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: 2017-08-16 08:13:32 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:17:26 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 233.6 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 3.4.1 (2017-06-30)
* 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    94.068  8.675 106.155
cisEffectTune 14.593  0.140  15.189
* 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	1.104	0.025	1.183
ExpressionSet2order	0.012	0.001	0.014
ExpressionSet2subset	0.010	0.001	0.012
ExpressionSet2weightedSubset	0.293	0.003	0.306
RCMestimation	0.979	0.035	1.057
RCMrandom	1.486	0.020	1.526
RCMtest	3.211	0.036	3.356
cghCall2cghSeg	0.149	0.001	0.162
cghCall2maximumSubset	0.405	0.004	0.419
cghCall2order	0.033	0.001	0.034
cghCall2subset	0.060	0.004	0.064
cghCall2weightedSubset	0.317	0.003	0.334
cghSeg2order	0.057	0.002	0.061
cghSeg2subset	0.060	0.001	0.061
cghSeg2weightedSubset	0.258	0.003	0.264
cisEffectPlot	0.231	0.003	0.243
cisEffectTable	1.672	0.044	1.783
cisEffectTest	1.849	0.038	1.959
cisEffectTune	14.593	0.140	15.189
cisTest-class	0.001	0.000	0.002
entTest-class	0.001	0.000	0.001
entropyTest	0.299	0.004	0.308
expandMatching2singleIDs	0.092	0.002	0.094
getSegFeatures	0.005	0.001	0.006
hdEntropy	0.008	0.001	0.010
hdMI	0.538	0.003	0.555
matchAnn2Ann	0.148	0.002	0.149
matchCGHcall2ExpressionSet	0.155	0.003	0.160
merge2ExpressionSets	0.067	0.000	0.075
merge2cghCalls	0.058	0.001	0.061
miTest-class	0.001	0.000	0.000
mutInfTest	94.068	8.675	106.155
nBreakpoints	0.159	0.003	0.172
pathway1sample	0.722	0.007	0.745
pathway2sample	3.736	0.652	4.534
pathwayFit-class	0.001	0.000	0.002
pathwayPlot	0.171	0.001	0.176
pollackCN16	0.005	0.001	0.006
pollackGE16	0.002	0.001	0.003
profilesPlot	0.179	0.016	0.219
rcmFit-class	0.001	0.000	0.001
rcmTest-class	0.001	0.000	0.001
splitMatchingAtBreakpoints	0.173	0.003	0.180
uniqGenomicInfo	0.006	0.001	0.007