BioC 3.4: CHECK report for sigaR on malbec1

Package: sigaR

Version: 1.22.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.22.0.tar.gz

StartedAt: 2017-04-15 01:16:49 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:20:06 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 197.1 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_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/sigaR.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 ‘sigaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigaR’ version ‘1.22.0’
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.alphabivariate’ ‘.alphaest’ ‘.pretest’
* 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
mutInfTest    98.472  2.032 100.590
cisEffectTune  9.788  0.000   9.794
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/sigaR.Rcheck/00check.log’
for details.

* 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	0.908	0.012	0.919
ExpressionSet2order	0.008	0.000	0.009
ExpressionSet2subset	0.012	0.000	0.012
ExpressionSet2weightedSubset	0.208	0.000	0.206
RCMestimation	0.516	0.008	0.524
RCMrandom	0.528	0.000	0.530
RCMtest	2.128	0.000	2.129
cghCall2cghSeg	0.032	0.000	0.035
cghCall2maximumSubset	0.280	0.004	0.284
cghCall2order	0.012	0.000	0.014
cghCall2subset	0.028	0.000	0.031
cghCall2weightedSubset	0.236	0.000	0.238
cghSeg2order	0.036	0.000	0.036
cghSeg2subset	0.056	0.004	0.058
cghSeg2weightedSubset	0.228	0.000	0.228
cisEffectPlot	0.052	0.000	0.050
cisEffectTable	1.232	0.000	1.234
cisEffectTest	1.072	0.000	1.070
cisEffectTune	9.788	0.000	9.794
cisTest-class	0.000	0.000	0.001
entTest-class	0.000	0.000	0.001
entropyTest	0.196	0.000	0.196
expandMatching2singleIDs	0.024	0.000	0.023
getSegFeatures	0.008	0.000	0.006
hdEntropy	0.008	0.000	0.006
hdMI	0.552	0.000	0.551
matchAnn2Ann	0.02	0.00	0.02
matchCGHcall2ExpressionSet	0.032	0.000	0.032
merge2ExpressionSets	0.048	0.000	0.046
merge2cghCalls	0.060	0.000	0.059
miTest-class	0	0	0
mutInfTest	98.472	2.032	100.590
nBreakpoints	0.100	0.004	0.105
pathway1sample	0.064	0.004	0.070
pathway2sample	2.824	0.048	2.875
pathwayFit-class	0	0	0
pathwayPlot	0.064	0.000	0.062
pollackCN16	0.004	0.000	0.003
pollackGE16	0.004	0.000	0.002
profilesPlot	0.076	0.000	0.077
rcmFit-class	0.000	0.000	0.001
rcmTest-class	0	0	0
splitMatchingAtBreakpoints	0.112	0.004	0.114
uniqGenomicInfo	0.008	0.000	0.006