BioC 3.5: CHECK report for sigaR on veracruz2

Package: sigaR

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.24.0.tar.gz

StartedAt: 2017-10-18 09:02:49 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:06:52 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 243.3 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/sigaR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.24.0’
* 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 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    98.444  9.737 112.782
cisEffectTune 14.570  0.119  15.115
* 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
  ‘/Users/biocbuild/bbs-3.5-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	1.059	0.028	1.120
ExpressionSet2order	0.010	0.001	0.012
ExpressionSet2subset	0.013	0.001	0.015
ExpressionSet2weightedSubset	0.263	0.003	0.282
RCMestimation	0.957	0.031	1.014
RCMrandom	1.355	0.026	1.414
RCMtest	3.108	0.024	3.266
cghCall2cghSeg	0.153	0.002	0.166
cghCall2maximumSubset	0.405	0.006	0.422
cghCall2order	0.035	0.001	0.037
cghCall2subset	0.048	0.002	0.054
cghCall2weightedSubset	0.291	0.003	0.313
cghSeg2order	0.067	0.002	0.070
cghSeg2subset	0.059	0.002	0.062
cghSeg2weightedSubset	0.277	0.002	0.283
cisEffectPlot	0.206	0.006	0.227
cisEffectTable	1.666	0.042	1.744
cisEffectTest	1.898	0.034	1.980
cisEffectTune	14.570	0.119	15.115
cisTest-class	0.002	0.000	0.002
entTest-class	0.000	0.000	0.001
entropyTest	0.289	0.003	0.297
expandMatching2singleIDs	0.083	0.003	0.089
getSegFeatures	0.007	0.001	0.008
hdEntropy	0.009	0.001	0.009
hdMI	0.571	0.005	0.592
matchAnn2Ann	0.159	0.003	0.166
matchCGHcall2ExpressionSet	0.158	0.004	0.168
merge2ExpressionSets	0.072	0.002	0.077
merge2cghCalls	0.057	0.002	0.061
miTest-class	0.001	0.000	0.001
mutInfTest	98.444	9.737	112.782
nBreakpoints	0.171	0.005	0.179
pathway1sample	0.650	0.008	0.674
pathway2sample	3.442	0.667	4.209
pathwayFit-class	0.001	0.000	0.002
pathwayPlot	0.190	0.003	0.195
pollackCN16	0.004	0.001	0.006
pollackGE16	0.002	0.001	0.004
profilesPlot	0.189	0.023	0.216
rcmFit-class	0.001	0.000	0.002
rcmTest-class	0.001	0.000	0.001
splitMatchingAtBreakpoints	0.185	0.003	0.195
uniqGenomicInfo	0.006	0.001	0.007