BioC 3.5: CHECK report for sigaR on oaxaca

Package: sigaR

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.23.0.tar.gz

StartedAt: 2017-03-04 09:06:40 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:10:42 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 242.0 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_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/sigaR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.23.0’
* 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    94.906 10.390 105.341
cisEffectTune 16.042  0.274  16.323
* 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	1.194	0.026	1.221
ExpressionSet2order	0.014	0.001	0.015
ExpressionSet2subset	0.017	0.001	0.019
ExpressionSet2weightedSubset	0.374	0.003	0.379
RCMestimation	1.190	0.058	1.249
RCMrandom	1.593	0.026	1.634
RCMtest	3.823	0.087	3.911
cghCall2cghSeg	0.201	0.002	0.204
cghCall2maximumSubset	0.411	0.005	0.416
cghCall2order	0.038	0.000	0.039
cghCall2subset	0.069	0.001	0.070
cghCall2weightedSubset	0.334	0.003	0.337
cghSeg2order	0.096	0.002	0.099
cghSeg2subset	0.060	0.002	0.061
cghSeg2weightedSubset	0.311	0.002	0.313
cisEffectPlot	0.290	0.010	0.301
cisEffectTable	1.864	0.056	1.922
cisEffectTest	1.970	0.049	2.019
cisEffectTune	16.042	0.274	16.323
cisTest-class	0.002	0.000	0.002
entTest-class	0.001	0.000	0.001
entropyTest	0.384	0.010	0.394
expandMatching2singleIDs	0.085	0.002	0.087
getSegFeatures	0.005	0.001	0.006
hdEntropy	0.007	0.001	0.008
hdMI	0.578	0.004	0.582
matchAnn2Ann	0.218	0.002	0.220
matchCGHcall2ExpressionSet	0.160	0.004	0.164
merge2ExpressionSets	0.066	0.000	0.067
merge2cghCalls	0.049	0.002	0.051
miTest-class	0.001	0.000	0.001
mutInfTest	94.906	10.390	105.341
nBreakpoints	0.233	0.005	0.238
pathway1sample	0.794	0.006	0.823
pathway2sample	3.437	0.653	4.109
pathwayFit-class	0.002	0.000	0.002
pathwayPlot	0.344	0.006	0.368
pollackCN16	0.004	0.001	0.005
pollackGE16	0.002	0.001	0.004
profilesPlot	0.195	0.025	0.220
rcmFit-class	0.001	0.001	0.001
rcmTest-class	0.001	0.000	0.002
splitMatchingAtBreakpoints	0.227	0.003	0.231
uniqGenomicInfo	0.008	0.001	0.010