Package: sigaR

Version: 1.26.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.26.0.tar.gz

StartedAt: 2018-04-12 02:55:42 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:58:58 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 196.5 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/sigaR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 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    102.812  2.032 104.913
cisEffectTune  10.204  0.000  10.207
* 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
  ‘/home/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	0.884	0.012	0.895
ExpressionSet2order	0.008	0.000	0.009
ExpressionSet2subset	0.012	0.000	0.011
ExpressionSet2weightedSubset	0.232	0.000	0.233
RCMestimation	0.844	0.008	0.854
RCMrandom	1.080	0.000	1.081
RCMtest	2.288	0.000	2.288
cghCall2cghSeg	0.108	0.000	0.109
cghCall2maximumSubset	0.324	0.000	0.324
cghCall2order	0.028	0.000	0.026
cghCall2subset	0.036	0.000	0.034
cghCall2weightedSubset	0.232	0.000	0.234
cghSeg2order	0.052	0.000	0.050
cghSeg2subset	0.044	0.000	0.045
cghSeg2weightedSubset	0.228	0.000	0.226
cisEffectPlot	0.16	0.00	0.16
cisEffectTable	1.216	0.000	1.215
cisEffectTest	1.492	0.000	1.495
cisEffectTune	10.204	0.000	10.207
cisTest-class	0.000	0.000	0.001
entTest-class	0.004	0.000	0.001
entropyTest	0.248	0.000	0.249
expandMatching2singleIDs	0.068	0.000	0.067
getSegFeatures	0.004	0.004	0.006
hdEntropy	0.004	0.000	0.006
hdMI	0.476	0.000	0.476
matchAnn2Ann	0.12	0.00	0.12
matchCGHcall2ExpressionSet	0.112	0.000	0.111
merge2ExpressionSets	0.060	0.000	0.061
merge2cghCalls	0.044	0.000	0.046
miTest-class	0.000	0.000	0.001
mutInfTest	102.812	2.032	104.913
nBreakpoints	0.108	0.000	0.107
pathway1sample	0.688	0.000	0.698
pathway2sample	3.000	0.092	3.097
pathwayFit-class	0.000	0.000	0.001
pathwayPlot	0.132	0.000	0.132
pollackCN16	0.000	0.004	0.004
pollackGE16	0.004	0.000	0.003
profilesPlot	0.132	0.000	0.131
rcmFit-class	0.000	0.000	0.001
rcmTest-class	0.000	0.000	0.001
splitMatchingAtBreakpoints	0.108	0.000	0.108
uniqGenomicInfo	0.000	0.004	0.005