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 03:42:52 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:47:47 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 295.1 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) (2019-03-18 r76245)
* 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   52.642  2.632  57.937
prepGraphite 46.239  1.918  48.799
mbpca         4.653  0.456   5.110
* 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’ ...
** 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	0.640	0.063	0.704
annotate.gs	0.229	0.039	0.268
bootMbpca	0	0	0
bootMoa	0.001	0.000	0.001
box.gs.feature	0.820	0.049	0.871
combine-methods	0.423	0.093	0.516
decompose.gs.group	0.256	0.031	0.287
decompose.gs.ind	0.168	0.036	0.205
distMoa	0.405	0.049	0.454
getmgsa	0.153	0.035	0.188
matpower	0.001	0.000	0.001
mbpca	4.653	0.456	5.110
mgsa-class	0.343	0.074	0.417
moGap	3.507	0.203	3.710
moa-class	0.122	0.016	0.138
moa	0.902	0.178	1.081
moa.sup-class	0.182	0.028	0.210
moaCoef	0.45	0.06	0.51
moaScore	0.425	0.051	0.475
mogsa-package	0.361	0.054	0.415
mogsa	0.406	0.066	0.472
pairwise.rv	0.408	0.017	0.425
plotGS	0.193	0.023	0.215
prepGraphite	46.239	1.918	48.799
prepMsigDB	0.005	0.001	0.007
prepSupMoa	52.642	2.632	57.937
softK	0.000	0.000	0.001
sup.moa	0.678	0.051	0.752
wsvd	0.002	0.000	0.002