Package: sigaR

Version: 1.32.0

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_1.32.0.tar.gz

StartedAt: 2019-10-16 06:52:22 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:57:52 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 330.1 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_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/sigaR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.32.0’
* 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     117.384 29.647 150.845
cisEffectTune   21.394  1.332  23.179
RCMtest          5.735  0.422   6.255
pathway2sample   3.576  1.459   5.055
* 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	1.288	0.040	1.329
ExpressionSet2order	0.020	0.004	0.024
ExpressionSet2subset	0.023	0.003	0.026
ExpressionSet2weightedSubset	0.387	0.006	0.396
RCMestimation	1.351	0.183	1.572
RCMrandom	1.440	0.144	1.583
RCMtest	5.735	0.422	6.255
cghCall2cghSeg	0.110	0.004	0.113
cghCall2maximumSubset	0.514	0.010	0.523
cghCall2order	0.029	0.005	0.034
cghCall2subset	0.078	0.006	0.085
cghCall2weightedSubset	0.422	0.008	0.430
cghSeg2order	0.044	0.002	0.046
cghSeg2subset	0.088	0.004	0.092
cghSeg2weightedSubset	0.361	0.010	0.370
cisEffectPlot	0.071	0.007	0.079
cisEffectTable	2.635	0.179	2.862
cisEffectTest	2.381	0.173	2.555
cisEffectTune	21.394	1.332	23.179
cisTest-class	0.001	0.000	0.002
entTest-class	0.001	0.000	0.001
entropyTest	0.34	0.02	0.36
expandMatching2singleIDs	0.048	0.007	0.054
getSegFeatures	0.010	0.004	0.013
hdEntropy	0.013	0.003	0.016
hdMI	0.815	0.013	0.829
matchAnn2Ann	0.042	0.006	0.048
matchCGHcall2ExpressionSet	0.068	0.008	0.076
merge2ExpressionSets	0.073	0.003	0.075
merge2cghCalls	0.094	0.005	0.098
miTest-class	0.001	0.001	0.002
mutInfTest	117.384	29.647	150.845
nBreakpoints	0.308	0.011	0.319
pathway1sample	0.090	0.013	0.103
pathway2sample	3.576	1.459	5.055
pathwayFit-class	0.002	0.001	0.002
pathwayPlot	0.117	0.030	0.147
pollackCN16	0.003	0.002	0.005
pollackGE16	0.003	0.004	0.007
profilesPlot	0.124	0.008	0.132
rcmFit-class	0.001	0.001	0.001
rcmTest-class	0.001	0.001	0.002
splitMatchingAtBreakpoints	0.219	0.012	0.232
uniqGenomicInfo	0.009	0.003	0.013