for copynumber on zin1

Package: copynumber

Version: 1.9.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings copynumber_1.9.0.tar.gz

StartedAt: 2015-08-23 22:55:20 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:57:23 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 123.5 seconds

RetCode: 0

Status:  OK

CheckDir: copynumber.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings copynumber_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/copynumber.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copynumber/DESCRIPTION’ ... OK
* this is package ‘copynumber’ version ‘1.9.0’
* 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 ... [6s/6s] 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 ... [53s/53s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
plotCircle 8.283  0.107   8.414
* 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
  ‘/home/biocbuild/bbs-3.2-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	0.014	0.004	0.018
aspcf	2.033	0.004	2.036
callAberrations	3.483	0.020	3.501
getGRangesFormat	3.453	0.000	3.457
imputeMissing	2.348	0.012	2.358
interpolate.pcf	0.504	0.000	0.504
lymphoma	0.002	0.000	0.002
micma	0.002	0.000	0.001
multipcf	0.559	0.000	0.558
pcf	0.749	0.000	0.749
pcfPlain	0.303	0.000	0.303
plotAberration	3.650	0.008	3.656
plotAllele	2.765	0.004	2.771
plotChrom	2.013	0.004	2.020
plotCircle	8.283	0.107	8.414
plotFreq	4.231	0.004	4.247
plotGamma	1.780	0.004	1.794
plotGenome	2.866	0.012	2.884
plotHeatmap	3.614	0.004	3.622
plotSample	2.530	0.020	2.553
selectSegments	1.057	0.004	1.071
subsetData	0.008	0.000	0.008
subsetSegments	3.497	0.000	3.502
winsorize	0.181	0.000	0.181