Package: sigaR

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.26.0.tar.gz

StartedAt: 2018-04-12 09:34:31 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 09:38:26 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 235.3 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 --no-vignettes --timings sigaR_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/sigaR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.26.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest    100.852  8.277 110.995
cisEffectTune  14.655  0.082  14.991
* 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-3.6-bioc/meat/sigaR.Rcheck/00check.log’
for details.

* installing *source* package ‘sigaR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	1.029	0.024	1.074
ExpressionSet2order	0.013	0.002	0.015
ExpressionSet2subset	0.016	0.003	0.019
ExpressionSet2weightedSubset	0.271	0.003	0.277
RCMestimation	1.022	0.037	1.077
RCMrandom	1.527	0.019	1.583
RCMtest	3.168	0.025	3.249
cghCall2cghSeg	0.135	0.001	0.140
cghCall2maximumSubset	0.372	0.007	0.381
cghCall2order	0.031	0.001	0.032
cghCall2subset	0.045	0.001	0.047
cghCall2weightedSubset	0.259	0.002	0.270
cghSeg2order	0.071	0.002	0.073
cghSeg2subset	0.060	0.002	0.061
cghSeg2weightedSubset	0.243	0.001	0.252
cisEffectPlot	0.213	0.003	0.219
cisEffectTable	1.636	0.027	1.689
cisEffectTest	1.808	0.022	1.849
cisEffectTune	14.655	0.082	14.991
cisTest-class	0.002	0.001	0.002
entTest-class	0.001	0.000	0.001
entropyTest	0.435	0.003	0.448
expandMatching2singleIDs	0.097	0.002	0.100
getSegFeatures	0.008	0.002	0.009
hdEntropy	0.008	0.001	0.009
hdMI	0.471	0.003	0.477
matchAnn2Ann	0.183	0.003	0.187
matchCGHcall2ExpressionSet	0.154	0.003	0.164
merge2ExpressionSets	0.083	0.002	0.086
merge2cghCalls	0.056	0.001	0.058
miTest-class	0.001	0.000	0.001
mutInfTest	100.852	8.277	110.995
nBreakpoints	0.169	0.005	0.178
pathway1sample	0.618	0.005	0.628
pathway2sample	3.341	0.678	4.111
pathwayFit-class	0.001	0.000	0.002
pathwayPlot	0.178	0.001	0.180
pollackCN16	0.005	0.001	0.006
pollackGE16	0.003	0.001	0.003
profilesPlot	0.174	0.019	0.199
rcmFit-class	0.001	0.000	0.002
rcmTest-class	0.002	0.000	0.002
splitMatchingAtBreakpoints	0.171	0.003	0.175
uniqGenomicInfo	0.007	0.001	0.008