BioC 3.5: CHECK report for rCGH on malbec2

Package: rCGH

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.6.0.tar.gz

StartedAt: 2017-10-18 01:51:58 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:57:57 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 358.6 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/rCGH.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘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 ‘rCGH’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
byGeneTable  13.252  0.244  13.616
multiplot    13.020  0.236  13.272
plotProfile  10.056  0.252  10.323
rCGH-package  7.472  0.188   7.677
EMnormalize   7.528  0.124   7.664
recenter      7.408  0.168   7.597
plotLOH       7.220  0.164   7.398
plotDensity   7.124  0.152   7.298
view          7.116  0.160   7.299
segmentCGH    6.492  0.156   6.666
adjustSignal  5.540  0.064   5.611
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.5-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	0.816	0.060	0.879
EMnormalize	7.528	0.124	7.664
adjustSignal	5.540	0.064	5.611
byGeneTable	13.252	0.244	13.616
hg18	0.004	0.000	0.002
hg19	0.004	0.000	0.003
hg38	0.004	0.000	0.003
multiplot	13.020	0.236	13.272
plotDensity	7.124	0.152	7.298
plotLOH	7.220	0.164	7.398
plotProfile	10.056	0.252	10.323
rCGH-Agilent-class	0.000	0.000	0.001
rCGH-SNP6-class	0	0	0
rCGH-class	0.000	0.000	0.001
rCGH-cytoScan-class	0	0	0
rCGH-generic-class	0.000	0.000	0.001
rCGH-oncoScan-class	0.000	0.000	0.001
rCGH-package	7.472	0.188	7.677
readAffyCytoScan	0.532	0.032	0.564
readAffyOncoScan	0.036	0.004	0.042
readAffySNP6	0.504	0.096	0.600
readAgilent	1.144	0.048	1.194
readGeneric	0.016	0.004	0.019
recenter	7.408	0.168	7.597
segmentCGH	6.492	0.156	6.666
setInfo	0.660	0.072	0.729
view	7.116	0.160	7.299