Package: mogsa

Version: 1.21.0

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_1.21.0.tar.gz

StartedAt: 2020-01-16 06:39:57 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 06:43:54 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 236.4 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/mogsa.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 ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.21.0’
* 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 ‘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 (user + system) or elapsed time > 5s
            user system elapsed
prepSupMoa 5.453  0.195   5.648
* 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/4.0/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	0.390	0.058	0.449
annotate.gs	0.704	0.038	0.743
bootMbpca	0.000	0.000	0.001
bootMoa	0.001	0.000	0.000
box.gs.feature	0.458	0.058	0.516
combine-methods	0.418	0.063	0.482
decompose.gs.group	0.243	0.027	0.271
decompose.gs.ind	0.231	0.031	0.264
distMoa	0.860	0.064	0.928
getmgsa	0.232	0.057	0.290
matpower	0.001	0.000	0.002
mbpca	4.224	0.556	4.784
mgsa-class	0.386	0.081	0.468
moGap	3.374	0.189	3.566
moa-class	0.150	0.017	0.166
moa	0.961	0.188	1.152
moa.sup-class	0.158	0.041	0.200
moaCoef	0.438	0.058	0.496
moaScore	0.451	0.054	0.505
mogsa-package	0.399	0.070	0.469
mogsa	0.599	0.108	0.708
pairwise.rv	0.017	0.004	0.022
plotGS	0.225	0.037	0.262
prepGraphite	0.437	0.020	0.458
prepMsigDB	0.004	0.001	0.006
prepSupMoa	5.453	0.195	5.648
softK	0.001	0.000	0.001
sup.moa	0.688	0.040	0.729
wsvd	0.002	0.000	0.002