BioC 3.4: CHECK report for sigaR on morelia

Package: sigaR

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.22.0.tar.gz

StartedAt: 2017-04-15 08:06:04 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:10:47 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 282.3 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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/sigaR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.22.0’
* 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 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    149.588  7.676 157.884
cisEffectTune  14.826  0.229  15.072
* 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-3.4-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	0.848	0.022	0.871
ExpressionSet2order	0.011	0.001	0.011
ExpressionSet2subset	0.017	0.001	0.018
ExpressionSet2weightedSubset	0.249	0.003	0.251
RCMestimation	0.905	0.036	0.942
RCMrandom	0.809	0.014	0.826
RCMtest	3.209	0.062	3.274
cghCall2cghSeg	0.037	0.001	0.037
cghCall2maximumSubset	0.394	0.009	0.402
cghCall2order	0.015	0.002	0.017
cghCall2subset	0.045	0.001	0.046
cghCall2weightedSubset	0.256	0.004	0.260
cghSeg2order	0.046	0.001	0.047
cghSeg2subset	0.075	0.002	0.078
cghSeg2weightedSubset	0.284	0.006	0.290
cisEffectPlot	0.088	0.002	0.090
cisEffectTable	1.666	0.040	1.708
cisEffectTest	1.668	0.038	1.710
cisEffectTune	14.826	0.229	15.072
cisTest-class	0.001	0.000	0.002
entTest-class	0.001	0.001	0.002
entropyTest	0.205	0.002	0.208
expandMatching2singleIDs	0.038	0.003	0.041
getSegFeatures	0.006	0.001	0.006
hdEntropy	0.010	0.001	0.012
hdMI	0.507	0.004	0.511
matchAnn2Ann	0.029	0.002	0.032
matchCGHcall2ExpressionSet	0.052	0.002	0.054
merge2ExpressionSets	0.063	0.002	0.065
merge2cghCalls	0.059	0.001	0.060
miTest-class	0.001	0.000	0.002
mutInfTest	149.588	7.676	157.884
nBreakpoints	0.175	0.005	0.180
pathway1sample	0.101	0.004	0.135
pathway2sample	2.847	0.590	3.440
pathwayFit-class	0.002	0.000	0.001
pathwayPlot	0.076	0.022	0.099
pollackCN16	0.004	0.000	0.003
pollackGE16	0.003	0.001	0.004
profilesPlot	0.142	0.002	0.144
rcmFit-class	0.001	0.001	0.001
rcmTest-class	0.002	0.000	0.001
splitMatchingAtBreakpoints	0.178	0.003	0.181
uniqGenomicInfo	0.005	0.001	0.006