BioC 3.4: CHECK report for rCGH on morelia

Package: rCGH

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.4.0.tar.gz

StartedAt: 2017-04-15 06:55:21 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 07:02:07 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 406.1 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/rCGH.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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 ... 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
byGeneTable  17.260  0.260  17.654
plotProfile  15.003  0.144  15.172
multiplot    13.007  0.134  13.150
rCGH-package 11.300  0.054  11.386
EMnormalize  10.485  0.087  10.578
recenter     10.411  0.036  10.459
view          9.109  0.029   9.143
plotLOH       7.568  0.039   8.184
plotDensity   7.379  0.033   8.991
adjustSignal  6.969  0.020   7.025
segmentCGH    6.729  0.025   6.756
* 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	0.926	0.018	0.944
EMnormalize	10.485	0.087	10.578
adjustSignal	6.969	0.020	7.025
byGeneTable	17.260	0.260	17.654
hg18	0.005	0.001	0.005
hg19	0.002	0.000	0.003
hg38	0.003	0.001	0.004
multiplot	13.007	0.134	13.150
plotDensity	7.379	0.033	8.991
plotLOH	7.568	0.039	8.184
plotProfile	15.003	0.144	15.172
rCGH-Agilent-class	0.001	0.000	0.001
rCGH-SNP6-class	0.001	0.001	0.001
rCGH-class	0.001	0.000	0.001
rCGH-cytoScan-class	0.002	0.001	0.001
rCGH-generic-class	0.001	0.000	0.001
rCGH-oncoScan-class	0.001	0.000	0.001
rCGH-package	11.300	0.054	11.386
readAffyCytoScan	0.731	0.004	0.735
readAffyOncoScan	0.025	0.000	0.025
readAffySNP6	0.744	0.006	0.750
readAgilent	1.051	0.011	1.062
readGeneric	0.012	0.001	0.013
recenter	10.411	0.036	10.459
segmentCGH	6.729	0.025	6.756
setInfo	0.752	0.002	0.755
view	9.109	0.029	9.143