Package: sigaR

Version: 1.34.0

Command: /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_1.34.0.tar.gz

StartedAt: 2020-04-15 05:41:17 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:45:40 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 262.6 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 --install=check:sigaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sigaR_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/sigaR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.34.0’
* 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    101.189 15.137 118.312
cisEffectTune  18.451  0.282  19.090
* 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-3.10-bioc/meat/sigaR.Rcheck/00check.log’
for details.

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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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	1.056	0.018	1.079
ExpressionSet2order	0.013	0.002	0.016
ExpressionSet2subset	0.015	0.001	0.019
ExpressionSet2weightedSubset	0.299	0.002	0.303
RCMestimation	1.237	0.094	1.401
RCMrandom	1.061	0.034	1.114
RCMtest	4.16	0.08	4.34
cghCall2cghSeg	0.075	0.001	0.077
cghCall2maximumSubset	0.410	0.005	0.419
cghCall2order	0.019	0.001	0.020
cghCall2subset	0.056	0.002	0.059
cghCall2weightedSubset	0.361	0.004	0.372
cghSeg2order	0.055	0.002	0.057
cghSeg2subset	0.083	0.002	0.085
cghSeg2weightedSubset	0.322	0.003	0.329
cisEffectPlot	0.083	0.003	0.086
cisEffectTable	2.057	0.076	2.149
cisEffectTest	1.971	0.050	2.042
cisEffectTune	18.451	0.282	19.090
cisTest-class	0.002	0.000	0.002
entTest-class	0.001	0.001	0.001
entropyTest	0.262	0.003	0.270
expandMatching2singleIDs	0.043	0.004	0.047
getSegFeatures	0.009	0.002	0.010
hdEntropy	0.012	0.002	0.014
hdMI	0.659	0.007	0.680
matchAnn2Ann	0.037	0.003	0.040
matchCGHcall2ExpressionSet	0.048	0.004	0.051
merge2ExpressionSets	0.058	0.002	0.060
merge2cghCalls	0.079	0.002	0.081
miTest-class	0.001	0.000	0.001
mutInfTest	101.189	15.137	118.312
nBreakpoints	0.245	0.006	0.258
pathway1sample	0.117	0.006	0.124
pathway2sample	2.944	0.643	3.668
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.071	0.010	0.083
pollackCN16	0.003	0.001	0.004
pollackGE16	0.003	0.002	0.005
profilesPlot	0.130	0.003	0.133
rcmFit-class	0.001	0.000	0.001
rcmTest-class	0.001	0.000	0.002
splitMatchingAtBreakpoints	0.275	0.016	0.291
uniqGenomicInfo	0.009	0.003	0.012