BioC 3.4: CHECK report for rCGH on malbec1

Package: rCGH

Version: 1.4.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.4.0.tar.gz

StartedAt: 2017-04-15 00:45:40 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:52:12 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 391.7 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_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/rCGH.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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 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  16.064  0.212  16.294
plotProfile  15.936  0.220  16.176
multiplot    15.712  0.208  15.944
EMnormalize  12.580  0.140  12.737
rCGH-package 11.788  0.176  11.978
recenter     11.444  0.172  11.626
plotDensity  11.004  0.184  11.206
plotLOH      10.716  0.132  10.868
view         10.524  0.104  10.645
segmentCGH    7.308  0.188   7.511
adjustSignal  6.608  0.064   6.682
* 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	0.828	0.068	0.898
EMnormalize	12.580	0.140	12.737
adjustSignal	6.608	0.064	6.682
byGeneTable	16.064	0.212	16.294
hg18	0.004	0.000	0.003
hg19	0.004	0.000	0.002
hg38	0.004	0.000	0.003
multiplot	15.712	0.208	15.944
plotDensity	11.004	0.184	11.206
plotLOH	10.716	0.132	10.868
plotProfile	15.936	0.220	16.176
rCGH-Agilent-class	0.000	0.000	0.001
rCGH-SNP6-class	0	0	0
rCGH-class	0.000	0.000	0.001
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	11.788	0.176	11.978
readAffyCytoScan	0.512	0.052	0.562
readAffyOncoScan	0.024	0.016	0.038
readAffySNP6	0.532	0.064	0.599
readAgilent	0.848	0.088	0.940
readGeneric	0.016	0.000	0.014
recenter	11.444	0.172	11.626
segmentCGH	7.308	0.188	7.511
setInfo	0.480	0.040	0.522
view	10.524	0.104	10.645