BioC 3.4: CHECK report for rCGH on zin1

Package: rCGH

Version: 1.3.3

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.3.3.tar.gz

StartedAt: 2016-09-20 11:18:27 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:27:29 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 541.8 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.3.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/rCGH.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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
byGeneTable  33.936  0.132  34.130
plotProfile  32.420  0.148  32.575
multiplot    32.300  0.224  32.527
plotLOH      29.648  0.136  29.784
rCGH-package 29.540  0.160  29.714
EMnormalize  29.184  0.112  29.297
view         28.904  0.124  29.033
plotDensity  28.752  0.120  28.876
recenter     28.528  0.108  28.641
segmentCGH   15.064  0.152  15.215
adjustSignal 14.340  0.104  14.449
* 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	1.076	0.068	1.143
EMnormalize	29.184	0.112	29.297
adjustSignal	14.340	0.104	14.449
byGeneTable	33.936	0.132	34.130
hg18	0.004	0.000	0.003
hg19	0.004	0.000	0.003
hg38	0.004	0.000	0.003
multiplot	32.300	0.224	32.527
plotDensity	28.752	0.120	28.876
plotLOH	29.648	0.136	29.784
plotProfile	32.420	0.148	32.575
rCGH-Agilent-class	0.000	0.000	0.002
rCGH-SNP6-class	0.000	0.000	0.001
rCGH-class	0.004	0.000	0.000
rCGH-cytoScan-class	0.000	0.000	0.001
rCGH-generic-class	0	0	0
rCGH-oncoScan-class	0.000	0.000	0.001
rCGH-package	29.540	0.160	29.714
readAffyCytoScan	0.780	0.084	0.867
readAffyOncoScan	0.028	0.008	0.039
readAffySNP6	0.452	0.104	0.555
readAgilent	0.668	0.076	0.746
readGeneric	0.012	0.000	0.012
recenter	28.528	0.108	28.641
segmentCGH	15.064	0.152	15.215
setInfo	0.50	0.04	0.54
view	28.904	0.124	29.033