BioC 3.4: CHECK report for rCGH on morelia

Package: rCGH

Version: 1.3.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.3.3.tar.gz

StartedAt: 2016-09-20 11:57:21 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:03:52 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 391.3 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_1.3.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/rCGH.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.3’
* 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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
multiplot    16.200  0.192  16.407
byGeneTable  14.859  0.251  17.966
plotProfile  14.271  0.136  14.443
plotDensity  11.126  0.061  11.203
plotLOH      10.964  0.061  11.043
rCGH-package 10.500  0.056  10.569
recenter      9.850  0.037   9.933
EMnormalize   9.090  0.051   9.146
view          9.058  0.027   9.093
segmentCGH    7.064  0.035   7.105
adjustSignal  6.407  0.029   6.441
* 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: OK

* 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	1.309	0.016	1.325
EMnormalize	9.090	0.051	9.146
adjustSignal	6.407	0.029	6.441
byGeneTable	14.859	0.251	17.966
hg18	0.005	0.001	0.005
hg19	0.004	0.001	0.005
hg38	0.003	0.000	0.004
multiplot	16.200	0.192	16.407
plotDensity	11.126	0.061	11.203
plotLOH	10.964	0.061	11.043
plotProfile	14.271	0.136	14.443
rCGH-Agilent-class	0.001	0.000	0.001
rCGH-SNP6-class	0.000	0.000	0.001
rCGH-class	0.001	0.000	0.000
rCGH-cytoScan-class	0.000	0.000	0.001
rCGH-generic-class	0.001	0.000	0.001
rCGH-oncoScan-class	0.001	0.000	0.001
rCGH-package	10.500	0.056	10.569
readAffyCytoScan	1.181	0.006	1.188
readAffyOncoScan	0.030	0.001	0.030
readAffySNP6	0.752	0.007	0.759
readAgilent	0.960	0.007	0.968
readGeneric	0.010	0.001	0.010
recenter	9.850	0.037	9.933
segmentCGH	7.064	0.035	7.105
setInfo	0.554	0.002	0.557
view	9.058	0.027	9.093