Multiple platform build/check report for BioC 3.8 - CHECK report for sigaR on merida1

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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_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/sigaR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.30.0’
* 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    92.155 17.295 111.696
cisEffectTune 18.265  0.257  18.889
* 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-3.8-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/3.5/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	1.189	0.078	1.275
ExpressionSet2order	0.015	0.002	0.017
ExpressionSet2subset	0.018	0.002	0.019
ExpressionSet2weightedSubset	0.293	0.009	0.303
RCMestimation	1.065	0.053	1.138
RCMrandom	1.135	0.032	1.176
RCMtest	4.266	0.096	4.459
cghCall2cghSeg	0.083	0.001	0.084
cghCall2maximumSubset	0.454	0.005	0.472
cghCall2order	0.022	0.003	0.026
cghCall2subset	0.066	0.001	0.069
cghCall2weightedSubset	0.361	0.005	0.369
cghSeg2order	0.057	0.002	0.059
cghSeg2subset	0.081	0.003	0.085
cghSeg2weightedSubset	0.318	0.003	0.328
cisEffectPlot	0.063	0.003	0.067
cisEffectTable	1.990	0.063	2.116
cisEffectTest	2.062	0.052	2.140
cisEffectTune	18.265	0.257	18.889
cisTest-class	0.001	0.001	0.002
entTest-class	0.001	0.000	0.000
entropyTest	0.288	0.008	0.296
expandMatching2singleIDs	0.045	0.004	0.048
getSegFeatures	0.010	0.002	0.012
hdEntropy	0.011	0.002	0.014
hdMI	0.692	0.005	0.700
matchAnn2Ann	0.037	0.003	0.042
matchCGHcall2ExpressionSet	0.058	0.003	0.061
merge2ExpressionSets	0.052	0.002	0.077
merge2cghCalls	0.070	0.002	0.101
miTest-class	0.001	0.000	0.001
mutInfTest	92.155	17.295	111.696
nBreakpoints	0.168	0.004	0.172
pathway1sample	0.102	0.005	0.110
pathway2sample	2.713	0.597	3.326
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.089	0.009	0.098
pollackCN16	0.005	0.001	0.006
pollackGE16	0.003	0.002	0.005
profilesPlot	0.113	0.003	0.123
rcmFit-class	0.001	0.000	0.002
rcmTest-class	0.001	0.001	0.001
splitMatchingAtBreakpoints	0.181	0.007	0.188
uniqGenomicInfo	0.005	0.001	0.006

CHECK report for sigaR on merida1

Summary

Command output

Installation output

Tests output

Example timings