BioC 3.5: CHECK report for sigaR on malbec2

Package: sigaR

Version: 1.24.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.24.0.tar.gz

StartedAt: 2017-08-16 02:16:58 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:19:58 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 180.0 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/sigaR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.24.0’
* 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    77.876   3.52  81.467
cisEffectTune 10.420   0.00  10.434
* 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-3.5-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	0.940	0.004	0.945
ExpressionSet2order	0.008	0.000	0.009
ExpressionSet2subset	0.012	0.000	0.011
ExpressionSet2weightedSubset	0.268	0.004	0.271
RCMestimation	0.728	0.008	0.737
RCMrandom	1.104	0.004	1.111
RCMtest	2.312	0.000	2.317
cghCall2cghSeg	0.104	0.000	0.107
cghCall2maximumSubset	0.344	0.000	0.345
cghCall2order	0.024	0.004	0.027
cghCall2subset	0.036	0.000	0.035
cghCall2weightedSubset	0.252	0.000	0.250
cghSeg2order	0.048	0.000	0.049
cghSeg2subset	0.048	0.000	0.044
cghSeg2weightedSubset	0.256	0.000	0.257
cisEffectPlot	0.152	0.000	0.153
cisEffectTable	1.268	0.000	1.269
cisEffectTest	1.528	0.000	1.532
cisEffectTune	10.420	0.000	10.434
cisTest-class	0.004	0.000	0.002
entTest-class	0	0	0
entropyTest	0.300	0.000	0.299
expandMatching2singleIDs	0.068	0.000	0.069
getSegFeatures	0.004	0.000	0.006
hdEntropy	0.008	0.000	0.006
hdMI	0.600	0.000	0.599
matchAnn2Ann	0.120	0.004	0.124
matchCGHcall2ExpressionSet	0.112	0.004	0.115
merge2ExpressionSets	0.06	0.00	0.06
merge2cghCalls	0.052	0.000	0.049
miTest-class	0.000	0.000	0.001
mutInfTest	77.876	3.520	81.467
nBreakpoints	0.108	0.000	0.109
pathway1sample	0.444	0.004	0.463
pathway2sample	3.252	0.076	3.336
pathwayFit-class	0	0	0
pathwayPlot	0.128	0.000	0.131
pollackCN16	0.004	0.000	0.004
pollackGE16	0.000	0.000	0.003
profilesPlot	0.144	0.000	0.145
rcmFit-class	0.000	0.000	0.001
rcmTest-class	0.004	0.000	0.000
splitMatchingAtBreakpoints	0.108	0.004	0.114
uniqGenomicInfo	0.008	0.000	0.005