Package: sigaR

Version: 1.31.0

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_1.31.0.tar.gz

StartedAt: 2019-04-09 05:30:09 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:35:22 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 313.2 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_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/sigaR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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    105.484 29.753 138.419
cisEffectTune  20.925  1.450  22.582
RCMtest         5.233  0.442   5.789
* 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.

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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	1.503	0.159	1.663
ExpressionSet2order	0.013	0.003	0.016
ExpressionSet2subset	0.017	0.003	0.020
ExpressionSet2weightedSubset	0.375	0.034	0.408
RCMestimation	1.459	0.125	1.584
RCMrandom	1.086	0.122	1.208
RCMtest	5.233	0.442	5.789
cghCall2cghSeg	0.130	0.002	0.136
cghCall2maximumSubset	0.581	0.032	0.613
cghCall2order	0.024	0.004	0.029
cghCall2subset	0.073	0.006	0.079
cghCall2weightedSubset	0.458	0.020	0.478
cghSeg2order	0.066	0.005	0.071
cghSeg2subset	0.101	0.005	0.106
cghSeg2weightedSubset	0.427	0.013	0.442
cisEffectPlot	0.074	0.007	0.081
cisEffectTable	2.214	0.183	2.397
cisEffectTest	2.211	0.178	2.394
cisEffectTune	20.925	1.450	22.582
cisTest-class	0.002	0.001	0.004
entTest-class	0.001	0.001	0.001
entropyTest	0.338	0.015	0.356
expandMatching2singleIDs	0.050	0.006	0.056
getSegFeatures	0.010	0.003	0.014
hdEntropy	0.014	0.003	0.018
hdMI	0.808	0.010	0.845
matchAnn2Ann	0.038	0.005	0.056
matchCGHcall2ExpressionSet	0.062	0.007	0.085
merge2ExpressionSets	0.049	0.003	0.052
merge2cghCalls	0.094	0.003	0.096
miTest-class	0.001	0.001	0.001
mutInfTest	105.484	29.753	138.419
nBreakpoints	0.273	0.010	0.331
pathway1sample	0.123	0.010	0.144
pathway2sample	3.195	1.375	4.687
pathwayFit-class	0.001	0.001	0.002
pathwayPlot	0.112	0.029	0.141
pollackCN16	0.006	0.003	0.009
pollackGE16	0.003	0.003	0.007
profilesPlot	0.142	0.007	0.149
rcmFit-class	0.001	0.000	0.002
rcmTest-class	0.001	0.001	0.003
splitMatchingAtBreakpoints	0.293	0.017	0.310
uniqGenomicInfo	0.011	0.004	0.016