Package: mogsa

Version: 1.18.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mogsa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mogsa_1.18.1.tar.gz

StartedAt: 2019-10-16 04:47:11 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:52:12 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 300.7 seconds

RetCode: 0

Status:  OK

CheckDir: mogsa.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mogsa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mogsa_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/mogsa.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.18.1’
* 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 ‘mogsa’ 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 ... OK
* 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 or elapsed time > 5s
               user system elapsed
prepSupMoa   49.562  1.984  51.558
prepGraphite 45.697  1.811  47.513
* 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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mogsa
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘mogsa’ ...
** 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 (mogsa)

name	user	system	elapsed
GIS	0.767	0.060	0.828
annotate.gs	0.190	0.044	0.233
bootMbpca	0.000	0.000	0.001
bootMoa	0.000	0.001	0.000
box.gs.feature	0.383	0.033	0.416
combine-methods	0.383	0.072	0.455
decompose.gs.group	0.220	0.042	0.262
decompose.gs.ind	0.631	0.038	0.670
distMoa	0.405	0.053	0.457
getmgsa	0.195	0.044	0.239
matpower	0.001	0.000	0.002
mbpca	4.214	0.566	4.783
mgsa-class	0.319	0.065	0.383
moGap	3.939	0.150	4.090
moa-class	0.165	0.056	0.221
moa	0.895	0.213	1.110
moa.sup-class	0.184	0.045	0.229
moaCoef	0.421	0.056	0.476
moaScore	0.350	0.038	0.388
mogsa-package	0.379	0.063	0.441
mogsa	1.023	0.123	1.147
pairwise.rv	0.016	0.002	0.017
plotGS	0.221	0.038	0.259
prepGraphite	45.697	1.811	47.513
prepMsigDB	0.006	0.001	0.007
prepSupMoa	49.562	1.984	51.558
softK	0.001	0.000	0.001
sup.moa	0.625	0.041	0.667
wsvd	0.002	0.001	0.002