Package: mogsa

Version: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2018-10-16 22:44:07 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:47:03 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 176.0 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/mogsa.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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
prepGraphite 9.08  1.042  10.206
* 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	0.586	0.035	0.627
annotate.gs	0.438	0.019	0.457
bootMbpca	0.001	0.000	0.001
box.gs.feature	0.287	0.026	0.314
combine-methods	0.290	0.030	0.322
decompose.gs.group	0.202	0.022	0.225
decompose.gs.ind	0.133	0.017	0.152
distMoa	0.362	0.023	0.388
getmgsa	0.168	0.020	0.190
matpower	0.003	0.000	0.003
mbpca	3.831	0.249	4.108
mgsa-class	0.316	0.042	0.362
moGap	1.520	0.037	1.567
moa-class	0.110	0.013	0.122
moa	0.177	0.009	0.188
moa.sup-class	0.138	0.017	0.155
moaCoef	0.404	0.027	0.431
moaScore	0.445	0.029	0.479
mogsa-package	0.277	0.038	0.318
mogsa	0.327	0.034	0.361
pairwise.rv	0.011	0.001	0.012
plotGS	0.147	0.016	0.165
prepGraphite	9.080	1.042	10.206
prepMsigDB	0.005	0.000	0.005
prepSupMoa	4.138	0.309	4.472
softK	0.002	0.000	0.002
sup.moa	0.458	0.026	0.489
wsvd	0.002	0.000	0.002