BioC 3.2: CHECK report for rCGH on zin1

Package: rCGH

Version: 0.99.7

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_0.99.7.tar.gz

StartedAt: 2015-08-24 03:02:35 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:10:25 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 470.2 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_0.99.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/rCGH.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 ‘rCGH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rCGH’ version ‘0.99.7’
* 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 ‘rCGH’ can be installed ... [26s/26s] OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    extdata   1.2Mb
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [241s/242s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
byGeneTable  26.634  0.167  27.036
multiplot    23.737  0.135  23.928
plotProfile  22.802  0.145  22.987
rCGH-package 22.263  0.137  22.416
plotLOH      21.830  0.141  22.063
recenter     21.213  0.113  21.339
view         21.067  0.078  21.206
EMnormalize  20.638  0.116  20.777
segmentCGH   20.225  0.114  20.349
plotDensity  20.135  0.108  20.283
adjustSignal  7.480  0.081   7.593
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [42s/42s]
 [42s/42s] OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/rCGH.Rcheck/00check.log’
for details.

* installing *source* package ‘rCGH’ ...
** 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 (rCGH)

name	user	system	elapsed
AllAccessors	0.711	0.088	0.801
EMnormalize	20.638	0.116	20.777
adjustSignal	7.480	0.081	7.593
byGeneTable	26.634	0.167	27.036
geneDB	0.031	0.000	0.031
hg19	0.003	0.000	0.003
multiplot	23.737	0.135	23.928
plotDensity	20.135	0.108	20.283
plotLOH	21.830	0.141	22.063
plotProfile	22.802	0.145	22.987
rCGH-Agilent-class	0.000	0.000	0.001
rCGH-SNP6-class	0.000	0.000	0.001
rCGH-class	0.001	0.000	0.001
rCGH-cytoScan-class	0.001	0.000	0.001
rCGH-package	22.263	0.137	22.416
readAffyCytoScan	0.489	0.020	0.509
readAffySNP6	0.523	0.076	0.598
readAgilent	1.055	0.088	1.144
recenter	21.213	0.113	21.339
segmentCGH	20.225	0.114	20.349
setInfo	0.455	0.052	0.510
view	21.067	0.078	21.206