Multiple platform build/check report for BioC 3.9 - CHECK report for sigaR on malbec2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sigaR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sigaR_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/sigaR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.31.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
mutInfTest    79.102  1.044  80.247
cisEffectTune 12.790  0.003  12.798
* 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-3.9-bioc/meat/sigaR.Rcheck/00check.log’
for details.

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL sigaR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output

Example timings

name	user	system	elapsed
CNGEheatmaps	0.921	0.036	0.957
ExpressionSet2order	0.014	0.000	0.014
ExpressionSet2subset	0.017	0.000	0.017
ExpressionSet2weightedSubset	0.311	0.000	0.311
RCMestimation	0.949	0.000	0.950
RCMrandom	0.861	0.000	0.864
RCMtest	2.827	0.000	2.828
cghCall2cghSeg	0.064	0.000	0.064
cghCall2maximumSubset	0.341	0.004	0.346
cghCall2order	0.018	0.000	0.018
cghCall2subset	0.048	0.000	0.047
cghCall2weightedSubset	0.359	0.000	0.359
cghSeg2order	0.049	0.000	0.049
cghSeg2subset	0.078	0.000	0.079
cghSeg2weightedSubset	0.351	0.000	0.351
cisEffectPlot	0.077	0.000	0.077
cisEffectTable	2.003	0.000	2.003
cisEffectTest	2.000	0.000	2.003
cisEffectTune	12.790	0.003	12.798
cisTest-class	0.001	0.000	0.001
entTest-class	0.001	0.000	0.000
entropyTest	0.21	0.00	0.21
expandMatching2singleIDs	0.020	0.000	0.021
getSegFeatures	0.006	0.000	0.006
hdEntropy	0.006	0.000	0.005
hdMI	0.602	0.000	0.603
matchAnn2Ann	0.022	0.000	0.021
matchCGHcall2ExpressionSet	0.028	0.000	0.029
merge2ExpressionSets	0.047	0.000	0.047
merge2cghCalls	0.064	0.003	0.068
miTest-class	0.000	0.000	0.001
mutInfTest	79.102	1.044	80.247
nBreakpoints	0.198	0.004	0.204
pathway1sample	0.110	0.000	0.109
pathway2sample	2.726	0.303	3.039
pathwayFit-class	0.001	0.000	0.000
pathwayPlot	0.089	0.008	0.098
pollackCN16	0.006	0.000	0.006
pollackGE16	0.000	0.003	0.003
profilesPlot	0.112	0.000	0.113
rcmFit-class	0.001	0.000	0.000
rcmTest-class	0.000	0.000	0.001
splitMatchingAtBreakpoints	0.196	0.000	0.197
uniqGenomicInfo	0.007	0.000	0.007

CHECK report for sigaR on malbec2

Summary

Command output

Installation output

Tests output

Example timings