Package: mogsa

Version: 1.16.0

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_1.16.0.tar.gz

StartedAt: 2019-04-16 01:23:20 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:27:19 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 238.8 seconds

RetCode: 0

Status:  OK

CheckDir: mogsa.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:mogsa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mogsa_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/mogsa.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.0’
* 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 or elapsed time > 5s
               user system elapsed
prepSupMoa   53.677  1.066  56.011
prepGraphite 40.505  1.034  42.196
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mogsa
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘mogsa’ ...
** 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 (mogsa)

name	user	system	elapsed
GIS	0.590	0.032	0.628
annotate.gs	0.442	0.021	0.464
bootMbpca	0	0	0
box.gs.feature	0.240	0.025	0.269
combine-methods	0.245	0.035	0.281
decompose.gs.group	0.176	0.014	0.193
decompose.gs.ind	0.165	0.017	0.185
distMoa	0.354	0.024	0.389
getmgsa	0.166	0.022	0.191
matpower	0.001	0.000	0.001
mbpca	3.928	0.252	4.230
mgsa-class	0.234	0.028	0.262
moGap	1.530	0.041	1.582
moa-class	0.123	0.008	0.136
moa	0.159	0.014	0.175
moa.sup-class	0.146	0.014	0.162
moaCoef	0.382	0.021	0.408
moaScore	0.421	0.025	0.457
mogsa-package	0.296	0.032	0.335
mogsa	0.310	0.037	0.357
pairwise.rv	0.015	0.001	0.017
plotGS	0.497	0.014	0.517
prepGraphite	40.505	1.034	42.196
prepMsigDB	0.005	0.000	0.006
prepSupMoa	53.677	1.066	56.011
softK	0.001	0.001	0.001
sup.moa	0.555	0.055	0.613
wsvd	0.001	0.000	0.002