BioC 3.5: CHECK report for sigaR on toluca2

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: 2017-04-23 09:54:03 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:58:33 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 270.0 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 r72187)
* 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    110.127 10.297 123.390
cisEffectTune  18.114  0.356  18.696
* 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	1.126	0.023	1.151
ExpressionSet2order	0.008	0.001	0.010
ExpressionSet2subset	0.015	0.002	0.017
ExpressionSet2weightedSubset	0.296	0.002	0.299
RCMestimation	1.181	0.040	1.223
RCMrandom	1.782	0.043	1.835
RCMtest	3.896	0.085	4.010
cghCall2cghSeg	0.181	0.001	0.182
cghCall2maximumSubset	0.481	0.007	0.489
cghCall2order	0.042	0.001	0.043
cghCall2subset	0.053	0.002	0.055
cghCall2weightedSubset	0.319	0.003	0.329
cghSeg2order	0.082	0.001	0.085
cghSeg2subset	0.069	0.001	0.077
cghSeg2weightedSubset	0.293	0.001	0.310
cisEffectPlot	0.277	0.006	0.288
cisEffectTable	1.900	0.051	1.964
cisEffectTest	2.233	0.052	2.288
cisEffectTune	18.114	0.356	18.696
cisTest-class	0.002	0.000	0.002
entTest-class	0.001	0.000	0.002
entropyTest	0.367	0.007	0.375
expandMatching2singleIDs	0.122	0.002	0.126
getSegFeatures	0.008	0.001	0.009
hdEntropy	0.011	0.002	0.013
hdMI	0.585	0.004	0.598
matchAnn2Ann	0.225	0.003	0.228
matchCGHcall2ExpressionSet	0.201	0.004	0.206
merge2ExpressionSets	0.098	0.001	0.101
merge2cghCalls	0.073	0.002	0.074
miTest-class	0.001	0.000	0.001
mutInfTest	110.127	10.297	123.390
nBreakpoints	0.221	0.004	0.279
pathway1sample	0.764	0.005	0.873
pathway2sample	3.537	0.616	4.193
pathwayFit-class	0.002	0.000	0.001
pathwayPlot	0.312	0.005	0.318
pollackCN16	0.005	0.001	0.006
pollackGE16	0.003	0.001	0.004
profilesPlot	0.212	0.018	0.231
rcmFit-class	0.002	0.000	0.001
rcmTest-class	0.001	0.001	0.002
splitMatchingAtBreakpoints	0.219	0.003	0.222
uniqGenomicInfo	0.008	0.001	0.008