BioC 3.2: CHECK report for rCGH on oaxaca

Package: rCGH

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.0.0.tar.gz

StartedAt: 2015-10-20 06:55:12 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 07:02:34 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 441.1 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rCGH.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.0’
* 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 ... [28s/31s] 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 ... [157s/157s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
byGeneTable  17.072  0.174  17.272
multiplot    14.706  0.109  14.833
rCGH-package 14.581  0.098  14.702
plotProfile  14.261  0.087  14.371
recenter     13.919  0.073  14.064
plotLOH      13.334  0.065  13.590
segmentCGH   12.951  0.059  13.020
view         12.706  0.054  12.771
plotDensity  11.831  0.057  11.929
EMnormalize  10.931  0.061  11.000
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [32s/32s]
 [32s/32s] 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	1.181	0.026	1.208
EMnormalize	10.931	0.061	11.000
adjustSignal	4.259	0.017	4.279
byGeneTable	17.072	0.174	17.272
geneDB	0.027	0.000	0.027
hg19	0.002	0.000	0.003
multiplot	14.706	0.109	14.833
plotDensity	11.831	0.057	11.929
plotLOH	13.334	0.065	13.590
plotProfile	14.261	0.087	14.371
rCGH-Agilent-class	0.002	0.000	0.002
rCGH-SNP6-class	0.001	0.000	0.001
rCGH-class	0.001	0.001	0.001
rCGH-cytoScan-class	0.001	0.000	0.001
rCGH-package	14.581	0.098	14.702
readAffyCytoScan	0.872	0.005	0.880
readAffySNP6	0.899	0.008	0.910
readAgilent	1.237	0.010	1.247
recenter	13.919	0.073	14.064
segmentCGH	12.951	0.059	13.020
setInfo	0.837	0.005	0.843
view	12.706	0.054	12.771