BioC 3.4: CHECK report for sigaR on zin1

Package: sigaR

Version: 1.20.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.20.0.tar.gz

StartedAt: 2016-08-18 12:06:34 -0700 (Thu, 18 Aug 2016)

EndedAt: 2016-08-18 12:09:56 -0700 (Thu, 18 Aug 2016)

EllapsedTime: 202.7 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.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 sigaR_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/sigaR.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 ‘sigaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigaR’ version ‘1.20.0’
* 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 ‘sigaR’ 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 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
mutInfTest    111.716  1.344 113.261
cisEffectTune  11.292  0.000  11.296
* 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 ‘sigaR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	0.792	0.000	0.792
ExpressionSet2order	0.004	0.004	0.007
ExpressionSet2subset	0.008	0.000	0.005
ExpressionSet2weightedSubset	0.196	0.000	0.194
RCMestimation	0.628	0.004	0.634
RCMrandom	0.636	0.000	0.636
RCMtest	2.592	0.000	2.594
cghCall2cghSeg	0.036	0.000	0.035
cghCall2maximumSubset	0.284	0.000	0.282
cghCall2order	0.008	0.004	0.011
cghCall2subset	0.036	0.000	0.037
cghCall2weightedSubset	0.228	0.000	0.230
cghSeg2order	0.036	0.000	0.034
cghSeg2subset	0.052	0.004	0.054
cghSeg2weightedSubset	0.216	0.004	0.220
cisEffectPlot	0.044	0.000	0.045
cisEffectTable	1.180	0.008	1.191
cisEffectTest	1.172	0.000	1.175
cisEffectTune	11.292	0.000	11.296
cisTest-class	0.000	0.000	0.002
entTest-class	0.000	0.000	0.001
entropyTest	0.172	0.000	0.174
expandMatching2singleIDs	0.028	0.004	0.029
getSegFeatures	0.008	0.000	0.007
hdEntropy	0.008	0.000	0.008
hdMI	0.428	0.000	0.428
matchAnn2Ann	0.028	0.000	0.025
matchCGHcall2ExpressionSet	0.036	0.000	0.034
merge2ExpressionSets	0.04	0.00	0.04
merge2cghCalls	0.060	0.000	0.058
miTest-class	0.000	0.000	0.001
mutInfTest	111.716	1.344	113.261
nBreakpoints	0.132	0.000	0.132
pathway1sample	0.084	0.012	0.095
pathway2sample	2.596	0.648	3.243
pathwayFit-class	0.000	0.000	0.001
pathwayPlot	0.076	0.000	0.079
pollackCN16	0.008	0.000	0.004
pollackGE16	0.000	0.000	0.002
profilesPlot	0.080	0.000	0.084
rcmFit-class	0	0	0
rcmTest-class	0.000	0.000	0.001
splitMatchingAtBreakpoints	0.140	0.000	0.143
uniqGenomicInfo	0.004	0.000	0.005