Multiple platform build/check report for BioC 3.7 - 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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/sigaR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.28.0’
* 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    78.425 14.863  93.781
cisEffectTune 14.782  0.303  15.170
* 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-3.7-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	1.166	0.074	1.250
ExpressionSet2order	0.012	0.001	0.014
ExpressionSet2subset	0.017	0.002	0.020
ExpressionSet2weightedSubset	0.298	0.008	0.308
RCMestimation	1.065	0.045	1.121
RCMrandom	0.974	0.026	1.003
RCMtest	3.707	0.079	3.813
cghCall2cghSeg	0.082	0.002	0.084
cghCall2maximumSubset	0.378	0.005	0.384
cghCall2order	0.019	0.004	0.023
cghCall2subset	0.057	0.002	0.059
cghCall2weightedSubset	0.334	0.003	0.339
cghSeg2order	0.050	0.001	0.052
cghSeg2subset	0.073	0.002	0.075
cghSeg2weightedSubset	0.307	0.004	0.312
cisEffectPlot	0.068	0.003	0.073
cisEffectTable	1.705	0.063	1.790
cisEffectTest	1.689	0.056	1.759
cisEffectTune	14.782	0.303	15.170
cisTest-class	0.002	0.000	0.002
entTest-class	0.001	0.000	0.002
entropyTest	0.255	0.011	0.268
expandMatching2singleIDs	0.034	0.003	0.036
getSegFeatures	0.011	0.002	0.013
hdEntropy	0.013	0.002	0.015
hdMI	0.620	0.004	0.626
matchAnn2Ann	0.023	0.002	0.025
matchCGHcall2ExpressionSet	0.057	0.004	0.061
merge2ExpressionSets	0.047	0.001	0.048
merge2cghCalls	0.073	0.002	0.077
miTest-class	0.002	0.000	0.002
mutInfTest	78.425	14.863	93.781
nBreakpoints	0.165	0.004	0.171
pathway1sample	0.103	0.006	0.112
pathway2sample	2.226	0.482	2.715
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.079	0.008	0.088
pollackCN16	0.006	0.001	0.007
pollackGE16	0.004	0.001	0.005
profilesPlot	0.087	0.002	0.091
rcmFit-class	0.002	0.000	0.002
rcmTest-class	0.001	0.001	0.002
splitMatchingAtBreakpoints	0.170	0.003	0.174
uniqGenomicInfo	0.007	0.001	0.009

CHECK report for sigaR on merida2

Summary

Command output

Installation output

Tests output

Example timings