Package: mogsa

Version: 1.17.5

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_1.17.5.tar.gz

StartedAt: 2019-04-09 02:19:46 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:23:44 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 237.2 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_1.17.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/mogsa.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.17.5’
* 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   43.200  0.856  44.445
prepGraphite 39.911  0.959  41.244
* 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/3.6/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	0.619	0.028	0.656
annotate.gs	0.160	0.017	0.183
bootMbpca	0	0	0
bootMoa	0.000	0.001	0.000
box.gs.feature	0.613	0.016	0.635
combine-methods	0.295	0.031	0.326
decompose.gs.group	0.196	0.017	0.214
decompose.gs.ind	0.185	0.024	0.212
distMoa	0.385	0.026	0.416
getmgsa	0.185	0.016	0.206
matpower	0.001	0.000	0.002
mbpca	4.002	0.244	4.309
mgsa-class	0.275	0.031	0.311
moGap	2.527	0.052	2.610
moa-class	0.109	0.009	0.121
moa	0.837	0.097	0.946
moa.sup-class	0.154	0.015	0.172
moaCoef	0.416	0.027	0.449
moaScore	0.418	0.025	0.452
mogsa-package	0.656	0.033	0.696
mogsa	0.430	0.054	0.487
pairwise.rv	0.013	0.001	0.014
plotGS	0.163	0.016	0.185
prepGraphite	39.911	0.959	41.244
prepMsigDB	0.003	0.000	0.003
prepSupMoa	43.200	0.856	44.445
softK	0.001	0.001	0.001
sup.moa	0.483	0.040	0.529
wsvd	0.002	0.000	0.001