BioC 3.2: CHECK report for rCGH on perceval

Package: rCGH

Version: 0.99.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_0.99.7.tar.gz

StartedAt: 2015-08-24 04:22:24 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:31:46 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 561.6 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.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 rCGH_0.99.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rCGH.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 ‘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 ... [44s/45s] OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  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 ... [203s/204s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
byGeneTable  24.566  0.366  25.527
multiplot    19.454  0.176  19.648
rCGH-package 18.531  0.147  18.713
plotProfile  18.426  0.136  18.626
plotLOH      17.204  0.130  17.453
recenter     16.383  0.103  16.496
segmentCGH   16.164  0.089  16.311
view         16.057  0.092  16.156
EMnormalize  15.098  0.105  15.296
plotDensity  15.085  0.117  15.384
adjustSignal  5.670  0.038   5.733
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [42s/42s]
 [43s/43s] 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
  ‘/Users/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	1.129	0.030	1.160
EMnormalize	15.098	0.105	15.296
adjustSignal	5.670	0.038	5.733
byGeneTable	24.566	0.366	25.527
geneDB	0.039	0.001	0.040
hg19	0.004	0.001	0.006
multiplot	19.454	0.176	19.648
plotDensity	15.085	0.117	15.384
plotLOH	17.204	0.130	17.453
plotProfile	18.426	0.136	18.626
rCGH-Agilent-class	0.002	0.000	0.002
rCGH-SNP6-class	0.001	0.000	0.001
rCGH-class	0.002	0.000	0.002
rCGH-cytoScan-class	0.001	0.000	0.002
rCGH-package	18.531	0.147	18.713
readAffyCytoScan	0.625	0.009	0.633
readAffySNP6	0.674	0.012	0.686
readAgilent	1.924	0.021	1.949
recenter	16.383	0.103	16.496
segmentCGH	16.164	0.089	16.311
setInfo	0.622	0.007	0.629
view	16.057	0.092	16.156