Package: sigaR

Version: 1.30.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:sigaR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings sigaR_1.30.0.tar.gz

StartedAt: 2019-04-16 03:03:22 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:06:30 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 188.1 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:sigaR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings sigaR_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/sigaR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.30.0’
* 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    79.944  1.532   81.79
cisEffectTune 12.996  0.004   13.05
* 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-3.8-bioc/meat/sigaR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL sigaR
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘sigaR’ ...
** 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
* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	0.956	0.044	0.999
ExpressionSet2order	0.008	0.000	0.010
ExpressionSet2subset	0.012	0.000	0.011
ExpressionSet2weightedSubset	0.260	0.004	0.261
RCMestimation	0.620	0.004	0.625
RCMrandom	0.736	0.000	0.741
RCMtest	3.640	0.000	3.659
cghCall2cghSeg	0.1	0.0	0.1
cghCall2maximumSubset	0.336	0.000	0.335
cghCall2order	0.02	0.00	0.02
cghCall2subset	0.056	0.000	0.056
cghCall2weightedSubset	0.388	0.000	0.388
cghSeg2order	0.056	0.000	0.057
cghSeg2subset	0.076	0.000	0.078
cghSeg2weightedSubset	0.340	0.000	0.344
cisEffectPlot	0.068	0.004	0.073
cisEffectTable	1.836	0.012	1.857
cisEffectTest	1.964	0.000	1.966
cisEffectTune	12.996	0.004	13.050
cisTest-class	0.004	0.000	0.001
entTest-class	0	0	0
entropyTest	0.236	0.000	0.238
expandMatching2singleIDs	0.024	0.000	0.026
getSegFeatures	0.008	0.000	0.006
hdEntropy	0.012	0.000	0.010
hdMI	0.652	0.004	0.656
matchAnn2Ann	0.032	0.000	0.032
matchCGHcall2ExpressionSet	0.048	0.000	0.049
merge2ExpressionSets	0.056	0.000	0.056
merge2cghCalls	0.072	0.000	0.072
miTest-class	0	0	0
mutInfTest	79.944	1.532	81.790
nBreakpoints	0.204	0.008	0.211
pathway1sample	0.108	0.000	0.140
pathway2sample	2.756	0.164	2.928
pathwayFit-class	0.004	0.000	0.000
pathwayPlot	0.048	0.008	0.056
pollackCN16	0.004	0.000	0.004
pollackGE16	0.000	0.000	0.001
profilesPlot	0.076	0.000	0.073
rcmFit-class	0.000	0.000	0.001
rcmTest-class	0.000	0.000	0.001
splitMatchingAtBreakpoints	0.112	0.004	0.115
uniqGenomicInfo	0.008	0.000	0.007