BioC 3.3: CHECK report for rCGH on zin2

Package: rCGH

Version: 1.2.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.2.2.tar.gz

StartedAt: 2016-10-13 05:48:02 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:55:26 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 443.2 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.2.2’
* 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  24.752  0.207  25.005
multiplot    21.895  0.174  22.092
plotProfile  21.691  0.205  21.905
plotLOH      20.186  0.124  20.320
rCGH-package 20.083  0.140  20.236
recenter     19.534  0.124  19.665
segmentCGH   19.215  0.145  19.370
view         19.132  0.116  19.252
plotDensity  19.045  0.146  19.180
EMnormalize  18.230  0.116  18.347
adjustSignal  6.713  0.050   6.761
* 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	0.959	0.084	1.043
EMnormalize	18.230	0.116	18.347
adjustSignal	6.713	0.050	6.761
byGeneTable	24.752	0.207	25.005
hg18	0.003	0.000	0.003
hg19	0.003	0.000	0.003
hg38	0.003	0.000	0.003
multiplot	21.895	0.174	22.092
plotDensity	19.045	0.146	19.180
plotLOH	20.186	0.124	20.320
plotProfile	21.691	0.205	21.905
rCGH-Agilent-class	0.001	0.000	0.001
rCGH-SNP6-class	0.001	0.000	0.001
rCGH-class	0.001	0.000	0.001
rCGH-cytoScan-class	0.001	0.000	0.001
rCGH-generic-class	0.001	0.000	0.000
rCGH-package	20.083	0.140	20.236
readAffyCytoScan	0.484	0.036	0.520
readAffySNP6	0.573	0.068	0.641
readAgilent	0.784	0.060	0.855
readGeneric	0.008	0.004	0.012
recenter	19.534	0.124	19.665
segmentCGH	19.215	0.145	19.370
setInfo	0.492	0.044	0.536
view	19.132	0.116	19.252