BioC 3.6: CHECK report for rCGH on malbec1

Package: rCGH

Version: 1.7.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.7.0.tar.gz

StartedAt: 2017-08-16 01:46:12 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:52:03 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 351.5 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/rCGH.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.0’
* 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  12.280  0.196  12.587
multiplot    12.040  0.292  12.347
plotProfile   9.928  0.216  10.160
rCGH-package  8.060  0.236   8.313
plotLOH       6.972  0.152   7.130
EMnormalize   6.792  0.080   6.883
plotDensity   6.672  0.168   6.847
view          6.544  0.152   6.719
recenter      6.508  0.148   6.670
adjustSignal  6.440  0.192   6.642
segmentCGH    6.040  0.124   6.187
* 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-3.6-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	0.784	0.068	0.852
EMnormalize	6.792	0.080	6.883
adjustSignal	6.440	0.192	6.642
byGeneTable	12.280	0.196	12.587
hg18	0.004	0.000	0.003
hg19	0.004	0.000	0.003
hg38	0.004	0.000	0.003
multiplot	12.040	0.292	12.347
plotDensity	6.672	0.168	6.847
plotLOH	6.972	0.152	7.130
plotProfile	9.928	0.216	10.160
rCGH-Agilent-class	0.004	0.000	0.001
rCGH-SNP6-class	0.000	0.000	0.001
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	0	0
rCGH-package	8.060	0.236	8.313
readAffyCytoScan	0.488	0.036	0.523
readAffyOncoScan	0.040	0.000	0.038
readAffySNP6	0.508	0.064	0.573
readAgilent	0.896	0.072	0.967
readGeneric	0.008	0.004	0.011
recenter	6.508	0.148	6.670
segmentCGH	6.040	0.124	6.187
setInfo	0.500	0.048	0.551
view	6.544	0.152	6.719