Multiple platform build/check report for BioC 3.9 - CHECK report for sigaR on merida2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sigaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sigaR_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/sigaR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.31.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
mutInfTest    94.308 15.729 111.017
cisEffectTune 18.442  0.339  19.015
* 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-3.9-bioc/meat/sigaR.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sigaR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘sigaR’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sigaR)

Tests output

Example timings

name	user	system	elapsed
CNGEheatmaps	1.158	0.073	1.242
ExpressionSet2order	0.012	0.002	0.014
ExpressionSet2subset	0.015	0.001	0.017
ExpressionSet2weightedSubset	0.272	0.005	0.280
RCMestimation	0.947	0.061	1.016
RCMrandom	1.000	0.026	1.036
RCMtest	3.919	0.074	4.035
cghCall2cghSeg	0.076	0.001	0.077
cghCall2maximumSubset	0.382	0.005	0.388
cghCall2order	0.019	0.002	0.021
cghCall2subset	0.056	0.002	0.057
cghCall2weightedSubset	0.346	0.005	0.354
cghSeg2order	0.041	0.002	0.043
cghSeg2subset	0.072	0.001	0.074
cghSeg2weightedSubset	0.334	0.003	0.348
cisEffectPlot	0.074	0.004	0.081
cisEffectTable	1.870	0.073	1.961
cisEffectTest	2.091	0.061	2.166
cisEffectTune	18.442	0.339	19.015
cisTest-class	0.001	0.000	0.002
entTest-class	0.000	0.000	0.001
entropyTest	0.268	0.002	0.278
expandMatching2singleIDs	0.043	0.002	0.047
getSegFeatures	0.009	0.002	0.011
hdEntropy	0.012	0.002	0.014
hdMI	0.693	0.004	0.703
matchAnn2Ann	0.037	0.003	0.040
matchCGHcall2ExpressionSet	0.055	0.004	0.059
merge2ExpressionSets	0.058	0.002	0.061
merge2cghCalls	0.064	0.001	0.066
miTest-class	0.001	0.000	0.001
mutInfTest	94.308	15.729	111.017
nBreakpoints	0.248	0.006	0.258
pathway1sample	0.118	0.005	0.125
pathway2sample	2.756	0.652	3.457
pathwayFit-class	0.001	0.000	0.002
pathwayPlot	0.107	0.015	0.122
pollackCN16	0.006	0.002	0.008
pollackGE16	0.004	0.002	0.005
profilesPlot	0.082	0.003	0.089
rcmFit-class	0.001	0.001	0.001
rcmTest-class	0.001	0.000	0.001
splitMatchingAtBreakpoints	0.140	0.005	0.145
uniqGenomicInfo	0.005	0.001	0.006

CHECK report for sigaR on merida2

Summary

Command output

Installation output

Tests output

Example timings