BioC 3.2: CHECK report for rCGH on perceval

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 11:05:29 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 11:15:46 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 617.1 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 Patched (2015-10-08 r69496)
* 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 ‘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 ... [35s/35s] 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 ... [226s/227s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
byGeneTable  26.734  0.316  27.143
multiplot    21.757  0.138  21.906
rCGH-package 21.647  0.120  21.787
recenter     19.596  0.073  19.672
plotProfile  19.470  0.105  19.576
plotLOH      19.460  0.082  19.551
view         18.502  0.072  18.590
segmentCGH   18.041  0.073  18.117
EMnormalize  17.483  0.064  17.554
plotDensity  16.494  0.114  16.652
adjustSignal  6.530  0.031   6.562
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [44s/45s]
 [45s/46s] 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	1.096	0.020	1.116
EMnormalize	17.483	0.064	17.554
adjustSignal	6.530	0.031	6.562
byGeneTable	26.734	0.316	27.143
geneDB	0.051	0.001	0.052
hg19	0.008	0.001	0.009
multiplot	21.757	0.138	21.906
plotDensity	16.494	0.114	16.652
plotLOH	19.460	0.082	19.551
plotProfile	19.470	0.105	19.576
rCGH-Agilent-class	0.003	0.000	0.003
rCGH-SNP6-class	0.002	0.000	0.002
rCGH-class	0.001	0.000	0.001
rCGH-cytoScan-class	0.001	0.000	0.002
rCGH-package	21.647	0.120	21.787
readAffyCytoScan	0.712	0.006	0.719
readAffySNP6	1.148	0.008	1.156
readAgilent	1.249	0.010	1.261
recenter	19.596	0.073	19.672
segmentCGH	18.041	0.073	18.117
setInfo	0.797	0.009	0.808
view	18.502	0.072	18.590