Package: sigaR

Version: 1.35.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sigaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sigaR_1.35.0.tar.gz

StartedAt: 2020-01-16 08:53:40 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:59:21 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 340.8 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 --install=check:sigaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sigaR_1.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/sigaR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.35.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
mutInfTest     122.761 27.465 151.676
cisEffectTune   23.124  1.503  24.938
RCMtest          4.893  0.435   5.327
pathway2sample   3.574  1.391   5.132
* 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-3.11-bioc/meat/sigaR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sigaR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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)

name	user	system	elapsed
CNGEheatmaps	1.515	0.181	1.695
ExpressionSet2order	0.018	0.004	0.023
ExpressionSet2subset	0.023	0.003	0.026
ExpressionSet2weightedSubset	0.388	0.046	0.434
RCMestimation	1.324	0.119	1.444
RCMrandom	1.266	0.131	1.397
RCMtest	4.893	0.435	5.327
cghCall2cghSeg	0.128	0.003	0.132
cghCall2maximumSubset	0.567	0.013	0.581
cghCall2order	0.028	0.004	0.033
cghCall2subset	0.072	0.005	0.078
cghCall2weightedSubset	0.474	0.024	0.498
cghSeg2order	0.070	0.005	0.075
cghSeg2subset	0.102	0.005	0.108
cghSeg2weightedSubset	0.385	0.014	0.398
cisEffectPlot	0.101	0.008	0.110
cisEffectTable	2.658	0.193	2.852
cisEffectTest	2.779	0.186	3.037
cisEffectTune	23.124	1.503	24.938
cisTest-class	0.002	0.001	0.010
entTest-class	0.001	0.000	0.001
entropyTest	0.351	0.029	0.400
expandMatching2singleIDs	0.051	0.007	0.057
getSegFeatures	0.010	0.003	0.013
hdEntropy	0.014	0.003	0.018
hdMI	0.828	0.009	0.846
matchAnn2Ann	0.045	0.007	0.057
matchCGHcall2ExpressionSet	0.071	0.007	0.079
merge2ExpressionSets	0.072	0.003	0.078
merge2cghCalls	0.098	0.004	0.104
miTest-class	0.001	0.001	0.001
mutInfTest	122.761	27.465	151.676
nBreakpoints	0.291	0.010	0.301
pathway1sample	0.103	0.010	0.114
pathway2sample	3.574	1.391	5.132
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.107	0.005	0.112
pollackCN16	0.006	0.003	0.009
pollackGE16	0.003	0.003	0.008
profilesPlot	0.158	0.008	0.167
rcmFit-class	0.001	0.001	0.001
rcmTest-class	0.001	0.000	0.001
splitMatchingAtBreakpoints	0.259	0.011	0.271
uniqGenomicInfo	0.010	0.003	0.012